R3302G last accessed: 2022-11-04

arrayexpress
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

Other names: functional genomics data, arrayexpress

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.

Webpage:

https://www.ebi.ac.uk/arrayexpress/

Licence:

Name: ArrayExpress Data Access Policy
URL: http://www.ebi.ac.uk/arrayexpress/help/data_availability.html

Publications:

Publications
More detailed information about this field from each metasource.

ArrayExpress update--simplifying data submissions
PMID: 25361974
metasource: Fairsharing.org
version: FAIRsharing.org: ArrayExpress; ArrayExpress; DOI: https://doi.org/10.25504/FAIRsharing.6k0kwd; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

ArrayExpress--a public repository for microarray gene expression data at the EBI
PMID: 12519949
metasource: Fairsharing.org
version: FAIRsharing.org: ArrayExpress; ArrayExpress; DOI: https://doi.org/10.25504/FAIRsharing.6k0kwd; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

ArrayExpress update - from bulk to single-cell expression data
PMID: 30357387
metasource: Fairsharing.org
version: FAIRsharing.org: ArrayExpress; ArrayExpress; DOI: https://doi.org/10.25504/FAIRsharing.6k0kwd; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
PMID: 21071405
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

ArrayExpress update--simplifying data submissions PubMed citations: 363.

363 articles citing: ArrayExpress update--simplifying data submissions

Evaluating the Link between BAFF System Gene Expression and Acute Rejection Development in Kidney Transplantation. PMID:35887720
In-silico analysis of interacting pathways through KIM-1 protein interaction in diabetic nephropathy. PMID:35843953
Integration of Transcriptomics Data and Metabolomic Data Using Biomedical Literature Mining and Pathway Analysis. PMID:35713871
Host protease activity classifies pneumonia etiology. PMID:35696579
Physiologically Based Pharmacokinetic (PBPK) Modeling of Clopidogrel and Its Four Relevant Metabolites for CYP2B6, CYP2C8, CYP2C19, and CYP3A4 Drug-Drug-Gene Interaction Predictions. PMID:35631502
PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool. PMID:35345455
The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective. PMID:35338126
A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape. PMID:35283898
Gene coexpression analysis in Arabidopsis thaliana based on public microarray data. PMID:35243384
Computational Prediction of Biomarkers, Pathways, and New Target Drugs in the Pathogenesis of Immune-Based Diseases Regarding Kidney Transplantation Rejection. PMID:34975915
DISCO: a database of Deeply Integrated human Single-Cell Omics data. PMID:34791375
PIK3CB is involved in metastasis through the regulation of cell adhesion to collagen I in pancreatic cancer. PMID:34603784
A framework for validating AI in precision medicine: considerations from the European ITFoC consortium. PMID:34600518
Synthetic Evaluation of MicroRNA-1-3p Expression in Head and Neck Squamous Cell Carcinoma Based on Microarray Chips and MicroRNA Sequencing. PMID:34485523
Identification of Immune-Related Genes in Sepsis due to Community-Acquired Pneumonia. PMID:34484417
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Pulmonary MicroRNA Changes Alter Angiogenesis in Chronic Obstructive Pulmonary Disease and Lung Cancer. PMID:34356894
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658
Si-C is a method for inferring super-resolution intact genome structure from single-cell Hi-C data. PMID:34272403
Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria. PMID:34238210
A comprehensive database for integrated analysis of omics data in autoimmune diseases. PMID:34167460
Analyzing Metabolic States of Adipogenic and Osteogenic Differentiation in Human Mesenchymal Stem Cells via Genome Scale Metabolic Model Reconstruction. PMID:34150750
Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification. PMID:34008752
A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers. PMID:33983435
Vaccine Inoculation Route Modulates Early Immunity and Consequently Antigen-Specific Immune Response. PMID:33959127
Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gestational diabetes mellitus. PMID:33890634
Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production. PMID:33762878
Identification of key genes in hepatitis B associated hepatocellular carcinoma based on WGCNA. PMID:33726794
Phytochrome regulates cellular response plasticity and the basic molecular machinery of leaf development. PMID:33693822
Epstein-Barr virus inactivates the transcriptome and disrupts the chromatin architecture of its host cell in the first phase of lytic reactivation. PMID:33675667
Myogenesis modelled by human pluripotent stem cells: a multi-omic study of Duchenne myopathy early onset. PMID:33586340
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. PMID:33535967
An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence. PMID:33417832
MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle. PMID:33338203
Detection of urinary miRNAs for diagnosis of clear cell renal cell carcinoma. PMID:33277569
Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. PMID:33251083
Inhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy. PMID:33247183
From ArrayExpress to BioStudies. PMID:33211879
Mutation bias within oncogene families is related to proliferation-specific codon usage. PMID:33199641
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. PMID:33174597
Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia. PMID:33108352
Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. PMID:32967293
Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. PMID:32967266
LAMA4 upregulation is associated with high liver metastasis potential and poor survival outcome of Pancreatic Cancer. PMID:32929348
Non-Coding RNA Databases in Cardiovascular Research. PMID:32887511
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. PMID:32850764
Respiratory Effects of Exposure to Aerosol From the Candidate Modified-Risk Tobacco Product THS 2.2 in an 18-Month Systems Toxicology Study With A/J Mice. PMID:32780831
Profiling the Course of Resolving vs. Persistent Inflammation in Human Monocytes: The Role of IL-1 Family Molecules. PMID:32754155
The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape. PMID:32693783
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Role of B Cell Lymphoma 2 in the Regulation of Liver Fibrosis in miR-122 Knockout Mice. PMID:32650615
The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. PMID:32646852
Mesenchymal to epithelial transition driven by canine distemper virus infection of canine histiocytic sarcoma cells contributes to a reduced cell motility in vitro. PMID:32627957
CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex. PMID:32621609
Novel HDAC inhibitor MAKV-8 and imatinib synergistically kill chronic myeloid leukemia cells via inhibition of BCR-ABL/MYC-signaling: effect on imatinib resistance and stem cells. PMID:32430012
Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke. PMID:32419906
Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data. PMID:32397130
MyoMiner: explore gene co-expression in normal and pathological muscle. PMID:32393257
BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization. PMID:32392297
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
Multi-Gene Prognostic Signatures and Prediction of Pathological Complete Response to Neoadjuvant Chemotherapy in ER-positive, HER2-negative Breast Cancer Patients. PMID:32369904
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer. PMID:32332866
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. PMID:32326418
The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension. PMID:32305042
Master Regulator Analysis of the SARS-CoV-2/Human Interactome. PMID:32244779
Fibration symmetries uncover the building blocks of biological networks. PMID:32234788
A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer's Disease. PMID:32231518
BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L. PMID:32133024
Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters. PMID:32112106
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Oxidative Stress in Canine Histiocytic Sarcoma Cells Induced by an Infection with Canine Distemper Virus Led to a Dysregulation of HIF-1α Downstream Pathway Resulting in a Reduced Expression of VEGF-B in vitro. PMID:32054075
Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots. PMID:32024696
All of gene expression (AOE): An integrated index for public gene expression databases. PMID:31978081
Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo. PMID:31921150
A dual druggable genome-wide siRNA and compound library screening approach identifies modulators of parkin recruitment to mitochondria. PMID:31911436
Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing. PMID:31882631
Broad-Spectrum Profiling of Drug Safety via Learning Complex Network. PMID:31868917
StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis. PMID:31856731
A Bioinformatics Approach to Explore MicroRNAs as Tools to Bridge Pathways Between Plants and Animals. Is DNA Damage Response (DDR) a Potential Target Process? PMID:31850028
NicheNet: modeling intercellular communication by linking ligands to target genes. PMID:31819264
HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis. PMID:31787073
An omics perspective on drug target discovery platforms. PMID:31774113
Mega-Analysis of Gene Expression in Mouse Models of Alzheimer's Disease. PMID:31767574
Identifying gene function and module connections by the integration of multispecies expression compendia. PMID:31754022
PCOSBase: a manually curated database of polycystic ovarian syndrome. PMID:31725861
DDBJ Database updates and computational infrastructure enhancement. PMID:31724722
Identification of 15 T Cell Restricted Genes Evaluates T Cell Infiltration of Human Healthy Tissues and Cancers and Shows Prognostic and Predictive Potential. PMID:31652661
The TargetMine Data Warehouse: Enhancement and Updates. PMID:31649722
Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments. PMID:31616468
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers. PMID:31521109
B cells sustain inflammation and predict response to immune checkpoint blockade in human melanoma. PMID:31519915
Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning. PMID:31504766
Considerations for Strategic Use of High-Throughput Transcriptomics Chemical Screening Data in Regulatory Decisions. PMID:31501805
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
MiR-376b-3p Is Associated With Long-term Response to Sunitinib in Metastatic Renal Cell Carcinoma Patients. PMID:31467229
Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features. PMID:31454993
Inhibition of GATA2 restrains cell proliferation and enhances apoptosis and chemotherapy mediated apoptosis in human GATA2 overexpressing AML cells. PMID:31434974
EdgeScaping: Mapping the spatial distribution of pairwise gene expression intensities. PMID:31386677
Differential gene expression analysis reveals novel genes and pathways in pediatric septic shock patients. PMID:31375728
Mining of Self-Organizing Map Gene-Expression Portraits Reveals Prognostic Stratification of HPV-Positive Head and Neck Squamous Cell Carcinoma. PMID:31357501
RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: Enhancing the retinal microarray data sets from GeneNetwork. PMID:31354228
Identification and Application of Gene Expression Signatures Associated with Lifespan Extension. PMID:31353263
The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay. PMID:31337399
Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. PMID:31311202
