Princeton University MicroArray database
Names
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Princeton University MicroArray database
metasource: Fairsharing.org
version: None
PUMAdb
metasource: Fairsharing.org
version: None
Names
More detailed information about this field from each metasource.
Princeton University MicroArray database
metasource: Fairsharing.orgversion: None
PUMAdb
metasource: Fairsharing.orgversion: None
Names
More detailed information about this field from each metasource.
Princeton University MicroArray database
metasource: Fairsharing.orgversion: None
PUMAdb
metasource: Fairsharing.orgversion: None
The Princeton University MicroArray database (PUMAdb) stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, PUMAdb provides interfaces for data retrieval, analysis and visualization.
Description
More detailed information about this field from each metasource.
The Princeton University MicroArray database (PUMAdb) stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, PUMAdb provides interfaces for data retrieval, analysis and visualization.
metasource: Fairsharing.orgversion: None
Webpage:
http://puma.princeton.eduWebpage
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Name: PUMAdb Privacy PolicyLicence name
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Publications
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The Stanford Microarray Database
PMID: 11125075
metasource: Fairsharing.org
version: None
The Stanford Microarray Database: data access and quality assessment tools
PMID: 12519956
metasource: Fairsharing.org
version: None
The Stanford Microarray Database accommodates additional microarray platforms and data formats
PMID: 15608265
metasource: Fairsharing.org
version: None
Publications
More detailed information about this field from each metasource.
The Stanford Microarray Database
PMID: 11125075
metasource: Fairsharing.org
version: None
The Stanford Microarray Database: data access and quality assessment tools
PMID: 12519956
metasource: Fairsharing.org
version: None
The Stanford Microarray Database accommodates additional microarray platforms and data formats
PMID: 15608265
metasource: Fairsharing.org
version: None
-
The Stanford Microarray Database
PubMed citations: 169.
169 articles citing: The Stanford Microarray Database
A Maximum Flow-Based Approach to Prioritize Drugs for Drug Repurposing of Chronic Diseases. PMID:34832991
Molecular subtyping of breast cancer intrinsic taxonomy with oligonucleotide microarray and NanoString nCounter. PMID:34387660
A framework using topological pathways for deeper analysis of transcriptome data. PMID:32138666
Gender differences in innate responses and gene expression profiles in memory CD4 T cells are apparent very early during acute simian immunodeficiency virus infection. PMID:31490965
Computational Analysis of Specific MicroRNA Biomarkers for Noninvasive Early Cancer Detection. PMID:28357401
Quantitative Proteomic Analysis of Human Airway Cilia Identifies Previously Uncharacterized Proteins of High Abundance. PMID:28282151
Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. PMID:25591752
Translating bioinformatics in oncology: guilt-by-profiling analysis and identification of KIF18B and CDCA3 as novel driver genes in carcinogenesis. PMID:25236463
Clinic-genomic association mining for colorectal cancer using publicly available datasets. PMID:24987669
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation. PMID:24565337
Weighted set enrichment of gene expression data. PMID:24565001
Array data extractor (ADE): a LabVIEW program to extract and merge gene array data. PMID:24289243
Specific mutation screening of TP53 gene by low-density DNA microarray. PMID:24198462
Saccharomyces cerevisiae genes involved in survival of heat shock. PMID:24142923
Differential expression analysis for pathways. PMID:23516350
Reuse of public genome-wide gene expression data. PMID:23269463
Cell-cycle and DNA damage regulation of the DNA mismatch repair protein Msh2 occurs at the transcriptional and post-transcriptional level. PMID:23261051
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
Cytotoxic necrotizing factor 1 and hemolysin from uropathogenic Escherichia coli elicit different host responses in the murine bladder. PMID:23090961
Comparative gene expression profiling of benign and malignant lesions reveals candidate therapeutic compounds for leiomyosarcoma. PMID:22919280
Identification of RARRES1 as a core regulator in liver fibrosis. PMID:22669512
Pathway detection from protein interaction networks and gene expression data using color-coding methods and A∗ search algorithms. PMID:22577352
