Published in Genome Biol on March 25, 2003
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics (2005) 22.22
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (2004) 20.23
GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol (2004) 15.61
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics (2005) 14.02
The Gene Ontology (GO) project in 2006. Nucleic Acids Res (2006) 13.79
WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res (2005) 12.88
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GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics (2004) 11.23
Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol (2010) 9.15
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res (2005) 9.05
Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A (2005) 8.75
ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics (2009) 8.60
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GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res (2008) 6.91
Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol (2012) 6.38
Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci U S A (2004) 4.89
A human functional protein interaction network and its application to cancer data analysis. Genome Biol (2010) 4.73
Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc Natl Acad Sci U S A (2006) 4.44
Identification of noninvasive imaging surrogates for brain tumor gene-expression modules. Proc Natl Acad Sci U S A (2008) 4.14
GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. Nucleic Acids Res (2004) 4.10
Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform (2008) 3.96
Recent additions and improvements to the Onto-Tools. Nucleic Acids Res (2005) 3.88
Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS One (2008) 3.87
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res (2007) 3.68
Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics (2004) 3.65
Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. BMC Bioinformatics (2004) 3.57
L2L: a simple tool for discovering the hidden significance in microarray expression data. Genome Biol (2005) 3.27
From genes to functional classes in the study of biological systems. BMC Bioinformatics (2007) 3.09
Comparing functional annotation analyses with Catmap. BMC Bioinformatics (2004) 2.92
Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics (2005) 2.78
Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One (2011) 2.74
Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol (2007) 2.73
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res (2009) 2.71
Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes. Nucleic Acids Res (2008) 2.70
DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet (2009) 2.56
Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda. J Transl Med (2008) 2.55
Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther (2006) 2.55
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics (2008) 2.53
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A (2009) 2.50
MicroRNA expression differentiates histology and predicts survival of lung cancer. Clin Cancer Res (2010) 2.48
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics (2006) 2.46
Sixty-five gene-based risk score classifier predicts overall survival in hepatocellular carcinoma. Hepatology (2012) 2.40
Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol (2014) 2.40
DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinformatics (2005) 2.33
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. Nucleic Acids Res (2008) 2.33
FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics (2007) 2.32
Comparative gene expression analysis of blood and brain provides concurrent validation of SELENBP1 up-regulation in schizophrenia. Proc Natl Acad Sci U S A (2005) 2.29
Coordinated changes in AHRR methylation in lymphoblasts and pulmonary macrophages from smokers. Am J Med Genet B Neuropsychiatr Genet (2012) 2.20
Activation of inflammation/NF-kappaB signaling in infants born to arsenic-exposed mothers. PLoS Genet (2007) 2.19
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res (2006) 2.19
ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics (2009) 2.11
A common gene signature across multiple studies relate biomarkers and functional regulation in tolerance to renal allograft. Kidney Int (2015) 2.02
A semantic analysis of the annotations of the human genome. Bioinformatics (2005) 2.01
Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics (2005) 2.01
Decreased expression of miR-125b and miR-100 in oral cancer cells contributes to malignancy. Genes Chromosomes Cancer (2009) 1.98
GeneTools--application for functional annotation and statistical hypothesis testing. BMC Bioinformatics (2006) 1.96
A general lack of compensation for gene dosage in yeast. Mol Syst Biol (2010) 1.96
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res (2007) 1.94
Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci U S A (2004) 1.93
BAFF controls B cell metabolic fitness through a PKC beta- and Akt-dependent mechanism. J Exp Med (2006) 1.93
Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res (2005) 1.93
Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice. Proc Natl Acad Sci U S A (2008) 1.91