Clinical update on head and neck cancer: molecular biology and ongoing challenges. PMID:31308358
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
Leveraging the Role of the Metastatic Associated Protein Anterior Gradient Homologue 2 in Unfolded Protein Degradation: A Novel Therapeutic Biomarker for Cancer. PMID:31247903
Co-expression Network Analysis Elucidated a Core Module in Association With Prognosis of Non-functioning Non-invasive Human Pituitary Adenoma. PMID:31244774
RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast. PMID:31235518
Essential guidelines for computational method benchmarking. PMID:31221194
MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature. PMID:31217513
Single Nucleotide Polymorphisms of CBX4 and CBX7 Decrease the Risk of Hepatocellular Carcinoma. PMID:31211140
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma. PMID:31197946
Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis. PMID:31182759
Differential analysis of combinatorial protein complexes with CompleXChange. PMID:31159772
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
An overview of publicly available patient-centered prostate cancer datasets. PMID:31143673
Genetic analyses led to the discovery of a super-active mutant of the RNA polymerase I. PMID:31136569
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. PMID:31121115
Large-scale in-silico identification of a tumor-specific antigen pool for targeted immunotherapy in triple-negative breast cancer. PMID:31069014
Molecular footprint of Medawar's mutation accumulation process in mammalian aging. PMID:31062469
Increasing Upstream Chromatin Long-Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells. PMID:31057422
Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field. PMID:31053169
Navigating in vitro bioactivity data by investigating available resources using model compounds. PMID:31036807
Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer. PMID:30974831
Translational PBPK Modeling of the Protein Therapeutic and CD95L Inhibitor Asunercept to Develop Dose Recommendations for Its First Use in Pediatric Glioblastoma Patients. PMID:30939793
Generally applicable transcriptome-wide analysis of translation using anota2seq. PMID:30926999
Network meta-analysis correlates with analysis of merged independent transcriptome expression data. PMID:30876387
Leveraging Big Data to Transform Drug Discovery. PMID:30848458
Drosophila melanogaster tPlus3a and tPlus3b ensure full male fertility by regulating transcription of Y-chromosomal, seminal fluid, and heat shock genes. PMID:30845228
YESdb: integrative analysis of environmental stress in yeast. PMID:30821814
Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects. PMID:30794641
Correlation-adjusted regression survival scores for high-dimensional variable selection. PMID:30793795
Circadian clock protein Rev-erbα regulates neuroinflammation. PMID:30792350
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. PMID:30777892
Comparative Transcriptomics Between Zebrafish and Mammals: A Roadmap for Discovery of Conserved and Unique Signaling Pathways in Physiology and Disease. PMID:30775367
CDRgator: An Integrative Navigator of Cancer Drug Resistance Gene Signatures. PMID:30759968
A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes. PMID:30727966
Functional homogeneity and specificity of topological modules in human proteome. PMID:30717667
Latent network-based representations for large-scale gene expression data analysis. PMID:30717663
Placental CX3CL1 is Deregulated by Angiotensin II and Contributes to a Pro-Inflammatory Trophoblast-Monocyte Interaction. PMID:30717334
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_. PMID:30691411
Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes. PMID:30657858
Isoprenylcysteine carboxy methyltransferase (ICMT) is associated with tumor aggressiveness and its expression is controlled by the p53 tumor suppressor. PMID:30655292
Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine. PMID:30631320
A Longitudinal Study of the Association between Mammographic Density and Gene Expression in Normal Breast Tissue. PMID:30613869
Transcriptomic meta-signatures identified in Anopheles gambiae populations reveal previously undetected insecticide resistance mechanisms. PMID:30538253
PDX Finder: A portal for patient-derived tumor xenograft model discovery. PMID:30535239
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. PMID:30481257
Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities. PMID:30469355
COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference. PMID:30462320
funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. PMID:30428831
Stemformatics: visualize and download curated stem cell data. PMID:30407577
BioSamples database: an updated sample metadata hub. PMID:30407529
Enabling precision medicine in neonatology, an integrated repository for preterm birth research. PMID:30398470
The PRIDE database and related tools and resources in 2019: improving support for quantification data. PMID:30395289
A call for public archives for biological image data. PMID:30377375
YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast. PMID:30371756
ArrayExpress update - from bulk to single-cell expression data. PMID:30357387
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data. PMID:30357349
Non-canonical Drosophila X chromosome dosage compensation and repressive topologically associated domains. PMID:30355339
Up-regulation of the kinase gene SGK1 by progesterone activates the AP-1-NDRG1 axis in both PR-positive and -negative breast cancer cells. PMID:30337371
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
CaSTLe - Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments. PMID:30304022
Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. PMID:30277459
Data-driven human transcriptomic modules determined by independent component analysis. PMID:30223787
Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis. PMID:30205792
Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. PMID:30202060
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. PMID:30137486
DNA topoisomerase 1 and 2A function as oncogenes in liver cancer and may be direct targets of nitidine chloride. PMID:30132517
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. PMID:30115066
A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing's family of tumors. PMID:30093970
Short-Term Exposure to Nitrogen Dioxide Provides Basal Pathogen Resistance. PMID:30076223
Downregulation of miR‑486‑5p in papillary thyroid carcinoma tissue: A study based on microarray and miRNA sequencing. PMID:30015845
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. PMID:29988723
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains. PMID:29985970
An Artificial Neural Network Integrated Pipeline for Biomarker Discovery Using Alzheimer's Disease as a Case Study. PMID:29977480
PASI: A novel pathway method to identify delicate group effects. PMID:29975740
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
HEAT INDUCIBLE LIPASE1 Remodels Chloroplastic Monogalactosyldiacylglycerol by Liberating α-Linolenic Acid in Arabidopsis Leaves under Heat Stress. PMID:29967047
Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells. PMID:29950180
RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. PMID:29931156
C-terminal truncation of IFN-γ inhibits proinflammatory macrophage responses and is deficient in autoimmune disease. PMID:29925830
Molecular and Cellular Dynamics in the Skin, the Lymph Nodes, and the Blood of the Immune Response to Intradermal Injection of Modified Vaccinia Ankara Vaccine. PMID:29922280
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. PMID:29900117
Transcriptomic immune profiling of ovarian cancers in paraneoplastic cerebellar degeneration associated with anti-Yo antibodies. PMID:29899393
Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice. PMID:29860357
Computational approaches for predicting key transcription factors in targeted cell reprogramming (Review). PMID:29845286
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson's Disease Data. PMID:29799491
Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. PMID:29785040
Identification of brain metastasis genes and therapeutic evaluation of histone deacetylase inhibitors in a clinically relevant model of breast cancer brain metastasis. PMID:29784888
The relative resistance of children to sepsis mortality: from pathways to drug candidates. PMID:29773677
Lysophospholipids induce innate immune transdifferentiation of endothelial cells, resulting in prolonged endothelial activation. PMID:29769317
A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells. PMID:29768462
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. PMID:29745848
Meta-Analysis and Experimental Validation Identified FREM2 and SPRY1 as New Glioblastoma Marker Candidates. PMID:29734672
PhytoNet: comparative co-expression network analyses across phytoplankton and land plants. PMID:29718316
Metabolic systems analysis of LPS induced endothelial dysfunction applied to sepsis patient stratification. PMID:29717213
BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology. PMID:29688366
Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability. PMID:29685133
Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio). PMID:29684067
ProtaBank: A repository for protein design and engineering data. PMID:29575358
A FAIR guide for data providers to maximise sharing of human genomic data. PMID:29543799
TRAP-seq identifies cystine/glutamate antiporter as a driver of recovery from liver injury. PMID:29517978
Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results. PMID:29507534
Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. PMID:29504919
STRENDA DB: enabling the validation and sharing of enzyme kinetics data. PMID:29498804
From gene networks to drugs: systems pharmacology approaches for AUD. PMID:29497781
Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer. PMID:29464091
Identification of common key genes in breast, lung and prostate cancer and exploration of their heterogeneous expression. PMID:29434863
Comparison, alignment, and synchronization of cell line information between CLO and EFO. PMID:29322915
Biology in the Dry Seed: Transcriptome Changes Associated with Dry Seed Dormancy and Dormancy Loss in the Arabidopsis GA-Insensitive sleepy1-2 Mutant. PMID:29312402
Integrated Analysis of Gene Expression Differences in Twins Discordant for Disease and Binary Phenotypes. PMID:29311748
Potential effect of tumor-specific Treg-targeted antibodies in the treatment of human cancers: A bioinformatics analysis. PMID:29308313
Cattle infection response network and its functional modules. PMID:29301495
Scalable non-negative matrix tri-factorization. PMID:29299064
Emerging whole-cell modeling principles and methods. PMID:29275251
Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D. PMID:29233860
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. PMID:29220461
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index. PMID:29216398
A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley. PMID:29202692
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. PMID:29192179
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
SATORI: a system for ontology-guided visual exploration of biomedical data repositories. PMID:29186292
Selection of internal references for qRT-PCR assays of human hepatocellular carcinoma cell lines. PMID:29180379
Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri. PMID:29179763
Expression Atlas: gene and protein expression across multiple studies and organisms. PMID:29165655
Regulation of Sucrose Transporters and Phloem Loading in Response to Environmental Cues. PMID:29158330
Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers. PMID:29156751
BCNTB bioinformatics: the next evolutionary step in the bioinformatics of breast cancer tissue banking. PMID:29136180
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. PMID:29126285
The BioStudies database-one stop shop for all data supporting a life sciences study. PMID:29069414
The Pancreatic Expression Database: 2018 update. PMID:29059374
CANcer-specific Evaluation System (CANES): a high-accuracy platform, for preclinical single/multi-biomarker discovery. PMID:29050243
The transcriptional regulator LysG (Rv1985c) of Mycobacterium tuberculosis activates lysE (Rv1986) in a lysine-dependent manner. PMID:29049397
DNA Data Bank of Japan: 30th anniversary. PMID:29040613
iSyTE 2.0: a database for expression-based gene discovery in the eye. PMID:29036527
'Multi-omic' data analysis using O-miner. PMID:28981577
AAgMarker 1.0: a resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases. PMID:28977551
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. PMID:28968850
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples. PMID:28968689
Statistically controlled identification of differentially expressed genes in one-to-one cell line comparisons of the CMAP database for drug repositioning. PMID:28962576
Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis. PMID:28955037
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster. PMID:28916647
A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research. PMID:28872130
Identification and characterization of Vibrio vulnificus plpA encoding a phospholipase A2 essential for pathogenesis. PMID:28855258
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. PMID:28850115
Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder. PMID:28848387
An improved analysis methodology for translational profiling by microarray. PMID:28842509
A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification. PMID:28830341
Automated assembly of species metabolomes through data submission into a public repository. PMID:28830114
Comparative transcriptomics indicate changes in cell wall organization and stress response in seedlings during spaceflight. PMID:28827451
Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study. PMID:28819158
Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. PMID:28819152
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
m6aViewer: software for the detection, analysis, and visualization of N6-methyladenosine peaks from m6A-seq/ME-RIP sequencing data. PMID:28724534
CSmiRTar: Condition-Specific microRNA targets database. PMID:28704505
RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes. PMID:28680265
Transcriptional mechanisms associated with seed dormancy and dormancy loss in the gibberellin-insensitive sly1-2 mutant of Arabidopsis thaliana. PMID:28628628
Transcriptomics technologies. PMID:28545146
SiGNet: A signaling network data simulator to enable signaling network inference. PMID:28545060
Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors. PMID:28542306
A Web Service Framework for Interactive Analysis of Metabolomics Data. PMID:28514166
Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection. PMID:28489074
DUX-family transcription factors regulate zygotic genome activation in placental mammals. PMID:28459456
IGF2BP3 functions as a potential oncogene and is a crucial target of miR-34a in gastric carcinogenesis. PMID:28399871
Drug repurposing from the perspective of pharmaceutical companies. PMID:28369768
Plant specimen contextual data consensus. PMID:28369359
The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data. PMID:28369191
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Orchestrating differential data access for translational research: a pilot implementation. PMID:28330491
Glycol porphyrin derivatives and temoporfin elicit resistance to photodynamic therapy by different mechanisms. PMID:28295025
The discovery of novel LPMO families with a new Hidden Markov model. PMID:28222763
Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization. PMID:28209199
Protein Bioinformatics Databases and Resources. PMID:28150231
Underexpression of Specific Interferon Genes Is Associated with Poor Prognosis of Melanoma. PMID:28114321
Gene Expression Profiling of Bronchoalveolar Lavage Cells Preceding a Clinical Diagnosis of Chronic Lung Allograft Dysfunction. PMID:28103284
Autophagy-related gene LRRK2 is likely a susceptibility gene for systemic lupus erythematosus in northern Han Chinese. PMID:28099919
Global open data management in metabolomics. PMID:28092796
Systemically identifying and prioritizing risk lncRNAs through integration of pan-cancer phenotype associations. PMID:28076842
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
The metastasis suppressor RARRES3 as an endogenous inhibitor of the immunoproteasome expression in breast cancer cells. PMID:28051153
Secreted Proteins Defy the Expression Level-Evolutionary Rate Anticorrelation. PMID:28007979
p53 Specifically Binds Triplex DNA In Vitro and in Cells. PMID:27907175
CEBS: a comprehensive annotated database of toxicological data. PMID:27899660
jPOSTrepo: an international standard data repository for proteomes. PMID:27899654
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. PMID:27899608
The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. PMID:27863463
Human Papillomavirus Drives Tumor Development Throughout the Head and Neck: Improved Prognosis Is Associated With an Immune Response Largely Restricted to the Oropharynx. PMID:27863190
Reduced angiogenic gene expression in morbillivirus-triggered oncolysis in a translational model for histiocytic sarcoma. PMID:27860224
HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development. PMID:27833533
Large-scale gene co-expression network as a source of functional annotation for cattle genes. PMID:27806696
Using Big Data to Discover Diagnostics and Therapeutics for Gastrointestinal and Liver Diseases. PMID:27773806
A computational interactome and functional annotation for the human proteome. PMID:27770567
Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly. PMID:27733515
The human-induced pluripotent stem cell initiative-data resources for cellular genetics. PMID:27733501
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). PMID:27679477
Phosphate uptake kinetics and tissue-specific transporter expression profiles in poplar (Populus × canescens) at different phosphorus availabilities. PMID:27663513
Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms. PMID:27654999
Meta-Analysis of Parkinson's Disease Transcriptome Data Using TRAM Software: Whole Substantia Nigra Tissue and Single Dopamine Neuron Differential Gene Expression. PMID:27611585
"Upstream Analysis": An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data. PMID:27600225
New insights in Rett syndrome using pathway analysis for transcriptomics data. PMID:27517371
Computational assessment of feature combinations for pathogenic variant prediction. PMID:27468419
Anesthetic Propofol-Induced Gene Expression Changes in Patients Undergoing Coronary Artery Bypass Graft Surgery Based on Dynamical Differential Coexpression Network Analysis. PMID:27437027
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. PMID:27402679
Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana. PMID:27352932
Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data. PMID:27349964
IGF2 knockdown in two colorectal cancer cell lines decreases survival, adhesion and modulates survival-associated genes. PMID:27337954
Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression. PMID:27322383
Gene expression prediction using low-rank matrix completion. PMID:27317252
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. PMID:27306882
Bioinformatics resources for pollen. PMID:27271281
Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned. PMID:27255914
Tissue- and Cell-Specific Cytokinin Activity in Populus × canescens Monitored by ARR5::GUS Reporter Lines in Summer and Winter. PMID:27242853
VESPUCCI: Exploring Patterns of Gene Expression in Grapevine. PMID:27242836
Altered gene expression in the lower respiratory tract of Car6 (-/-) mice. PMID:27209317
The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity? PMID:27184366
Changes in Gene Expression and Estrogen Receptor Cistrome in Mouse Liver Upon Acute E2 Treatment. PMID:27164166
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
GIANT API: an application programming interface for functional genomics. PMID:27098035
HIC1 Expression Distinguishes Intestinal Carcinomas Sensitive to Chemotherapy. PMID:27084425
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system. PMID:27078110
Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections. PMID:27058578
Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates. PMID:27042287
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PMID:27028627
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations. PMID:26925399
Osteogenic Differentiation of MSC through Calcium Signaling Activation: Transcriptomics and Functional Analysis. PMID:26828589
A genomics-based framework for identifying biomarkers of human neurodevelopmental toxicity. PMID:26827931
Pluralistic and stochastic gene regulation: examples, models and consistent theory. PMID:26823500
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA. PMID:26757983
Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment. PMID:26753519
Blood transcriptomics and metabolomics for personalized medicine. PMID:26702339
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
Fundamentals of protein interaction network mapping. PMID:26681426
HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. PMID:26657893
Dimeric peroxiredoxins are druggable targets in human Burkitt lymphoma. PMID:26636537
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. PMID:26586805
BioGPS: building your own mash-up of gene annotations and expression profiles. PMID:26578587
ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression. PMID:26546318
A measure of the impact of CV incompleteness on prediction error estimation with application to PCA and normalization. PMID:26537575
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. PMID:26527724
Public data and open source tools for multi-assay genomic investigation of disease. PMID:26463000
Joint Transcriptomic and Metabolomic Analyses Reveal Changes in the Primary Metabolism and Imbalances in the Subgenome Orchestration in the Bread Wheat Molecular Response to Fusarium graminearum. PMID:26438291
Mating induces the expression of immune- and pH-regulatory genes in the utero-vaginal junction containing mucosal sperm-storage tubuli of hens. PMID:26370241
ExAtlas: An interactive online tool for meta-analysis of gene expression data. PMID:26223199
Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice. PMID:26206757
Empirical comparison of structure-based pathway methods. PMID:26197809
A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal. PMID:26122086
Revealing protein-lncRNA interaction. PMID:26041786
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. PMID:26013488
NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning. PMID:25940629
Differential gene expression in liver tissues of streptozotocin-induced diabetic rats in response to resveratrol treatment. PMID:25905778
Influence of vascular endothelial growth factor stimulation and serum deprivation on gene activation patterns of human adipose tissue-derived stromal cells. PMID:25889587
KPP: KEGG Pathway Painter. PMID:25879163
The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. PMID:25831060
ArrayExpress--a public repository for microarray gene expression data at the EBI PubMed citations: 308.