Antibody therapy targeting the CD47 protein is effective in a model of aggressive metastatic leiomyosarcoma. PMID:22451919
Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule data. PMID:22363412
Increased expression of NuSAP in recurrent prostate cancer is mediated by E2F1. PMID:22349817
A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers. PMID:22295108
A network flow approach to predict drug targets from microarray data, disease genes and interactome network - case study on prostate cancer. PMID:22239822
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PMID:22144874
MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. PMID:22116060
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. PMID:22078224
G-DOC: a systems medicine platform for personalized oncology. PMID:21969811
ParkDB: a Parkinson's disease gene expression database. PMID:21593080
Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. PMID:21592396
Gene-expression signatures can distinguish gastric cancer grades and stages. PMID:21445269
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer. PMID:20965966
MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. PMID:20958970
Ontology-based meta-analysis of global collections of high-throughput public data. PMID:20927376
In silico models of cancer. PMID:20836040
High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. PMID:20610602
Systematizing the generation of missing metabolic knowledge. PMID:20589842
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. PMID:20587029
Connective tissue growth factor in regulation of RhoA mediated cytoskeletal tension associated osteogenesis of mouse adipose-derived stromal cells. PMID:20585662
Characterization of molecular subtypes of Korean breast cancer: an ethnically and clinically distinct population. PMID:20514396
Microarray analysis of Shigella flexneri-infected epithelial cells identifies host factors important for apoptosis inhibition. PMID:20429941
Targeting monoamine oxidase A in advanced prostate cancer. PMID:20204405
DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines. PMID:20179752
The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database. PMID:20174471
Novel early response genes in osteoblasts exposed to dynamic fluid flow. PMID:20047941
Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency. PMID:20025723
Systems biology of embryogenesis. PMID:20003850
Biomarker detection in the integration of multiple multi-class genomic studies. PMID:19965884
Using a state-space model and location analysis to infer time-delayed regulatory networks. PMID:19841683
Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression. PMID:19801443
MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary. PMID:19798417
Anti-oncogenic and pro-differentiation effects of clorgyline, a monoamine oxidase A inhibitor, on high grade prostate cancer cells. PMID:19691856
TableButler - a Windows based tool for processing large data tables generated with high-throughput methods. PMID:19640300
Disorders of sex development expose transcriptional autonomy of genetic sex and androgen-programmed hormonal sex in human blood leukocytes. PMID:19570224
Construction and clarification of dynamic gene regulatory network of cancer cell cycle via microarray data. PMID:19458769
TRUNCATULIX--a data warehouse for the legume community. PMID:19210766
WebFlow: a software package for high-throughput analysis of flow cytometry data. PMID:19187010
ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets. PMID:19014503
Temporal changes in gene expression induced by sulforaphane in human prostate cancer cells. PMID:18973173
Physical protein-protein interactions predicted from microarrays. PMID:18829707
Genomic expression profiling of TNF-alpha-treated BDC2.5 diabetogenic CD4+ T cells. PMID:18632574
StressDB: a locally installable web-based relational microarray database designed for small user communities. PMID:18628845
Identification of fevR, a novel regulator of virulence gene expression in Francisella novicida. PMID:18559431
Genetic weighted k-means algorithm for clustering large-scale gene expression data. PMID:18541047
Enabling integrative genomic analysis of high-impact human diseases through text mining. PMID:18229717
Genome-wide expression profiling Arabidopsis at the stage of Golovinomyces cichoracearum haustorium formation. PMID:18218973
Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. PMID:17963508
Gene ordering in partitive clustering using microarray expressions. PMID:17914244
Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers. PMID:17907811