Resistance exercise reverses aging in human skeletal muscle. PLoS One (2007) 1.90
VirtualPlant: a software platform to support systems biology research. Plant Physiol (2009) 1.88
Information Visualization Techniques in Bioinformatics during the Postgenomic Era. Drug Discov Today Biosilico (2004) 1.85
Large-scale and high-confidence proteomic analysis of human seminal plasma. Genome Biol (2006) 1.84
Deciphering cellular states of innate tumor drug responses. Genome Biol (2006) 1.83
Upregulation of miR-142-3p in peripheral blood mononuclear cells of operationally tolerant patients with a renal transplant. J Am Soc Nephrol (2012) 1.81
Adaptively inferring human transcriptional subnetworks. Mol Syst Biol (2006) 1.81
In vivo functional and transcriptional profiling of bone marrow stem cells after transplantation into ischemic myocardium. Arterioscler Thromb Vasc Biol (2011) 1.80
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res (2004) 1.79
GOAL: automated Gene Ontology analysis of expression profiles. Nucleic Acids Res (2004) 1.79
GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data. BMC Bioinformatics (2006) 1.72
A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model. BMC Genomics (2006) 1.71
RNA quality in frozen breast cancer samples and the influence on gene expression analysis--a comparison of three evaluation methods using microcapillary electrophoresis traces. BMC Mol Biol (2007) 1.70
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res (2006) 1.69
Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One (2009) 1.68
Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart. Genome Biol (2005) 1.64
Cellular effect of high doses of silica-coated quantum dot profiled with high throughput gene expression analysis and high content cellomics measurements. Nano Lett (2006) 1.63
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PLoS Biol (2010) 1.62
Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics (2010) 1.59
ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res (2005) 1.58
Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics (2004) 1.57
Oncogenic ETS proteins mimic activated RAS/MAPK signaling in prostate cells. Genes Dev (2011) 1.56
DNA replication licensing and progenitor numbers are increased by progesterone in normal human breast. Endocrinology (2009) 1.55
Toxicogenomic analysis of Caenorhabditis elegans reveals novel genes and pathways involved in the resistance to cadmium toxicity. Genome Biol (2007) 1.55
Signal transduction pathway profiling of individual tumor samples. BMC Bioinformatics (2005) 1.55
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res (2008) 1.53
ZEB1 enhances transendothelial migration and represses the epithelial phenotype of prostate cancer cells. Mol Biol Cell (2009) 1.52
Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci U S A (2011) 1.50
VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics (2008) 1.49
Functional genomics unique to week 20 post wounding in the deep cone/fat dome of the Duroc/Yorkshire porcine model of fibroproliferative scarring. PLoS One (2011) 1.48
Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans. Genome Biol (2007) 1.41
Proteomic studies reveal coordinated changes in T-cell expression patterns upon infection with human immunodeficiency virus type 1. J Virol (2008) 1.40
Evolutionary plasticity of segmentation clock networks. Development (2011) 1.39
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol (2003) 20.83
Profiling gene expression using onto-express. Genomics (2002) 12.65
MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol (2003) 8.66
MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques (1999) 5.56
'Omic' and hypothesis-driven research in the molecular pharmacology of cancer. Curr Opin Pharmacol (2002) 4.54
Fishing expeditions. Science (1998) 4.09
Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping. Cancer Res (2003) 3.52
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87
Revised Bethesda Guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability. J Natl Cancer Inst (2004) 14.97
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics (2005) 14.02
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science (2011) 11.12
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol (2003) 8.66
Genomic instability and aging-like phenotype in the absence of mammalian SIRT6. Cell (2006) 8.48
In vivo tumor targeting and spectroscopic detection with surface-enhanced Raman nanoparticle tags. Nat Biotechnol (2007) 7.33
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins. Mol Biol Cell (2005) 6.79
Nova regulates brain-specific splicing to shape the synapse. Nat Genet (2005) 6.58
Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer (2005) 6.46
SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. Nature (2008) 6.02
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Senescing human cells and ageing mice accumulate DNA lesions with unrepairable double-strand breaks. Nat Cell Biol (2004) 4.87
HIF-1alpha induces cell cycle arrest by functionally counteracting Myc. EMBO J (2004) 4.26
The contribution of VHL substrate binding and HIF1-alpha to the phenotype of VHL loss in renal cell carcinoma. Cancer Cell (2002) 4.13
Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Mol Cancer Ther (2006) 4.09