308 articles citing: ArrayExpress--a public repository for microarray gene expression data at the EBI

An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer. PMID:35884419
A Genomic Information Management System for Maintaining Healthy Genomic States and Application of Genomic Big Data in Clinical Research. PMID:35682641
Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health. PMID:35628666
Wristwatch PCR: A Versatile and Efficient Genome Walking Strategy. PMID:35497369
A Cancer Associated Fibroblasts-Related Six-Gene Panel for Anti-PD-1 Therapy in Melanoma Driven by Weighted Correlation Network Analysis and Supervised Machine Learning. PMID:35479936
Identification and Validation of Hub Genes with Poor Prognosis in Hepatocellular Carcinoma by Integrated Bioinformatical Analysis. PMID:35431572
Network meta-analysis of transcriptome expression changes in different manifestations of dengue virus infection. PMID:35220956
Identification of Nifurtimox and Chrysin as Anti-Influenza Virus Agents by Clinical Transcriptome Signature Reversion. PMID:35216485
Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data. PMID:35205414
Novel insight into pancreatic adenocarcinoma pathogenesis using liquid association analysis. PMID:35180880
Analysis of transcriptomic data sets supports the role of IL-6 in NETosis and immunothrombosis in severe COVID-19. PMID:34775962
Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. PMID:34686726
Deep Large-Scale Multitask Learning Network for Gene Expression Inference. PMID:34014778
Acyl-Acyl Carrier Protein Desaturases and Plant Biotic Interactions. PMID:33803674
Large-scale labeling and assessment of sex bias in publicly available expression data. PMID:33784977
Juxtapose: a gene-embedding approach for comparing co-expression networks. PMID:33726666
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. PMID:33647482
Human pathways in animal models: possibilities and limitations. PMID:33524155
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:33396976
From ArrayExpress to BioStudies. PMID:33211879
Correcting for experiment-specific variability in expression compendia can remove underlying signals. PMID:33140829
A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. PMID:33092028
Mining genetic and transcriptomic data using machine learning approaches in Parkinson's disease. PMID:32964109
Integrated PPI- and WGCNA-Retrieval of Hub Gene Signatures Shared Between Barrett's Esophagus and Esophageal Adenocarcinoma. PMID:32903837
Protective Role of Decorin in Primary Hepatocellular Carcinoma. PMID:32477937
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. PMID:32449934
Understanding the Molecular Mechanisms of Asthma through Transcriptomics. PMID:32141255
Identification of key genes associated with multiple sclerosis based on gene expression data from peripheral blood mononuclear cells. PMID:32117605
A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. PMID:31992182
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. PMID:31956905
Identification of differentially expressed genes between the colon and ileum of patients with inflammatory bowel disease by gene co-expression analysis. PMID:31822145
Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination. PMID:31787983
Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. PMID:31733513
Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease. PMID:31730674
Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. PMID:31590277
EWAS Data Hub: a resource of DNA methylation array data and metadata. PMID:31584095
HENA, heterogeneous network-based data set for Alzheimer's disease. PMID:31413325
Identification of gene expression logical invariants in Arabidopsis. PMID:31245766
T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection. PMID:31223533
Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. PMID:31182013
Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease. PMID:31068785
Atlas of RNA sequencing profiles for normal human tissues. PMID:31015567
The variable quality of metadata about biological samples used in biomedical experiments. PMID:30778255
Shambhala: a platform-agnostic data harmonizer for gene expression data. PMID:30727942
Whole-Genome Sequencing Identifies a Novel Variation of WAS Gene Coordinating With Heterozygous Germline Mutation of APC to Enhance Hepatoblastoma Oncogenesis. PMID:30619485
Gene Expression Studies for the Development of Particle Therapy. PMID:30555854
LCE: an open web portal to explore gene expression and clinical associations in lung cancer. PMID:30532070
Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk. PMID:30453964
ArrayExpress update - from bulk to single-cell expression data. PMID:30357387
SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks. PMID:30102702
Random forest versus logistic regression: a large-scale benchmark experiment. PMID:30016950
Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. PMID:29809142
Identification of key candidate genes and pathways in hepatocellular carcinoma by integrated bioinformatical analysis. PMID:29805517
DANUBE: Data-driven meta-ANalysis using UnBiased Empirical distributions-applied to biological pathway analysis. PMID:29706661
EPHB6 augments both development and drug sensitivity of triple-negative breast cancer tumours. PMID:29700392
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system. PMID:29688349
Transcriptome Network Analysis Reveals Aging-Related Mitochondrial and Proteasomal Dysfunction and Immune Activation in Human Thyroid. PMID:29652618
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones. PMID:29387079
Gene annotation bias impedes biomedical research. PMID:29358745
Transcriptomics Evidence for Common Pathways in Human Major Depressive Disorder and Glioblastoma. PMID:29329273
Cancer transcriptome profiling at the juncture of clinical translation. PMID:29279605
Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology. PMID:29246152
A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley. PMID:29202692
Impact of sequencing depth and read length on single cell RNA sequencing data of T cells. PMID:28986563
A link prediction approach to cancer drug sensitivity prediction. PMID:28984192
Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker. PMID:28973476
The CINSARC signature as a prognostic marker for clinical outcome in multiple neoplasms. PMID:28710396
Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks. PMID:28623317
A Transcriptomics and Comparative Genomics Analysis Reveals Gene Families with a Role in Body Plan Complexity. PMID:28611798
Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens. PMID:28540497
CSTEA: a webserver for the Cell State Transition Expression Atlas. PMID:28486666
Study of Meta-analysis strategies for network inference using information-theoretic approaches. PMID:28484519
Synergistic drug combinations from electronic health records and gene expression. PMID:27940607
EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY. PMID:27896970
GEN3VA: aggregation and analysis of gene expression signatures from related studies. PMID:27846806
A Modular Repository-based Infrastructure for Simulation Model Storage and Execution Support in the Context of In Silico Oncology and In Silico Medicine. PMID:27812280
Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans. PMID:27790248
Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells. PMID:27703845
Meta-analysis of clinical metabolic profiling studies in cancer: challenges and opportunities. PMID:27601137
Genomic-Wide Analysis with Microarrays in Human Oncology. PMID:27600234
The metabolic background is a global player in Saccharomyces gene expression epistasis. PMID:27572163
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
Matricellular TSP-1 as a target of interest for impeding melanoma spreading: towards a therapeutic use for TAX2 peptide. PMID:27349907
Approaches to uncovering cancer diagnostic and prognostic molecular signatures. PMID:27308330
Breast cancer subtype predictors revisited: from consensus to concordance? PMID:27259591
GFOD1 and peejar are promising markers for clear-cell renal cell carcinoma disease progression. PMID:27191742
Learning from Co-expression Networks: Possibilities and Challenges. PMID:27092161
An individualized prognostic signature and multi‑omics distinction for early stage hepatocellular carcinoma patients with surgical resection. PMID:27006471
Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms. PMID:26944083
MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation. PMID:26881263
FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks. PMID:26872036
Big Data Application in Biomedical Research and Health Care: A Literature Review. PMID:26843812
Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner. PMID:26684652
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Data standards can boost metabolomics research, and if there is a will, there is a way. PMID:26612985
Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma. PMID:26558755
Gene expression profiling of the inner ear. PMID:26403558
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
Turning publicly available gene expression data into discoveries using gene set context analysis. PMID:26350211
In silico analysis of the molecular mechanism of postmenopausal osteoporosis. PMID:26329309
MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data. PMID:26314578
Identification of reproducible drug-resistance-related dysregulated genes in small-scale cancer cell line experiments. PMID:26173481
Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms. PMID:26173225
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. PMID:25983554
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. PMID:25969447
Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability. PMID:25966034
Investigation into the annotation of protocol sequencing steps in the sequence read archive. PMID:25960871
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8. PMID:25654111
Proteomics for systems toxicology. PMID:25379146
Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in a Drosophila melanogaster population. PMID:25371429
ArrayExpress update--simplifying data submissions. PMID:25361974
DEOP: a database on osmoprotectants and associated pathways. PMID:25326239
Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy. PMID:25303361
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters. PMID:25204982
We are all individuals... bioinformatics in the personalized medicine era. PMID:25204962
Developmental stage dependent metabolic regulation during meiotic differentiation in budding yeast. PMID:25178389
CSEO - the Cigarette Smoke Exposure Ontology. PMID:25093069
Clinic-genomic association mining for colorectal cancer using publicly available datasets. PMID:24987669
Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation. PMID:24967636
Amerindian-specific regions under positive selection harbour new lipid variants in Latinos. PMID:24886709
Copy-neutral loss of heterozygosity is prevalent and a late event in the pathogenesis of FLT3/ITD AML. PMID:24786392
INsPeCT: INtegrative Platform for Cancer Transcriptomics. PMID:24653643
Deubiquitylating enzymes and their emerging role in plant biology. PMID:24600466
Meta-analysis of pathway enrichment: combining independent and dependent omics data sets. PMID:24586671
Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions. PMID:24576339
Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data. PMID:24564491
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. PMID:24451627
Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma. PMID:24379610
FUT11 as a potential biomarker of clear cell renal cell carcinoma progression based on meta-analysis of gene expression data. PMID:24318988
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. PMID:24309898
Integrating in silico resources to map a signaling network. PMID:24233784
Ten simple rules for reproducible computational research. PMID:24204232
Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes. PMID:24058882
Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. PMID:24009894
Analysis of the transcriptome in molecular epidemiology studies. PMID:23907930
PLANEX: the plant co-expression database. PMID:23688397
Genome-wide analysis of the GH3 family in apple (Malus × domestica). PMID:23638690
Two-way AIC: detection of differentially expressed genes from large scale microarray meta-dataset. PMID:23445621
The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization. PMID:23445545
Data submission and quality in microarray-based microRNA profiling. PMID:23358751
Exact statistical tests for the intersection of independent lists of genes. PMID:23335952
Overview of DNA microarrays: types, applications, and their future. PMID:23288464
Reuse of public genome-wide gene expression data. PMID:23269463
Expression of microRNAs in the NCI-60 cancer cell-lines. PMID:23209617
miRNA profiles of monocyte-lineage cells are consistent with complicated roles in HIV-1 restriction. PMID:23202444
ArrayExpress update--trends in database growth and links to data analysis tools. PMID:23193272
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