Identification of novel stem cell markers using gap analysis of gene expression data. PMID:17875203
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation. PMID:17784952
New insights about host response to smallpox using microarray data. PMID:17718913
An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PMID:17684564
Gene expression changes associated with Barrett's esophagus and Barrett's-associated adenocarcinoma cell lines after acid or bile salt exposure. PMID:17597535
Cerebellar gene expression profiles of mouse models for Rett syndrome reveal novel MeCP2 targets. PMID:17584923
Autocorrelation analysis reveals widespread spatial biases in microarray experiments. PMID:17565680
The mouse polyubiquitin gene UbC is essential for fetal liver development, cell-cycle progression and stress tolerance. PMID:17491588
A promoting role of androgen receptor in androgen-sensitive and -insensitive prostate cancer cells. PMID:17426117
A meta-data based method for DNA microarray imputation. PMID:17394658
A method of microarray data storage using array data type. PMID:17392028
Gene expression patterns in pancreatic tumors, cells and tissues. PMID:17389914
Sharing detailed research data is associated with increased citation rate. PMID:17375194
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
Clues to neuro-degeneration in Niemann-Pick type C disease from global gene expression profiling. PMID:17183645
Distinctive gene expression of prostatic stromal cells cultured from diseased versus normal tissues. PMID:17044071
Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation. PMID:17003113
Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis. PMID:17000729
Gene expression profiling reveals stromal genes expressed in common between Barrett's esophagus and adenocarcinoma. PMID:16952561
Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein. PMID:16931877
Integrated functional visualization of eukaryotic genomes. PMID:16848887
A classification based framework for quantitative description of large-scale microarray data. PMID:16626502
Identifying metabolic enzymes with multiple types of association evidence. PMID:16571130
Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. PMID:16381818
Iron and pH homeostasis intersect at the level of Fur regulation in the gastric pathogen Helicobacter pylori. PMID:16369017
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data. PMID:16280078
Differential expression of alphaB-crystallin and Hsp27-1 in anaplastic thyroid carcinomas because of tumor-specific alphaB-crystallin gene (CRYAB) silencing. PMID:16184762
The role of antigenic drive and tumor-infiltrating accessory cells in the pathogenesis of helicobacter-induced mucosa-associated lymphoid tissue lymphoma. PMID:16127158
Microarray-based detection of Salmonella enterica serovar Typhimurium transposon mutants that cannot survive in macrophages and mice. PMID:16113260
Variation in gene expression patterns in effusions and primary tumors from serous ovarian cancer patients. PMID:16042759
The bioinformatics resource for oral pathogens. PMID:15980574
Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma. PMID:15882461
Confirmation of human protein interaction data by human expression data. PMID:15877815
Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures. PMID:15833139
Transcript AA454543 is a novel prognostic marker for hepatocellular carcinoma after curative partial hepatectomy. PMID:15810144
Quantitative inference of dynamic regulatory pathways via microarray data. PMID:15748298
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:15608260
Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. PMID:15547264
Global analysis of host cell gene expression late during cytomegalovirus infection reveals extensive dysregulation of cell cycle gene expression and induction of Pseudomitosis independent of US28 function. PMID:15479839
Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. PMID:15470261
GeneXplorer: an interactive web application for microarray data visualization and analysis. PMID:15458579
Major human cytomegalovirus structural protein pp65 (ppUL83) prevents interferon response factor 3 activation in the interferon response. PMID:15452220
Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. PMID:15371544
Chronic Helicobacter pylori infection with Sydney strain 1 and a newly identified mouse-adapted strain (Sydney strain 2000) in C57BL/6 and BALB/c mice. PMID:15271928
Delineation of upstream signaling events in the salmonella pathogenicity island 2 transcriptional activation pathway. PMID:15231802
Global survey of chromatin accessibility using DNA microarrays. PMID:15231753
