GeneSigDB

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GeneSigDB

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

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genesigdb

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

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Other names: genesigdb

Gene Signature DataBase

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Publications:

Publications

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GeneSigDB--a curated database of gene expression signatures
PMID: 19934259

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

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GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
PMID: 22110038

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

---

http://dx.doi.org/10.1093/nar/GKR901

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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• GeneSigDB--a curated database of gene expression signatures PubMed citations: 62.

  62 articles citing: GeneSigDB--a curated database of gene expression signatures

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  Application of weighted gene co-expression network analysis to identify the hub genes in H1N1. PMID:34336131

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  HGNChelper: identification and correction of invalid gene symbols for human and mouse. PMID:33564398

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  A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024

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  A dichotomy of gene regulatory associations during the activated B-cell to plasmablast transition. PMID:32843533

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  netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis. PMID:31992614

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  A Novel Discovery: Holistic Efficacy at the Special Organ Level of Pungent Flavored Compounds from Pungent Traditional Chinese Medicine. PMID:30754631

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  Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response. PMID:29331675

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  Drug repurposing for the treatment of glioblastoma multiforme. PMID:29179732

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  Non-Small Cell Lung Cancer Radiogenomics Map Identifies Relationships between Molecular and Imaging Phenotypes with Prognostic Implications. PMID:28727543

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  The CINSARC signature as a prognostic marker for clinical outcome in multiple neoplasms. PMID:28710396

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  annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq. PMID:28169395

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  The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120

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  Network Analysis Identifies Proinflammatory Plasma Cell Polarization for Secretion of ISG15 in Human Autoimmunity. PMID:27357150

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  Finding New Order in Biological Functions from the Network Structure of Gene Annotations. PMID:26588252

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  Gene expression meta-analysis reveals immune response convergence on the IFNγ-STAT1-IRF1 axis and adaptive immune resistance mechanisms in lymphoma. PMID:26362649

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  Inhibition of Thrombopoietin/Mpl Signaling in Adult Hematopoiesis Identifies New Candidates for Hematopoietic Stem Cell Maintenance. PMID:26147434

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  DSigDB: drug signatures database for gene set analysis. PMID:25990557

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  Pancancer analysis of DNA methylation-driven genes using MethylMix. PMID:25631659

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  Transcriptional coexpression network reveals the involvement of varying stem cell features with different dysregulations in different gastric cancer subtypes. PMID:24917244

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  Pathway and network analysis in proteomics. PMID:24911777

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  SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity. PMID:24875472

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  Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. PMID:24569707

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  Identification of ovarian cancer driver genes by using module network integration of multi-omics data. PMID:24511378

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  Polymorphic cytochrome P450 enzymes (CYPs) and their role in personalized therapy. PMID:24340040

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  Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data. PMID:24266983

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  Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data. PMID:23895370

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  Network2Canvas: network visualization on a canvas with enrichment analysis. PMID:23749960

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  GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis. PMID:23650583

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  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463

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  Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis. PMID:23536770

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  A microarray platform-independent classification tool for cell of origin class allows comparative analysis of gene expression in diffuse large B-cell lymphoma. PMID:23424639

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  Identifying master regulators of cancer and their downstream targets by integrating genomic and epigenomic features. PMID:23424118

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  A data similarity-based strategy for meta-analysis of transcriptional profiles in cancer. PMID:23383020

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  Exact statistical tests for the intersection of independent lists of genes. PMID:23335952

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  Expression profiling of archival tumors for long-term health studies. PMID:23136189

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  Transcriptional data: a new gateway to drug repositioning? PMID:22897878

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  Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape. PMID:22820642

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  iBBiG: iterative binary bi-clustering of gene sets. PMID:22789589

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  Integration of breast cancer gene signatures based on graph centrality. PMID:22784616

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  Genes2FANs: connecting genes through functional association networks. PMID:22748121

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  Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer. PMID:22710433

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  Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. PMID:22499558

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  Liverome: a curated database of liver cancer-related gene signatures with self-contained context information. PMID:22369201

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  Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer. PMID:22348002

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  A three-gene model to robustly identify breast cancer molecular subtypes. PMID:22262870

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  Comprehensive literature review and statistical considerations for microarray meta-analysis. PMID:22262733

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  Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment. PMID:22235100

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  The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. PMID:22121217

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  GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. PMID:22110038

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  Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. PMID:22096235

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  SIGNATURE: a workbench for gene expression signature analysis. PMID:22078435

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  Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. PMID:22064864

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  Network based consensus gene signatures for biomarker discovery in breast cancer. PMID:22046239

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  3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. PMID:21959866

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  Integrative computational biology for cancer research. PMID:21691773

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  Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence. PMID:21672909

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  Molecular signatures database (MSigDB) 3.0. PMID:21546393

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  Conceptual aspects of large meta-analyses with publicly available microarray data: a case study in oncology. PMID:21423405

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  Breast cancer biomarker discovery in the functional genomic age: a systematic review of 42 gene expression signatures. PMID:21082037

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  A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database. PMID:20699007

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  Discovering causal signaling pathways through gene-expression patterns. PMID:20494976

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  Data reporting standards: making the things we use better. PMID:19939294
• GeneSigDB: a manually curated database and resource for analysis of gene expression signatures PubMed citations: 62.