Reconstruction of the evolutionary history of Saccharomyces cerevisiae x S. kudriavzevii hybrids based on multilocus sequence analysis. PMID:23049811
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
Transcriptome classification reveals molecular subtypes in psoriasis. PMID:22971201
Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins. PMID:22906207
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. PMID:22898396
Context-specific ontology integration: a bayesian approach. PMID:22779057
Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs--a comparative study. PMID:22723911
Detection of simultaneous group effects in microRNA expression and related target gene sets. PMID:22723856
How can microarrays unlock asthma? PMID:22500180
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice. PMID:22307325
Toxicogenomic biomarkers for liver toxicity. PMID:22271975
Predicting gene ontology from a global meta-analysis of 1-color microarray experiments. PMID:22166114
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. PMID:22166002
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PMID:22144874
Hyperactivation of oxidative mitochondrial metabolism in epithelial cancer cells in situ: visualizing the therapeutic effects of metformin in tumor tissue. PMID:22134189
The BioSample Database (BioSD) at the European Bioinformatics Institute. PMID:22096232
Construction of regulatory networks using expression time-series data of a genotyped population. PMID:22084118
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. PMID:22078224
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
Gene expression analysis characterizes antemortem stress and has implications for establishing cause of death. PMID:21693618
Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. PMID:21672904
Plant-pathogen interactions: what microarray tells about it? PMID:21618071
Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation. PMID:21615920
Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach. PMID:21595873
ParkDB: a Parkinson's disease gene expression database. PMID:21593080
Evidence for a stromal-epithelial "lactate shuttle" in human tumors: MCT4 is a marker of oxidative stress in cancer-associated fibroblasts. PMID:21558814
Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers. PMID:21521946
Ketones and lactate increase cancer cell "stemness," driving recurrence, metastasis and poor clinical outcome in breast cancer: achieving personalized medicine via Metabolo-Genomics. PMID:21512313
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data. PMID:21453538
Conceptual aspects of large meta-analyses with publicly available microarray data: a case study in oncology. PMID:21423405
GCOD - GeneChip Oncology Database. PMID:21291543
Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PMID:21151926
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. PMID:21071405
Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies. PMID:21052526
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
Practical application of toxicogenomics for profiling toxicant-induced biological perturbations. PMID:20957103
RB-pathway disruption in breast cancer: differential association with disease subtypes, disease-specific prognosis and therapeutic response. PMID:20948315
Ontology-based meta-analysis of global collections of high-throughput public data. PMID:20927376
Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. PMID:20875095
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PMID:20824171
Enhancing interdisciplinary mathematics and biology education: a microarray data analysis course bridging these disciplines. PMID:20810954
Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. PMID:20698961
Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. PMID:20660011
Application of genetic/genomic approaches to allergic disorders. PMID:20638111
Genome-wide identification of new Wnt/beta-catenin target genes in the human genome using CART method. PMID:20515496
Advances in genetical genomics of plants. PMID:20514216
Comparative gene expression analysis in mouse models for multiple sclerosis, Alzheimer's disease and stroke for identifying commonly regulated and disease-specific gene changes. PMID:20435134
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. PMID:20222994
A markov classification model for metabolic pathways. PMID:20047667
Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data. PMID:20015947
Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. PMID:19956698
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability. PMID:19941644
Data reporting standards: making the things we use better. PMID:19939294
Allergen databases: current status and perspectives. PMID:19671381
Beta-arrestin2 regulates parathyroid hormone effects on a p38 MAPK and NFkappaB gene expression network in osteoblasts. PMID:19560570
Orymold: ontology based gene expression data integration and analysis tool applied to rice. PMID:19463186
MYCN-non-amplified metastatic neuroblastoma with good prognosis and spontaneous regression: a molecular portrait of stage 4S. PMID:19383347
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. PMID:19200358
Repeatability of published microarray gene expression analyses. PMID:19174838
Using pathway signatures as means of identifying similarities among microarray experiments. PMID:19125200
SPRINT: a new parallel framework for R. PMID:19114001
Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality. PMID:19105848
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. PMID:19015125
Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. PMID:18851746
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. PMID:18803840
Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. PMID:18769540
Key issues in conducting a meta-analysis of gene expression microarray datasets. PMID:18767902
A decade of genome-wide gene expression profiling in acute myeloid leukemia: flashback and prospects. PMID:18703705
Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis. PMID:18637193
Standardization Initiatives in the (eco)toxicogenomics domain: a review. PMID:18629184
Navigating public microarray databases. PMID:18629145
The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data. PMID:18629134
Bioinformatic tools for inferring functional information from plant microarray data: tools for the first steps. PMID:18528524
Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. PMID:18487259
HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0. PMID:18487092
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. PMID:18463138
A software framework for microarray and gene expression object model (MAGE-OM) array design annotation. PMID:18366695
Enabling integrative genomic analysis of high-impact human diseases through text mining. PMID:18229717
Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. PMID:18177501
Determinants of protein abundance and translation efficiency in S. cerevisiae. PMID:18159940
Computational prediction of protein-protein interactions. PMID:18095187
BioCAD: an information fusion platform for bio-network inference and analysis. PMID:18047703
Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. PMID:17980019
Genetic and molecular epidemiology. PMID:17699527
PHIDIAS: a pathogen-host interaction data integration and analysis system. PMID:17663773
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. PMID:17651921
Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres. PMID:17651496
Integrated olfactory receptor and microarray gene expression databases. PMID:17603910
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. PMID:17567993
Sensitive and robust gene expression changes in fish exposed to estrogen--a microarray approach. PMID:17555559
PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories. PMID:17553161
The genopolis microarray database. PMID:17430566
Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME. PMID:17389643
Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation. PMID:17352823
High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations. PMID:17244361
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. PMID:17182626
Databases of free expression. PMID:17143588
Converting a breast cancer microarray signature into a high-throughput diagnostic test. PMID:17074082
The reactive oxygen species network pathways:an essential prerequisite for perception of pathogen attack and the acquired disease resistance in plants. PMID:17006022
Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana. PMID:16969662
Development and validation of a bovine macrophage specific cDNA microarray. PMID:16948847
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. PMID:16845058
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. PMID:16756676
Expression profiling of the mouse early embryo: reflections and perspectives. PMID:16739220
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. PMID:16597336
Development of a chicken 5 K microarray targeted towards immune function. PMID:16533398
Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use. PMID:16507466
The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development. PMID:16428600
Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. PMID:16420668
Recent applications of DNA microarray technology to toxicology and ecotoxicology. PMID:16393650
Mining published lists of cancer related microarray experiments: identification of a gene expression signature having a critical role in cell-cycle control. PMID:16351740
Analysis of microarray studies performed in the neurosciences. PMID:16280595
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data. PMID:16280078
Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH. PMID:16274472
Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. PMID:16254600
Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling. PMID:16224098
L2L: a simple tool for discovering the hidden significance in microarray expression data. PMID:16168088
A molecular map of mesenchymal tumors. PMID:16168083
Storing, linking, and mining microarray databases using SRS. PMID:16048644
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. PMID:15998450
How to improve quality assurance in fluorometry: fluorescence-inherent sources of error and suited fluorescence standards. PMID:15986157
T-profiler: scoring the activity of predefined groups of genes using gene expression data. PMID:15980543
Single-feature polymorphism discovery in the barley transcriptome. PMID:15960806
Toward supportive data collection tools for plant metabolomics. PMID:15888680
MARS: microarray analysis, retrieval, and storage system. PMID:15836795
Quantitative inference of dynamic regulatory pathways via microarray data. PMID:15748298
Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays. PMID:15653641
BarleyBase--an expression profiling database for plant genomics. PMID:15608273
The Stanford Microarray Database accommodates additional microarray platforms and data formats. PMID:15608265
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:15608260
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. PMID:15608201
Combining gene expression data from different generations of oligonucleotide arrays. PMID:15504239
In control: systematic assessment of microarray performance. PMID:15459748
PEDRo: a database for storing, searching and disseminating experimental proteomics data. PMID:15377392
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. PMID:15375207
Standards for microarray data: an open letter. PMID:15345376
Improving identification of differentially expressed genes in microarray studies using information from public databases. PMID:15345054
Submission of microarray data to public repositories. PMID:15340489
GOAL: automated Gene Ontology analysis of expression profiles. PMID:15215435
Expression Profiler: next generation--an online platform for analysis of microarray data. PMID:15215431
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states. PMID:15053844
Database development in toxicogenomics: issues and efforts. PMID:15033600
Toxicogenomics in risk assessment: an overview of an HESI collaborative research program. PMID:15033589
Scratching the (T cell) surface. PMID:14709166
EnsMart: a generic system for fast and flexible access to biological data. PMID:14707178
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. PMID:14681484
CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. PMID:14681477
yMGV: a cross-species expression data mining tool. PMID:14681424
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. PMID:14681408
The EMBL Nucleotide Sequence Database. PMID:14681351
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. PMID:14630514
Microarray analysis of gene expression during the cell cycle. PMID:14577836
New methods for finding disease-susceptibility genes: impact and potential. PMID:14519189
The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). PMID:12930545
REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data. PMID:12824350
GenePublisher: Automated analysis of DNA microarray data. PMID:12824347
The European Bioinformatics Institute's data resources. PMID:12519944
ArrayExpress update - from bulk to single-cell expression data PubMed citations: 207.