Consequences of a deletion in dspA on transcript accumulation in Synechocystis sp. strain PCC6803. PMID:15175303
Coexpression analysis of human genes across many microarray data sets. PMID:15173114
Cancer characterization and feature set extraction by discriminative margin clustering. PMID:15070405
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. PMID:15034139
Diverse and specific gene expression responses to stresses in cultured human cells. PMID:15004229
Similarities and differences in genome-wide expression data of six organisms. PMID:14737187
CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. PMID:14681477
Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells. PMID:14617803
MgrA, an orthologue of Mga, Acts as a transcriptional repressor of the genes within the rlrA pathogenicity islet in Streptococcus pneumoniae. PMID:14594838
Growth phase-dependent response of Helicobacter pylori to iron starvation. PMID:14573673
Reconciling gene expression data with known genome-scale regulatory network structures. PMID:14559784
wCLUTO: a Web-enabled clustering toolkit. PMID:14555780
Systemic and cell type-specific gene expression patterns in scleroderma skin. PMID:14530402
Protective immunity against Helicobacter is characterized by a unique transcriptional signature. PMID:14528007
Detection of mutations in RET proto-oncogene codon 634 through double tandem hybridization. PMID:14526122
Endothelial cell diversity revealed by global expression profiling. PMID:12963823
Gene expression patterns in ovarian carcinomas. PMID:12960427
The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). PMID:12930545
Variation in gene expression patterns in human gastric cancers. PMID:12925757
An Arabidopsis mutant resistant to thaxtomin A, a cellulose synthesis inhibitor from Streptomyces species. PMID:12897252
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. PMID:12844359
pH-regulated gene expression of the gastric pathogen Helicobacter pylori. PMID:12761138
Genomewide view of gene silencing by small interfering RNAs. PMID:12730368
Gene expression profiling of Helicobacter pylori reveals a growth-phase-dependent switch in virulence gene expression. PMID:12704139
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. PMID:12631705
Distinct gene expression profiles characterize the histopathological stages of disease in Helicobacter-induced mucosa-associated lymphoid tissue lymphoma. PMID:12552104
Identification of frequent cytogenetic aberrations in hepatocellular carcinoma using gene-expression microarray data. PMID:12537564
A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes. PMID:12537547
Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. PMID:12511502
Microarray analysis of host cell gene transcription in response to varicella-zoster virus infection of human T cells and fibroblasts in vitro and SCIDhu skin xenografts in vivo. PMID:12502844
The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors. PMID:12486061
YMD: a microarray database for large-scale gene expression analysis. PMID:12463803
Fuzzy neural network applied to gene expression profiling for predicting the prognosis of diffuse large B-cell lymphoma. PMID:12460461
Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. PMID:12456890
Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. PMID:12445333
Improved analytical methods for microarray-based genome-composition analysis. PMID:12429064
Induction of the arginine decarboxylase ADC2 gene provides evidence for the involvement of polyamines in the wound response in Arabidopsis. PMID:12428010
Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection. PMID:12411577
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. PMID:12384605
The predicted candidates of Arabidopsis plastid inner envelope membrane proteins and their expression profiles. PMID:12376647
BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. PMID:12186655
Transcriptional programs activated by exposure of human prostate cancer cells to androgen. PMID:12184806
Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. PMID:12167669
Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. PMID:12097350
The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae. PMID:12084816
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. PMID:12058064
Gene expression patterns in human liver cancers. PMID:12058060
Gene expression pattern in Caco-2 cells following rotavirus infection. PMID:11932413
Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium. PMID:11860205 -
The Stanford Microarray Database: data access and quality assessment tools
PubMed citations: 103.