A gene signature predicting for survival in suboptimally debulked patients with ovarian cancer. Cancer Res (2008) 4.05
Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther (2007) 3.84
A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery. Proc Natl Acad Sci U S A (2007) 3.78
Predicting drug sensitivity and resistance: profiling ABC transporter genes in cancer cells. Cancer Cell (2004) 3.72
Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci U S A (2003) 3.66
Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics (2004) 3.65
Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest (2012) 3.64
Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping. Cancer Res (2003) 3.52
An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin Cancer Res (2012) 3.48
Karyotypic complexity of the NCI-60 drug-screening panel. Cancer Res (2003) 3.42
Calorie restriction, aging, and cancer prevention: mechanisms of action and applicability to humans. Annu Rev Med (2001) 3.22
MicroRNAs modulate the chemosensitivity of tumor cells. Mol Cancer Ther (2008) 3.06
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics (2007) 2.93
Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell (2005) 2.82
Gene expression profiles of serous, endometrioid, and clear cell subtypes of ovarian and endometrial cancer. Clin Cancer Res (2005) 2.72
Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov (2012) 2.68
BRCA1, histone H2AX phosphorylation, and male meiotic sex chromosome inactivation. Curr Biol (2004) 2.67
CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Res (2012) 2.57
Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther (2006) 2.55
DNA fingerprinting of the NCI-60 cell line panel. Mol Cancer Ther (2009) 2.53
MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol Cancer Ther (2007) 2.53
Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biol (2003) 2.52
Gene expression analysis reveals chemical-specific profiles. Toxicol Sci (2002) 2.50
Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov (2013) 2.49
Expression profiling of serous low malignant potential, low-grade, and high-grade tumors of the ovary. Cancer Res (2005) 2.48
Bioconjugated quantum dots for multiplexed and quantitative immunohistochemistry. Nat Protoc (2007) 2.45
Scientific collaboration results in higher citation rates of published articles. Pharmacotherapy (2006) 2.39
Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics (2005) 2.29
The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Res (2013) 2.27
A stromal gene signature associated with inflammatory breast cancer. Int J Cancer (2008) 2.18
Clinical proteomics: translating benchside promise into bedside reality. Nat Rev Drug Discov (2002) 2.15
PIK3CA mutations may be discordant between primary and corresponding metastatic disease in breast cancer. Clin Cancer Res (2010) 2.13
A gene signature predictive for outcome in advanced ovarian cancer identifies a survival factor: microfibril-associated glycoprotein 2. Cancer Cell (2009) 2.13
Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance. Cancer Res (2004) 2.10
Conditional expression of the CTCF-paralogous transcriptional factor BORIS in normal cells results in demethylation and derepression of MAGE-A1 and reactivation of other cancer-testis genes. Cancer Res (2005) 2.08
Thymidylate synthase as an oncogene: a novel role for an essential DNA synthesis enzyme. Cancer Cell (2004) 2.05
Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen. Cancer Res (2008) 2.01
mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities. Mol Cancer Ther (2010) 2.00
Pathology imaging informatics for quantitative analysis of whole-slide images. J Am Med Inform Assoc (2013) 1.93
Chronic inorganic arsenic exposure induces hepatic global and individual gene hypomethylation: implications for arsenic hepatocarcinogenesis. Carcinogenesis (2004) 1.91
The microcephaly ASPM gene is expressed in proliferating tissues and encodes for a mitotic spindle protein. Hum Mol Genet (2005) 1.88
Role of ETS transcription factors in the hypoxia-inducible factor-2 target gene selection. Cancer Res (2006) 1.87
Gene expression profiles associated with response to chemotherapy in epithelial ovarian cancers. Clin Cancer Res (2005) 1.86
Desorption electrospray ionization mass spectrometry reveals surface-mediated antifungal chemical defense of a tropical seaweed. Proc Natl Acad Sci U S A (2009) 1.86
Evaluation of current methods used to analyze the expression profiles of ATP-binding cassette transporters yields an improved drug-discovery database. Mol Cancer Ther (2009) 1.83
Prediction of compound signature using high density gene expression profiling. Toxicol Sci (2002) 1.82
Transcriptional regulation of the telomerase hTERT gene as a target for cellular and viral oncogenic mechanisms. Carcinogenesis (2003) 1.82
Solid renal tumor severity in von Hippel Lindau disease is related to germline deletion length and location. Hum Mutat (2004) 1.78
Regulation of HIF prolyl hydroxylases by hypoxia-inducible factors. J Cell Biochem (2004) 1.76
Reciprocal binding of CTCF and BORIS to the NY-ESO-1 promoter coincides with derepression of this cancer-testis gene in lung cancer cells. Cancer Res (2005) 1.74