207 articles citing: ArrayExpress update - from bulk to single-cell expression data

The Potential Anti-remodeling Effect of Paroxetine After Myocardial Infarction May Be Blunted by Beta-Blockers. PMID:35898267
Identifying significant genes and functionally enriched pathways in familial hypercholesterolemia using integrated gene co-expression network analysis. PMID:35844366
Ecosystem-specific microbiota and microbiome databases in the era of big data. PMID:35842686
Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. PMID:35819579
Gene Co-Expression Network Tools and Databases for Crop Improvement. PMID:35807577
Computational Analysis Identifies Novel Biomarkers for High-Risk Bladder Cancer Patients. PMID:35806060
DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies. PMID:35798798
A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex. PMID:35736244
A Robust Immuno-Prognostic Model of Non-Muscle-Invasive Bladder Cancer Indicates Dynamic Interaction in Tumor Immune Microenvironment Contributes to Cancer Progression. PMID:35719408
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues. PMID:35714157
A comparative meta-proteomic pipeline for the identification of plasmodesmata proteins and regulatory conditions in diverse plant species. PMID:35655273
Artificial neural networks enable genome-scale simulations of intracellular signaling. PMID:35654811
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. PMID:35649389
Cold atmospheric plasmas target breast cancer stemness via modulating AQP3-19Y mediated AQP3-5K and FOXO1 K48-ubiquitination. PMID:35637961
Low Dose Gamma Irradiation of Trypanosoma evansi Parasites Identifies Molecular Changes That Occur to Repair Radiation Damage and Gene Transcripts That May Be Involved in Establishing Disease in Mice Post-Irradiation. PMID:35634275
Proteomic and transcriptomic profiles of human urothelial cancer cells with histone deacetylase 5 overexpression. PMID:35624179
Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages. PMID:35619054
Perception of a conserved family of plant signalling peptides by the receptor kinase HSL3. PMID:35617122
Gene co-expression network based on part mutual information for gene-to-gene relationship and gene-cancer correlation analysis. PMID:35610556
Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs. PMID:35587924
Multiomic Profiling Identified EGF Receptor Signaling as a Potential Inhibitor of Type I Interferon Response in Models of Oncolytic Therapy by Vesicular Stomatitis Virus. PMID:35563635
Cloning and Functional Characterization of Dog OCT1 and OCT2: Another Step in Exploring Species Differences in Organic Cation Transporters. PMID:35563491
Novel brown adipose tissue candidate genes predicted by the human gene connectome. PMID:35534514
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
Bringing machine learning to research on intellectual and developmental disabilities: taking inspiration from neurological diseases. PMID:35501679
Metabolomics-based phenotypic screens for evaluation of drug synergy via direct-infusion mass spectrometry. PMID:35494234
The Landscape of Novel Expressed Chimeric RNAs in Rheumatoid Arthritis. PMID:35406656
Insight Into the Long Noncoding RNA and mRNA Coexpression Profile in the Human Blood Transcriptome Upon Leishmania infantum Infection. PMID:35370994
Current progress and open challenges for applying deep learning across the biosciences. PMID:35365602
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells. PMID:35363305
Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers. PMID:35316277
Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model. PMID:35310659
Cardiac protection by pirfenidone after myocardial infarction: a bioinformatic analysis. PMID:35304529
Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions. PMID:35288573
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States. PMID:35269470
Advancing discovery in hearing research via biologist-friendly access to multi-omic data. PMID:35235019
Targeting Apoptosis Pathways With BCL2 and MDM2 Inhibitors in Adult B-cell Acute Lymphoblastic Leukemia. PMID:35233509
Identification of UBE2I as a Novel Biomarker in ccRCC Based on a Large-Scale CRISPR-Cas9 Screening Database and Immunohistochemistry. PMID:35211510
Impact of Maternal Obesity on Liver Disease in the Offspring: A Comprehensive Transcriptomic Analysis and Confirmation of Results in a Murine Model. PMID:35203502
Integrative OMICS Data-Driven Procedure Using a Derivatized Meta-Analysis Approach. PMID:35186042
Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model. PMID:35164671
PlantGF: an analysis and annotation platform for plant gene families. PMID:35134149
Transcriptional Control of Hypoxic Hyphal Growth in the Fungal Pathogen Candida albicans. PMID:35127551
gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues. PMID:35102184
Ontology-based identification and prioritization of candidate drugs for epilepsy from literature. PMID:35073996
Dictionary learning allows model-free pseudotime estimation of transcriptomic data. PMID:35033004
The Vulnerability of the Developing Brain: Analysis of Highly Expressed Genes in Infant C57BL/6 Mouse Hippocampus in Relation to Phenotypic Annotation Derived From Mutational Studies. PMID:35023907
Meta-analysis of whole-genome gene expression datasets assessing the effects of IDH1 and IDH2 mutations in isogenic disease models. PMID:34997121
Significance of CD47 and Its Association With Tumor Immune Microenvironment Heterogeneity in Ovarian Cancer. PMID:34966389
Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes. PMID:34944646
Characterization of SLC34A2 as a Potential Prognostic Marker of Oncological Diseases. PMID:34944522
Fibroblast growth factor (FGF), FGF receptor (FGFR), and cyclin D1 (CCND1) DNA methylation in head and neck squamous cell carcinomas is associated with transcriptional activity, gene amplification, human papillomavirus (HPV) status, and sensitivity to tyrosine kinase inhibitors. PMID:34933671
Supervised Methods for Biomarker Detection from Microarray Experiments. PMID:34902125
Improving Analysis and Annotation of Microarray Data with Protein Interactions. PMID:34902122
Cystic Fibrosis: Systems Biology Analysis from Homozygous p.Phe508del Variant Patients' Samples Reveals Perturbations in Tissue-Specific Pathways. PMID:34901273
Integrative analysis of immune-related multi-omics profiles identifies distinct prognosis and tumor microenvironment patterns in osteosarcoma. PMID:34894177
Chemical biology-whole genome engineering datasets predict new antibacterial combinations. PMID:34874820
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
recount3: summaries and queries for large-scale RNA-seq expression and splicing. PMID:34844637
Automatic cell type identification methods for single-cell RNA sequencing. PMID:34815832
Defective cytokinin signaling reprograms lipid and flavonoid gene-to-metabolite networks to mitigate high salinity in Arabidopsis. PMID:34815339
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. PMID:34791440
DNA Data Bank of Japan (DDBJ) update report 2021. PMID:34751405
BioSamples database: FAIRer samples metadata to accelerate research data management. PMID:34747489
Computational workflow for functional characterization of COVID-19 through secondary data analysis. PMID:34746856
Identification of an Autophagy-Related Risk Signature Correlates With Immunophenotype and Predicts Immune Checkpoint Blockade Efficacy of Neuroblastoma. PMID:34746127
Band-based similarity indices for gene expression classification and clustering. PMID:34732744
Relationships between type 2 diabetes, cell dysfunction, and redox signaling: A meta-analysis of single-cell gene expression of human pancreatic α- and β-cells. PMID:34725923
Identification of Key eRNAs for Spinal Cord Injury by Integrated Multinomial Bioinformatics Analysis. PMID:34708039
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
Investigations on the Degradation of the Bile Salt Cholate via the 9,10-Seco-Pathway Reveals the Formation of a Novel Recalcitrant Steroid Compound by a Side Reaction in Sphingobium sp. Strain Chol11. PMID:34683472
SysInflam HuDB, a Web Resource for Mining Human Blood Cells Transcriptomic Data Associated with Systemic Inflammatory Responses to Sepsis. PMID:34663591
The network interplay of interferon and Toll-like receptor signaling pathways in the anti-Candida immune response. PMID:34645905
CancerSCEM: a database of single-cell expression map across various human cancers. PMID:34643725
Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival. PMID:34639124
VThunter: a database for single-cell screening of virus target cells in the animal kingdom. PMID:34634807
Prediction of Biochemical Recurrence-Free Survival of Prostate Cancer Patients Leveraging Multiple Gene Expression Profiles in Tumor Microenvironment. PMID:34631510
A proteomics sample metadata representation for multiomics integration and big data analysis. PMID:34615866
PIK3CB is involved in metastasis through the regulation of cell adhesion to collagen I in pancreatic cancer. PMID:34603784
ISA API: An open platform for interoperable life science experimental metadata. PMID:34528664
KCa channel blockers increase effectiveness of the EGF receptor TK inhibitor erlotinib in non-small cell lung cancer cells (A549). PMID:34526525
Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism. PMID:34521731
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. PMID:34493866
Genotypes of informative loci from 1000 Genomes data allude evolution and mixing of human populations. PMID:34493766
ARMT: An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research. PMID:34471489
Reproducibility and robustness of high-throughput S1500+ transcriptomics on primary rat hepatocytes for chemical-induced hepatotoxicity assessment. PMID:34467220
RNA Sequencing Analyses for Deciphering Potato Molecular Responses. PMID:34448155
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Non-Tumor CCAAT/Enhancer-Binding Protein Delta Potentiates Tumor Cell Extravasation and Pancreatic Cancer Metastasis Formation. PMID:34439745
A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer. PMID:34412551
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. PMID:34403477
Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study. PMID:34394179
A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression. PMID:34381057
Clinical significance and molecular mechanism of angiotensin-converting enzyme 2 in hepatocellular carcinoma tissues. PMID:34369278
PSMB7 Is a Key Gene Involved in the Development of Multiple Myeloma and Resistance to Bortezomib. PMID:34367968
Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function. PMID:34353905
Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis. PMID:34282769
Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis. PMID:34281497
The Progenetix oncogenomic resource in 2021. PMID:34272855
CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking. PMID:34255742
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. PMID:34211498
Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models. PMID:34205912
Screen Key Genes Associated with Distraction-Induced Osteogenesis of Stem Cells Using Bioinformatics Methods. PMID:34204414
Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct Carcinoma. PMID:34200770
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity. PMID:34172724
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue. PMID:34136521
Decoding empagliflozin's molecular mechanism of action in heart failure with preserved ejection fraction using artificial intelligence. PMID:34103605
Multiomic analysis of stretched osteocytes reveals processes and signalling linked to bone regeneration and cancer. PMID:34099736
MiR-15a-5p Confers Chemoresistance in Acute Myeloid Leukemia by Inhibiting Autophagy Induced by Daunorubicin. PMID:34068078
Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. PMID:34065451
SIK2 kinase synthetic lethality is driven by spindle assembly defects in FANCA-deficient cells. PMID:34058059
A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers. PMID:33983435
Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization. PMID:33963293
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. PMID:33937763
Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling. PMID:33922083
Disentangling age-dependent DNA methylation: deterministic, stochastic, and nonlinear. PMID:33911141
EPISPOT: An epigenome-driven approach for detecting and interpreting hotspots in molecular QTL studies. PMID:33909991
Analysis workflow of publicly available RNA-sequencing datasets. PMID:33907739
Cleavage of the vaspin N-terminus releases cell-penetrating peptides that affect early stages of adipogenesis and inhibit lipolysis in mature adipocytes. PMID:33866927
Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer. PMID:33803328
Consensus Transcriptional Landscape of Human End-Stage Heart Failure. PMID:33787284
De novo histidine biosynthesis protects Mycobacterium tuberculosis from host IFN-γ mediated histidine starvation. PMID:33767335
Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework. PMID:33732286
Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future. PMID:33711481
Meta-Analysis of Oxidative Transcriptomes in Insects. PMID:33669076
Fast searches of large collections of single-cell data using scfind. PMID:33649586
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation. PMID:33575256
A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression. PMID:33546472
Independent component analysis recovers consistent regulatory signals from disparate datasets. PMID:33529205
Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies. PMID:33526761
Screening of disease-related biomarkers related to neuropathic pain (NP) after spinal cord injury (SCI). PMID:33494823
Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators. PMID:33458747
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. PMID:33441124
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes. PMID:33430123
Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk. PMID:33339112
MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle. PMID:33338203
RNA-Seq transcriptome data of human cells infected with influenza A/Puerto Rico/8/1934 (H1N1) virus. PMID:33318985
Hearing impairment due to Mir183/96/182 mutations suggests both loss and gain of function effects. PMID:33318051
Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast. PMID:33313903
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. PMID:33279989
miR-15a-5p and miR-21-5p contribute to chemoresistance in cytogenetically normal acute myeloid leukaemia by targeting PDCD4, ARL2 and BTG2. PMID:33270982
The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase. PMID:33225887
From ArrayExpress to BioStudies. PMID:33211879
Tracing the footsteps of autophagy in computational biology. PMID:33201177
Guidelines for reporting single-cell RNA-seq experiments. PMID:33188371
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. PMID:33179754
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. PMID:33174603
DDBJ update: streamlining submission and access of human data. PMID:33156332
GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions. PMID:33151298
Heavy Metal Transporters-Associated Proteins in S. tuberosum: Genome-Wide Identification, Comprehensive Gene Feature, Evolution and Expression Analysis. PMID:33126505
The mouse Gene Expression Database (GXD): 2021 update. PMID:33104772
A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes. PMID:33074331
Exploiting oxidative phosphorylation to promote the stem and immunoevasive properties of pancreatic cancer stem cells. PMID:33067432
Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients. PMID:33051456
iMOKA: k-mer based software to analyze large collections of sequencing data. PMID:33050927
Therapeutic Opportunities for Intestinal Angioectasia- Targeting PPARγ and Oxidative Stress. PMID:33048460
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
A meta-analysis of microRNAs expressed in human aerodigestive epithelial cultures and their role as potential biomarkers of exposure response to nicotine-containing products. PMID:33014713
Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses. PMID:32998684
A simple, scalable approach to building a cross-platform transcriptome atlas. PMID:32986694
Bioinformatic Identification of Neuroblastoma Microenvironment-Associated Biomarkers with Prognostic Value. PMID:32963529
Global reprogramming of virulence and antibiotic resistance in Pseudomonas aeruginosa by a single nucleotide polymorphism in elongation factor, fusA1. PMID:32943550
The Expression and Potential Role of Tubulin Alpha 1b in Wilms' Tumor. PMID:32908931
Cross-sectional study of human coding- and non-coding RNAs in progressive stages of Helicobacter pylori infection. PMID:32901043
Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants. PMID:32880574
BrassicaEDB: A Gene Expression Database for Brassica Crops. PMID:32823802
Circuits Regulating Superoxide and Nitric Oxide Production and Neutralization in Different Cell Types: Expression of Participating Genes and Changes Induced by Ionizing Radiation. PMID:32756515
Scion genotypes exert long distance control over rootstock transcriptome responses to low phosphate in grafted grapevine. PMID:32746781
Merging microarray studies to identify a common gene expression signature to several structural heart diseases. PMID:32670412
Moderate Mechanical Stimulation Protects Rats against Osteoarthritis through the Regulation of TRAIL via the NF-κB/NLRP3 Pathway. PMID:32566090
Integrative computational epigenomics to build data-driven gene regulation hypotheses. PMID:32543653
Scoring functions for drug-effect similarity. PMID:32484516
Available Software for Meta-analyses of Genome-wide Expression Studies. PMID:32476989
ISG15 and ISGylation is required for pancreatic cancer stem cell mitophagy and metabolic plasticity. PMID:32472071
Putative cell type discovery from single-cell gene expression data. PMID:32424270
The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds. PMID:32423144
Prediction of condition-specific regulatory genes using machine learning. PMID:32329779
Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine. PMID:32296688
Detection and Comparative Analysis of Methylomic Biomarkers of Rheumatoid Arthritis. PMID:32292416
In silico analysis of the immunological landscape of pituitary adenomas. PMID:32236778
Building blocks are synthesized on demand during the yeast cell cycle. PMID:32213592
RASflow: an RNA-Seq analysis workflow with Snakemake. PMID:32183729
GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest. PMID:32140729
Evaluating the Use of Circulating MicroRNA Profiles for Lung Cancer Detection in Symptomatic Patients. PMID:32134442
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Data libraries - the missing element for modeling biological systems. PMID:32100391
Vitamin D Receptor Overexpression in β-Cells Ameliorates Diabetes in Mice. PMID:32086292
Personalized Assessment of Normal Tissue Radiosensitivity via Transcriptome Response to Photon, Proton and Carbon Irradiation in Patient-Derived Human Intestinal Organoids. PMID:32085439
A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. PMID:31992182
Open Data for Differential Network Analysis in Glioma. PMID:31952211
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. PMID:31950984
Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammation. PMID:31944177
Meta-Analysis of Hypoxic Transcriptomes from Public Databases. PMID:31936636
Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans. PMID:31822273
Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions. PMID:31781177
ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. PMID:31743345
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. PMID:31701143
Expression Atlas update: from tissues to single cells. PMID:31665515
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
Transcriptome visualization and data availability at the Saccharomyces Genome Database. PMID:31612944
Unique Gene Expression Signatures in the Intestinal Mucosa and Organoids Derived from Germ-Free and Monoassociated Mice. PMID:30934845
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. PMID:30626175
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments PubMed citations: 186.