103 articles citing: The Stanford Microarray Database: data access and quality assessment tools
The unequivocal preponderance of biocomputation in clinical virology. PMID:35539262
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Analysis of a single Helicobacter pylori strain over a 10-year period in a primate model. PMID:25804332
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. PMID:25089180
Review of biological network data and its applications. PMID:24465231
The putative Poc complex controls two distinct Pseudomonas aeruginosa polar motility mechanisms. PMID:24102920
A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology. PMID:23865555
Loss of a 20S proteasome activator in Saccharomyces cerevisiae downregulates genes important for genomic integrity, increases DNA damage, and selectively sensitizes cells to agents with diverse mechanisms of action. PMID:22908043
eXframe: reusable framework for storage, analysis and visualization of genomics experiments. PMID:22103807
The collagen chaperone HSP47 is a new interactor of APP that affects the levels of extracellular beta-amyloid peptides. PMID:21829458
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
AphA and LuxR/HapR reciprocally control quorum sensing in vibrios. PMID:21325136
Characterization of molecular subtypes of Korean breast cancer: an ethnically and clinically distinct population. PMID:20514396
Quality assessment of transcriptome data using intrinsic statistical properties. PMID:20451162
The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database. PMID:20174471
Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments. PMID:20056002
Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation. PMID:19324962
Co-expression among constituents of a motif in the protein-protein interaction network. PMID:19226657
A complex-based reconstruction of the Saccharomyces cerevisiae interactome. PMID:19176519
MiMiR--an integrated platform for microarray data sharing, mining and analysis. PMID:18801157
Navigating public microarray databases. PMID:18629145
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. PMID:18613949
Microarray data mining: a novel optimization-based approach to uncover biologically coherent structures. PMID:18538024
Prediction of human disease genes by human-mouse conserved coexpression analysis. PMID:18369433
Genome-wide expression profiling Arabidopsis at the stage of Golovinomyces cichoracearum haustorium formation. PMID:18218973
Computational prediction of protein-protein interactions. PMID:18095187
BioStar models of clinical and genomic data for biomedical data warehouse design. PMID:18048122
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PMID:17912365
Orthologous transcription factors in bacteria have different functions and regulate different genes. PMID:17845071
Gene copy number variation spanning 60 million years of human and primate evolution. PMID:17666543
Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface. PMID:17645793
Integrated olfactory receptor and microarray gene expression databases. PMID:17603910
Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system. PMID:17588127
Extracting binary signals from microarray time-course data. PMID:17517782
Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection. PMID:17337568
Analysis of the quality of contact-pin fabricated oligonucleotide microarrays. PMID:17284778
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. PMID:17182626
Target discovery and validation in pancreatic cancer. PMID:17172725
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it. PMID:17169146
Cell-line and tissue-specific signatures of androgen receptor-coregulator transcription. PMID:16932916
The life-cycle of operons. PMID:16789824
Analysis of gene expression in operons of Streptomyces coelicolor. PMID:16749941
Empirical array quality weights in the analysis of microarray data. PMID:16712727
Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse. PMID:16518469
Genome-scale identification of membrane-associated human mRNAs. PMID:16415983
Gene expression profiling predicts survival in conventional renal cell carcinoma. PMID:16318415
Gene expression profiling differentiates germ cell tumors from other cancers and defines subtype-specific signatures. PMID:16306258
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data. PMID:16280078
Protocols for the assurance of microarray data quality and process control. PMID:16272462
Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling. PMID:16224098
Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer. PMID:16036106
Trends in the quality of data from 5168 oligonucleotide microarrays from a single facility. PMID:16030321