  62 articles citing: GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

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  Amadis: A Comprehensive Database for Association Between Microbiota and Disease. PMID:34335304

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  Declined expressions of vast mitochondria-related genes represented by CYCS and transcription factor ESRRA in skeletal muscle aging. PMID:34229541

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  Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. PMID:33861732

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  Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams. PMID:33627109

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  Identification of a Transcriptomic Prognostic Signature by Machine Learning Using a Combination of Small Cohorts of Prostate Cancer. PMID:33324443

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  An Improved, Assay Platform Agnostic, Absolute Single Sample Breast Cancer Subtype Classifier. PMID:33255759

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  Transcriptome Analysis Identifies SenZfp536, a Sense LncRNA that Suppresses Self-renewal of Cortical Neural Progenitors. PMID:33196962

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  signatureSearch: environment for gene expression signature searching and functional interpretation. PMID:33068417

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  The transcription factor C/EBPβ orchestrates dendritic cell maturation and functionality under homeostatic and malignant conditions. PMID:33020261

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  Gene Set Analysis: Challenges, Opportunities, and Future Research. PMID:32695141

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  Identification and Analysis of Glioblastoma Biomarkers Based on Single Cell Sequencing. PMID:32195242

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  The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer. PMID:31871106

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  Dissection of gene expression datasets into clinically relevant interaction signatures via high-dimensional correlation maximization. PMID:31780653

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  The TargetMine Data Warehouse: Enhancement and Updates. PMID:31649722

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  BEERE: a web server for biomedical entity expansion, ranking and explorations. PMID:31114876

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  Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays. PMID:30169535

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  "Super Gene Set" Causal Relationship Discovery from Functional Genomics Data. PMID:30040650

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  GSEA-InContext: identifying novel and common patterns in expression experiments. PMID:29950010

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  GEsture: an online hand-drawing tool for gene expression pattern search. PMID:29942676

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  CancerDiscover: an integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data. PMID:29416792

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  PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. PMID:29126216

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  NFPscanner: a webtool for knowledge-based deciphering of biomedical networks. PMID:28521733

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  MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets. PMID:28472340

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  Detecting gene signature activation in breast cancer in an absolute, single-patient manner. PMID:28327201

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  pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. PMID:27899558

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  The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120

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  The Role of Proliferation in Determining Response to Neoadjuvant Chemotherapy in Breast Cancer: A Gene Expression-Based Meta-Analysis. PMID:27330058

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  Efficient Test and Visualization of Multi-Set Intersections. PMID:26603754

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  Finding New Order in Biological Functions from the Network Structure of Gene Annotations. PMID:26588252

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  Profiling of Discrete Gynecological Cancers Reveals Novel Transcriptional Modules and Common Features Shared by Other Cancer Types and Embryonic Stem Cells. PMID:26559525

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  Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations. PMID:26444668

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  GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature. PMID:26199946

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  Multiple signatures of a disease in potential biomarker space: Getting the signatures consensus and identification of novel biomarkers. PMID:26100469

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  PAGER: constructing PAGs and new PAG-PAG relationships for network biology. PMID:26072489

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  Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles. PMID:26040557

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  Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues. PMID:25937617

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  Molecular portrait of breast cancer in China reveals comprehensive transcriptomic likeness to Caucasian breast cancer and low prevalence of luminal A subtype. PMID:25787708

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  Aging-like changes in the transcriptome of irradiated microglia. PMID:25690519

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  Resistance to everolimus driven by epigenetic regulation of MYC in ER+ breast cancers. PMID:25537515

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  Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells. PMID:25519510

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  Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology. PMID:25412710

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  Proteomics for systems toxicology. PMID:25379146

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  Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation. PMID:25350763

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  iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PMID:25058159

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  LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. PMID:24906883

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  BioPlat: a software for human cancer biomarker discovery. PMID:24574115

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  Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. PMID:24569707

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  Bronchial airway gene expression in smokers with lung or head and neck cancer. PMID:24497500

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  Genome-wide methylation and gene expression changes in newborn rats following maternal protein restriction and reversal by folic acid. PMID:24391732

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  Ensemble of gene signatures identifies novel biomarkers in colorectal cancer activated through PPARγ and TNFα signaling. PMID:24133572

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  Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data. PMID:23895370

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  Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes. PMID:23748561

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  Age-specific gene expression signatures for breast tumors and cross-species conserved potential cancer progression markers in young women. PMID:23704896

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  Steiner tree methods for optimal sub-network identification: an empirical study. PMID:23627667

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  Multiscale integration of -omic, imaging, and clinical data in biomedical informatics. PMID:23231990

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  PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. PMID:23046413

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  Multi-edge gene set networks reveal novel insights into global relationships between biological themes. PMID:23028852

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  Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions. PMID:23019221

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  Brain and testicular tumors in mice with progenitor cells lacking BAX and BAK. PMID:22986529

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  omniBiomarker: A Web-Based Application for Knowledge-Driven Biomarker Identification. PMID:22893372

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  iBBiG: iterative binary bi-clustering of gene sets. PMID:22789589

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  Systems biology approach to identify gene network signatures for colorectal cancer. PMID:22629282
• http://dx.doi.org/10.1093/nar/GKR901

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More detailed information about this field from each metasource. ×

microarray data and other gene expression databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

---

gene expression

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

---

oncology

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

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mapping

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

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gene transcripts

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

---

pathology

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:58.708643

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microarray data and other gene expression gene expression oncology mapping gene transcripts pathology