186 articles citing: ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. PMID:35501320
Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders. PMID:34563116
ITGA2, LAMB3, and LAMC2 may be the potential therapeutic targets in pancreatic ductal adenocarcinoma: an integrated bioinformatics analysis. PMID:34007003
Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk. PMID:33339112
From ArrayExpress to BioStudies. PMID:33211879
First Steps in the Successful Fertilization of Rice and Arabidopsis: Pollen Longevity, Adhesion and Hydration. PMID:32751098
Integrated analysis of DNA methylation and transcriptome profiling of polycystic ovary syndrome. PMID:32323770
A Direct Comparison of Thyroid Hormone Receptor Protein Levels in Mice Provides Unexpected Insights into Thyroid Hormone Action. PMID:32122258
Identification of Monotonically Differentially Expressed Genes for IFN-β-Treated Multiple Sclerosis Patients. PMID:31915697
Identification of Transcriptional Metabolic Dysregulation in Subtypes of Pituitary Adenoma by Integrated Bioinformatics Analysis. PMID:31819570
Reduced expression of microRNA-139-5p in hepatocellular carcinoma results in a poor outcome: An exploration the roles of microRNA-139-5p in tumorigenesis, advancement and prognosis at the molecular biological level using an integrated meta-analysis and bioinformatic investigation. PMID:31807180
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. PMID:31799603
Elevated CD44 expression predicts poor prognosis in patients with low-grade glioma. PMID:31516582
Incorporating Pathway Information into Feature Selection towards Better Performed Gene Signatures. PMID:31073522
Personalized Medicine and Molecular Interaction Networks in Amyotrophic Lateral Sclerosis (ALS): Current Knowledge. PMID:30551677
ArrayExpress update - from bulk to single-cell expression data. PMID:30357387
A radiogenomic dataset of non-small cell lung cancer. PMID:30325352
Cyclin D1-mediated microRNA expression signature predicts breast cancer outcome. PMID:29721077
When Transcriptomics and Metabolomics Work Hand in Hand: A Case Study Characterizing Plant CDF Transcription Factors. PMID:29495643
Quantitative or qualitative transcriptional diagnostic signatures? A case study for colorectal cancer. PMID:29378509
Drug repurposing for the treatment of glioblastoma multiforme. PMID:29179732
Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments. PMID:29134529
Genome build information is an essential part of genomic track files. PMID:28911336
Identification of the Consistently Altered Metabolic Targets in Human Hepatocellular Carcinoma. PMID:28840186
Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm. PMID:28828699
Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis. PMID:28789679
Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions. PMID:28683715
C9ORF135 encodes a membrane protein whose expression is related to pluripotency in human embryonic stem cells. PMID:28345668
A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without. PMID:27846842
Identification of Genes Discriminating Multiple Sclerosis Patients from Controls by Adapting a Pathway Analysis Method. PMID:27846233
Dies1/VISTA expression loss is a recurrent event in gastric cancer due to epigenetic regulation. PMID:27721458
Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes. PMID:27681389
CardioTF, a database of deconstructing transcriptional circuits in the heart system. PMID:27635320
Improving Spleen Volume Estimation Via Computer-assisted Segmentation on Clinically Acquired CT Scans. PMID:27519156
Databases and tools for constructing signal transduction networks in cancer. PMID:27502015
GEE: An Informatics Tool for Gene Expression Data Explore. PMID:27200217
Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. PMID:27100087
A physiome interoperability roadmap for personalized drug development. PMID:27051513
A molecular classification of human mesenchymal stromal cells. PMID:27042394
A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor. PMID:26692761
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions. PMID:26452147
Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection. PMID:26162090
Competition-cooperation relationship networks characterize the competition and cooperation between proteins. PMID:26108281
The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. PMID:26093607
BioMiner: Paving the Way for Personalized Medicine. PMID:26005322
Comparison of merging and meta-analysis as alternative approaches for integrative gene expression analysis. PMID:25937953
EPMA position paper in cancer: current overview and future perspectives. PMID:25908947
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. PMID:25819073
Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. PMID:25774498
Biological databases for human research. PMID:25712261
Identifying genetic interactions associated with late-onset Alzheimer's disease. PMID:25649863
Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data. PMID:25628763
High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology. PMID:25437800
Expression and evolution of the Tiki1 and Tiki2 genes in vertebrates. PMID:25354456
Measuring the effect of inter-study variability on estimating prediction error. PMID:25330348
DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. PMID:25267467
Translating bioinformatics in oncology: guilt-by-profiling analysis and identification of KIF18B and CDCA3 as novel driver genes in carcinogenesis. PMID:25236463
ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions. PMID:25228922
Radiogenomic imaging-linking diagnostic imaging and molecular diagnostics. PMID:25170389
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool. PMID:24904397
Co-expression network analysis identifies transcriptional modules in the mouse liver. PMID:24816893
categoryCompare, an analytical tool based on feature annotations. PMID:24808906
Bridging the gaps in systems biology. PMID:24728588
The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences. PMID:24682735
PATHOME: an algorithm for accurately detecting differentially expressed subpathways. PMID:24681952
Translational research platforms integrating clinical and omics data: a review of publicly available solutions. PMID:24608524
CorrelaGenes: a new tool for the interpretation of the human transcriptome. PMID:24564370
Photoperiodic control of carbon distribution during the floral transition in Arabidopsis. PMID:24563199
Identification of core T cell network based on immunome interactome. PMID:24528953
Sources of high variance between probe signals in Affymetrix short oligonucleotide microarrays. PMID:24385030
PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. PMID:24312499
Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data. PMID:24280533
Updates to BioSamples database at European Bioinformatics Institute. PMID:24265224
Integrating in silico resources to map a signaling network. PMID:24233784
Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia. PMID:24219996
SPIEDw: a searchable platform-independent expression database web tool. PMID:24199845
Computational approaches for discovery of common immunomodulators in fungal infections: towards broad-spectrum immunotherapeutic interventions. PMID:24099000
Ontology based molecular signatures for immune cell types via gene expression analysis. PMID:24004649
ESTOOLS Data@Hand: human stem cell gene expression resource. PMID:23985726
Structural and logical analysis of a comprehensive hedgehog signaling pathway to identify alternative drug targets for glioma, colon and pancreatic cancer. PMID:23935937
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. PMID:23935057
A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. PMID:23874666
NanoMiner - integrative human transcriptomics data resource for nanoparticle research. PMID:23874618
Insights into TREM2 biology by network analysis of human brain gene expression data. PMID:23855984
Gene expression analysis of peripheral blood cells reveals Toll-like receptor pathway deregulation in colorectal cancer. PMID:23650534
Iterative rank-order normalization of gene expression microarray data. PMID:23647742
A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis. PMID:23638386
Chapter 15: disease gene prioritization. PMID:23633938
When is hub gene selection better than standard meta-analysis? PMID:23613865
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. PMID:23563154
curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. PMID:23550061
Global gene expression profiling reveals SPINK1 as a potential hepatocellular carcinoma marker. PMID:23527199
Uncovering hidden duplicated content in public transcriptomics data. PMID:23487185
ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. PMID:23457041
virtualArray: a R/bioconductor package to merge raw data from different microarray platforms. PMID:23452776
The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization. PMID:23445545
A novel method for cross-species gene expression analysis. PMID:23444967
Intravenous glial growth factor 2 (GGF2) isoform of neuregulin-1β improves left ventricular function, gene and protein expression in rats after myocardial infarction. PMID:23437060
Developmental and environmental regulation of Aquaporin gene expression across Populus species: divergence or redundancy? PMID:23393587
Characterization of transcriptional changes in ERG rearrangement-positive prostate cancer identifies the regulation of metabolic sensors such as neuropeptide Y. PMID:23390522
Evaluation of methods for modeling transcription factor sequence specificity. PMID:23354101
Multi-parameter systematic strategies for predictive, preventive and personalised medicine in cancer. PMID:23339750
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. PMID:23325622
An integrative approach to inferring gene regulatory module networks. PMID:23285197
StRAP: an integrated resource for profiling high-throughput cancer genomic data from stress response studies. PMID:23284744
Reuse of public genome-wide gene expression data. PMID:23269463
Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages. PMID:23259851
CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data. PMID:23241162
Exploiting parallel R in the cloud with SPRINT. PMID:23223611
Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli. PMID:23222720
Analysis of gene expression data from non-small cell lung carcinoma cell lines reveals distinct sub-classes from those identified at the phenotype level. PMID:23209689
Identification of pharmacological targets in amyotrophic lateral sclerosis through genomic analysis of deregulated genes and pathways. PMID:23204922
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. PMID:23203880
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. PMID:23203868
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
ArrayExpress update--trends in database growth and links to data analysis tools. PMID:23193272
NCBI GEO: archive for functional genomics data sets--update. PMID:23193258
Molecular pathways involved in prostate carcinogenesis: insights from public microarray datasets. PMID:23185449
RiceFREND: a platform for retrieving coexpressed gene networks in rice. PMID:23180784
RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. PMID:23180765
Application of genomic tools in plant breeding. PMID:23115520
BirdsEyeView (BEV): graphical overviews of experimental data. PMID:23046276
Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. PMID:22978381
Evaluation of research in biomedical ontologies. PMID:22962340
Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. PMID:22961666
Characterization of a viral synergism in the monocot Brachypodium distachyon reveals distinctly altered host molecular processes associated with disease. PMID:22961132
The chordate proteome history database. PMID:22904610
Toward a combinatorial nature of microRNA regulation in human cells. PMID:22904063
Influence of common genetic variation on lung cancer risk: meta-analysis of 14 900 cases and 29 485 controls. PMID:22899653
Transcriptional data: a new gateway to drug repositioning? PMID:22897878
BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. PMID:22847375
Molecular typing and epidemiological investigation of clinical populations of Pseudomonas aeruginosa using an oligonucleotide-microarray. PMID:22840192
Computational tools for prioritizing candidate genes: boosting disease gene discovery. PMID:22751426
Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results. PMID:22723499
Leukemia gene atlas--a public platform for integrative exploration of genome-wide molecular data. PMID:22720055
Identification of metagenes and their interactions through large-scale analysis of Arabidopsis gene expression data. PMID:22694750
First insights into the unexplored two-component system YehU/YehT in Escherichia coli. PMID:22685278
A novel strategy for selection and validation of reference genes in dynamic multidimensional experimental design in yeast. PMID:22675547
Identification of RARRES1 as a core regulator in liver fibrosis. PMID:22669512
Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. PMID:22645320
arrayMap: a reference resource for genomic copy number imbalances in human malignancies. PMID:22629346
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
O-miner: an integrative platform for automated analysis and mining of -omics data. PMID:22600742
Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PMID:22589741
Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. PMID:22582075
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. PMID:22570409
graph2tab, a library to convert experimental workflow graphs into tabular formats. PMID:22556367
Paternal Benzo[a]pyrene Exposure Modulates MicroRNA Expression Patterns in the Developing Mouse Embryo. PMID:22548065
Molecular signatures from omics data: from chaos to consensus. PMID:22528809
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. PMID:22369666
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. PMID:22369646
Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. PMID:22307966
A searchable cross-platform gene expression database reveals connections between drug treatments and disease. PMID:22233519
Mechanisms of resistance to chloramphenicol in Pseudomonas putida KT2440. PMID:22143519
MetaBase--the wiki-database of biological databases. PMID:22139927
neXtProt: a knowledge platform for human proteins. PMID:22139911
A unified framework for managing provenance information in translational research. PMID:22126369
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. PMID:22110025
The BioSample Database (BioSD) at the European Bioinformatics Institute. PMID:22096232
PLEXdb: gene expression resources for plants and plant pathogens. PMID:22084198
Disease Ontology: a backbone for disease semantic integration. PMID:22080554
The International Nucleotide Sequence Database Collaboration. PMID:22080546
WormBase 2012: more genomes, more data, new website. PMID:22067452
Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks. PMID:22035155
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
A framework to select clinically relevant cancer cell lines for investigation by establishing their molecular similarity with primary human cancers. PMID:22012889
The Sequence Read Archive: explosive growth of sequencing data. PMID:22009675
Chipster: user-friendly analysis software for microarray and other high-throughput data. PMID:21999641
Systems-biology approaches to discover anti-viral effectors of the human innate immune response. PMID:21994773
pubmed2ensembl: a resource for mining the biological literature on genes. PMID:21980353
ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. PMID:21967760
Genomic and phenotypic analysis of BRCA2 mutated breast cancers reveals co-occurring changes linked to progression. PMID:21958427
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. PMID:21884636
The real cost of sequencing: higher than you think! PMID:21867570
The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins. PMID:21695268
Leucine-rich repeat kinase 2 modulates retinoic acid-induced neuronal differentiation of murine embryonic stem cells. PMID:21695257
g:Profiler--a web server for functional interpretation of gene lists (2011 update). PMID:21646343
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. PMID:21531804
Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. PMID:21441235
Elucidation of the regulon and cis-acting regulatory element of HrpB, the AraC-type regulator of a plant pathogen-like type III secretion system in Burkholderia pseudomallei. PMID:21335458