How to improve quality assurance in fluorometry: fluorescence-inherent sources of error and suited fluorescence standards. PMID:15986157
Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. PMID:15942025
Operon formation is driven by co-regulation and not by horizontal gene transfer. PMID:15930492
Local coexpression domains of two to four genes in the genome of Arabidopsis. PMID:15923337
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
MARS: microarray analysis, retrieval, and storage system. PMID:15836795
A DNA microarray survey of gene expression in normal human tissues. PMID:15774023
Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. PMID:15758028
Atlas - a data warehouse for integrative bioinformatics. PMID:15723693
Evolutionary significance of gene expression divergence. PMID:15716085
A novel method for accurate operon predictions in all sequenced prokaryotes. PMID:15701760
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. PMID:15693947
BarleyBase--an expression profiling database for plant genomics. PMID:15608273
The Stanford Microarray Database accommodates additional microarray platforms and data formats. PMID:15608265
CLOE: identification of putative functional relationships among genes by comparison of expression profiles between two species. PMID:15550177
Combining gene expression data from different generations of oligonucleotide arrays. PMID:15504239
Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. PMID:15470261
GeneXplorer: an interactive web application for microarray data visualization and analysis. PMID:15458579
Major human cytomegalovirus structural protein pp65 (ppUL83) prevents interferon response factor 3 activation in the interferon response. PMID:15452220
PEDRo: a database for storing, searching and disseminating experimental proteomics data. PMID:15377392
Improving identification of differentially expressed genes in microarray studies using information from public databases. PMID:15345054
Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells. PMID:15345050
Global nucleosome occupancy in yeast. PMID:15345046
Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering. PMID:15324460
A specific gene expression program triggered by Gram-positive bacteria in the cytosol. PMID:15269347
New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. PMID:15240831
Nutritional homeostasis in batch and steady-state culture of yeast. PMID:15240820
Delineation of upstream signaling events in the salmonella pathogenicity island 2 transcriptional activation pathway. PMID:15231802
GOAL: automated Gene Ontology analysis of expression profiles. PMID:15215435
ArrayProspector: a web resource of functional associations inferred from microarray expression data. PMID:15215427
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. PMID:15215383
Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? PMID:15186489
Consequences of a deletion in dspA on transcript accumulation in Synechocystis sp. strain PCC6803. PMID:15175303
LuxS is required for persistent pneumococcal carriage and expression of virulence and biosynthesis genes. PMID:15102809
Charting gene regulatory networks: strategies, challenges and perspectives. PMID:15080794
Quantifying the relationship between co-expression, co-regulation and gene function. PMID:15053845
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. PMID:15034139
Database development in toxicogenomics: issues and efforts. PMID:15033600
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PMID:15024427
Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. PMID:14981237
Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. PMID:14718068
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. PMID:14681484
PlantGDB, plant genome database and analysis tools. PMID:14681433
Gene expression in the normal adult human kidney assessed by complementary DNA microarray. PMID:14657249
Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. PMID:14633610
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. PMID:14604444
MgrA, an orthologue of Mga, Acts as a transcriptional repressor of the genes within the rlrA pathogenicity islet in Streptococcus pneumoniae. PMID:14594838
Position specific variation in the rate of evolution in transcription factor binding sites. PMID:12946282
The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). PMID:12930545
Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. PMID:12750471
Development and validation of a T7 based linear amplification for genomic DNA. PMID:12740028 -
The Stanford Microarray Database accommodates additional microarray platforms and data formats
PubMed citations: 73.
73 articles citing: The Stanford Microarray Database accommodates additional microarray platforms and data formats
A novel intronic circular RNA, circGNG7, inhibits head and neck squamous cell carcinoma progression by blocking the phosphorylation of heat shock protein 27 at Ser78 and Ser82. PMID:34498800
Identification of gene expression logical invariants in Arabidopsis. PMID:31245766
The Global Response of Cronobacter sakazakii Cells to Amino Acid Deficiency. PMID:30154778
Discovering missing reactions of metabolic networks by using gene co-expression data. PMID:28150713
Recent Advances in Understanding the Molecular Mechanisms Regulating the Root System Response to Phosphate Deficiency in Arabidopsis. PMID:27499680
Plant systems biology: insights, advances and challenges. PMID:24671625
Wig-1 regulates cell cycle arrest and cell death through the p53 targets FAS and 14-3-3σ. PMID:24469038
Recent developments in plant zinc homeostasis and the path toward improved biofortification and phytoremediation programs. PMID:23221755
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. PMID:22898396
Extracting regulatory modules from gene expression data by sequential pattern mining. PMID:22369275
Construction of regulatory networks using expression time-series data of a genotyped population. PMID:22084118
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. PMID:21884636
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. PMID:21749690
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
Association between translation efficiency and horizontal gene transfer within microbial communities. PMID:21343180
Recent advances in clustering methods for protein interaction networks. PMID:21143777
The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database. PMID:20174471
Internet Resources for Gene Expression Analysis in Arabidopsis thaliana. PMID:19506727
ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets. PMID:19014503
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PMID:18776931
Accessing and integrating data and knowledge for biomedical research. PMID:18660883
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. PMID:18541053
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. PMID:18414481
Pharmacogenomics of interferon-beta therapy in multiple sclerosis: baseline IFN signature determines pharmacological differences between patients. PMID:18382694
Prediction of protein-protein interactions using protein signature profiling. PMID:18267299
CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining. PMID:17942411
Systematic condition-dependent annotation of metabolic genes. PMID:17895423
Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli. PMID:17873044
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer. PMID:17868458
PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. PMID:17854489
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation. PMID:17784952
The PhenoGen informatics website: tools for analyses of complex traits. PMID:17760997
Semantic integration to identify overlapping functional modules in protein interaction networks. PMID:17650343
Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface. PMID:17645793
Strategy for encoding and comparison of gene expression signatures. PMID:17612401
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. PMID:17586824
DGEM--a microarray gene expression database for primary human disease tissues. PMID:17570735
A method of microarray data storage using array data type. PMID:17392028
Sharing detailed research data is associated with increased citation rate. PMID:17375194
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. PMID:17356713
Improved precision and accuracy for microarrays using updated probe set definitions. PMID:17288599
Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. PMID:17223656
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. PMID:17202170
SIGMA: a system for integrative genomic microarray analysis of cancer genomes. PMID:17192189
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. PMID:17182626
AthaMap web tools for the analysis and identification of co-regulated genes. PMID:17148485
SLIMarray: lightweight software for microarray facility management. PMID:17147785
Databases of free expression. PMID:17143588
Characterization of a large, stable, high-copy-number Streptomyces plasmid that requires stability and transfer functions for heterologous polyketide overproduction. PMID:17142363
The mouse Gene Expression Database (GXD): 2007 update. PMID:17130151
Using local gene expression similarities to discover regulatory binding site modules. PMID:17109764
Identification of Helicobacter pylori genes that contribute to stomach colonization. PMID:17101654
PathoPlant: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. PMID:17099232
Infection with Toxoplasma gondii bradyzoites has a diminished impact on host transcript levels relative to tachyzoite infection. PMID:17088349
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. PMID:17087822
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. PMID:16982645
A direct comparison of protein interaction confidence assignment schemes. PMID:16872496
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. PMID:16845059
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. PMID:16756676
Global analysis of gene function in yeast by quantitative phenotypic profiling. PMID:16738548
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. PMID:16685651
QPath: a method for querying pathways in a protein-protein interaction network. PMID:16606460
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. PMID:16597336
Protein evolutionary rates correlate with expression independently of synonymous substitutions in Helicobacter pylori. PMID:16586017
The Gaggle: an open-source software system for integrating bioinformatics software and data sources. PMID:16569235
More robust detection of motifs in coexpressed genes by using phylogenetic information. PMID:16549017
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. PMID:16537387
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. PMID:16381943
Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700/Panther probe-to-gene annotations. PMID:16372901
MicroGen: a MIAME compliant web system for microarray experiment information and workflow management. PMID:16351755
GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. PMID:16343346
Storage and retrieval of microarray data and open source microarray database software. PMID:15988049
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
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dna microarray
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gene expression data
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microarray experiment
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raw microarray data
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More detailed information about this field from each metasource.
dna microarray
metasource: Fairsharing.orgversion: None
gene expression data
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microarray experiment
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raw microarray data
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dna microarray gene expression microarray experiment raw microarray data
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