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chromatin immunoprecipitation - dna microarray
metasource: Fairsharing.org
version: FAIRsharing.org: ArrayExpress; ArrayExpress; DOI: https://doi.org/10.25504/FAIRsharing.6k0kwd; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: ArrayExpress; ArrayExpress; DOI: https://doi.org/10.25504/FAIRsharing.6k0kwd; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

dna microarray
metasource: Fairsharing.org
version: FAIRsharing.org: ArrayExpress; ArrayExpress; DOI: https://doi.org/10.25504/FAIRsharing.6k0kwd; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: ArrayExpress; ArrayExpress; DOI: https://doi.org/10.25504/FAIRsharing.6k0kwd; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

experimentally determined
metasource: Fairsharing.org
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gene expression
metasource: Fairsharing.org
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metasource: re3data.org
version: re3data.org: ArrayExpress; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3302G last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: ArrayExpress; ArrayExpress; DOI: https://doi.org/10.25504/FAIRsharing.6k0kwd; Last edited: Feb. 8, 2021, 8:54 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

genotyping
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methylation
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nucleotide
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protocol
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rna sequencing
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dna & rna
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bioinformatics
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version: re3data.org: ArrayExpress; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3302G last accessed: 2022-11-04

functional genomics data
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genomics
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ontologies
metasource: re3data.org
version: re3data.org: ArrayExpress; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3302G last accessed: 2022-11-04

proteins
metasource: re3data.org
version: re3data.org: ArrayExpress; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3302G last accessed: 2022-11-04

sequencing application
metasource: re3data.org
version: re3data.org: ArrayExpress; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3302G last accessed: 2022-11-04

functional genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.707124

chromatin immunoprecipitation - dna microarray chromatin immunoprecipitation - dna sequencing dna microarray experimental measurement experimentally determined gene expression gene expression genotyping methylation nucleotide protocol rna sequence dna & rna bioinformatics functional genomics data genomics ontologies proteins sequencing application functional genomics

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Tomato Functional Genomics Database

Gemma

GeneProf

Functional Genomics Experiment Markup Language

Minimum Information About a Microarray Experiment

BioSamples at the European Bioinformatics Institute

modMine

caArray

The European Bioinformatics Institute Tools

Gene Expression Barcode

European Nucleotide Archive

COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia

Stanford Microarray Database

XenMine

MGnify