Published in Bioinformatics on October 22, 2010
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Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods. Biol Direct (2012) 0.88
Expressomal approach for comprehensive analysis and visualization of ligand sensitivities of xenoestrogen responsive genes. Proc Natl Acad Sci U S A (2013) 0.84
Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules. PLoS Comput Biol (2013) 0.79
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The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
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Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58
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An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci U S A (2005) 13.54
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A (2005) 8.75
The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res (2008) 5.69
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Integrative analysis of the cancer transcriptome. Nat Genet (2005) 4.44
A general modular framework for gene set enrichment analysis. BMC Bioinformatics (2009) 3.92
Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics (2007) 3.59
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. BMC Bioinformatics (2006) 3.39
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics (2008) 2.53
Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays. Proc Natl Acad Sci U S A (2005) 2.37
Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics (2009) 2.24
ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinformatics (2007) 1.68
A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. Bioinformatics (2009) 1.65
A gene recommender algorithm to identify coexpressed genes in C. elegans. Genome Res (2003) 1.45
MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Nucleic Acids Res (2010) 1.45
CLEAN: CLustering Enrichment ANalysis. BMC Bioinformatics (2009) 1.29
Anti-proliferative effect of estrogen in breast cancer cells that re-express ERalpha is mediated by aberrant regulation of cell cycle genes. J Mol Endocrinol (2005) 1.29
Strategy for encoding and comparison of gene expression signatures. Genome Biol (2007) 1.18
Expression-based Pathway Signature Analysis (EPSA): mining publicly available microarray data for insight into human disease. BMC Med Genomics (2008) 1.16
Gene expression module-based chemical function similarity search. Nucleic Acids Res (2008) 1.01
GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. BMC Genomics (2009) 0.88
Influence of fatty acid diets on gene expression in rat mammary epithelial cells. Physiol Genomics (2009) 0.84
Genomics Portals: integrative web-platform for mining genomics data. BMC Genomics (2010) 0.82
Similar compounds searching system by using the gene expression microarray database. Toxicol Lett (2008) 0.80
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. BMC Bioinformatics (2006) 3.39
Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics (2002) 2.56
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics (2008) 2.53
Clustering gene-expression data with repeated measurements. Genome Biol (2003) 2.37
MicroRNA-494 targeting both proapoptotic and antiapoptotic proteins protects against ischemia/reperfusion-induced cardiac injury. Circulation (2010) 2.03
Statistical assessment of mediational effects for logistic mediational models. Stat Med (2004) 1.96
Persistent hypomethylation in the promoter of nucleosomal binding protein 1 (Nsbp1) correlates with overexpression of Nsbp1 in mouse uteri neonatally exposed to diethylstilbestrol or genistein. Endocrinology (2008) 1.95
Conditional activation of RET/PTC3 and BRAFV600E in thyroid cells is associated with gene expression profiles that predict a preferential role of BRAF in extracellular matrix remodeling. Cancer Res (2006) 1.62
Control of nutrient stress-induced metabolic reprogramming by PKCζ in tumorigenesis. Cell (2013) 1.44
From co-expression to co-regulation: how many microarray experiments do we need? Genome Biol (2004) 1.40
Expression of genes in the TGF-beta signaling pathway is significantly deregulated in smooth muscle cells from aorta of aryl hydrocarbon receptor knockout mice. Toxicol Appl Pharmacol (2004) 1.37
Microarray results improve significantly as hybridization approaches equilibrium. Biotechniques (2004) 1.35
Genomic profile of matrix and vasculature remodeling in TGF-alpha induced pulmonary fibrosis. Am J Respir Cell Mol Biol (2007) 1.29
CLEAN: CLustering Enrichment ANalysis. BMC Bioinformatics (2009) 1.29
The role of metallothionein in the pathogenesis of acute lung injury. Am J Respir Cell Mol Biol (2005) 1.25
Genomewide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs. Environ Health Perspect (2009) 1.22
A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res (2006) 1.17
Gene expression changes during the development of acute lung injury: role of transforming growth factor beta. Am J Respir Crit Care Med (2005) 1.10
Loss of the miR-144/451 cluster impairs ischaemic preconditioning-mediated cardioprotection by targeting Rac-1. Cardiovasc Res (2012) 1.09
Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure. Physiol Genomics (2007) 1.08
Different global gene expression profiles in benzo[a]pyrene- and dioxin-treated vascular smooth muscle cells of AHR-knockout and wild-type mice. Cardiovasc Toxicol (2004) 1.08
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset. Bioinformatics (2006) 1.05
Identification of a NF-κB cardioprotective gene program: NF-κB regulation of Hsp70.1 contributes to cardioprotection after permanent coronary occlusion. J Mol Cell Cardiol (2011) 1.02
NF-kappaB driven cardioprotective gene programs; Hsp70.3 and cardioprotection after late ischemic preconditioning. J Mol Cell Cardiol (2010) 0.99
A semi-parametric Bayesian model for unsupervised differential co-expression analysis. BMC Bioinformatics (2010) 0.98
4-aminobiphenyl-induced liver and urinary bladder DNA adduct formation in Cyp1a2(-/-) and Cyp1a2(+/+) mice. J Natl Cancer Inst (2003) 0.98
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. BMC Bioinformatics (2007) 0.97
Disruption of aryl hydrocarbon receptor homeostatic levels during embryonic stem cell differentiation alters expression of homeobox transcription factors that control cardiomyogenesis. Environ Health Perspect (2013) 0.97
c-Myc phosphorylation by PKCζ represses prostate tumorigenesis. Proc Natl Acad Sci U S A (2013) 0.96
Neural system-enriched gene expression: relationship to biological pathways and neurological diseases. Physiol Genomics (2004) 0.96
Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin. Biochim Biophys Acta (2006) 0.92
Haplotype association mapping of acute lung injury in mice implicates activin a receptor, type 1. Am J Respir Crit Care Med (2011) 0.91
Regeneration of the adult thymus is preceded by the expansion of K5+K8+ epithelial cell progenitors and by increased expression of Trp63, cMyc and Tcf3 transcription factors in the thymic stroma. Int Immunol (2007) 0.91
Critical regulation of genes for tumor cell migration by AP-1. Clin Exp Metastasis (2004) 0.90
Epigenetic changes with dietary soy in cynomolgus monkeys. PLoS One (2011) 0.89
Integrative assessment of chlorine-induced acute lung injury in mice. Am J Respir Cell Mol Biol (2012) 0.89
Gene expression profiles of mouse aorta and cultured vascular smooth muscle cells differ widely, yet show common responses to dioxin exposure. Cardiovasc Toxicol (2004) 0.89
Transcriptome analyses in normal prostate epithelial cells exposed to low-dose cadmium: oncogenic and immunomodulations involving the action of tumor necrosis factor. Environ Health Perspect (2008) 0.88
Developmental characteristics of adapting mouse small intestine crypt cells. Gastroenterology (2006) 0.88
Rapid and weight-independent improvement of glucose tolerance induced by a peptide designed to elicit apoptosis in adipose tissue endothelium. Diabetes (2012) 0.87
Identification of secretaglobin Scgb2a1 as a target for developmental reprogramming by BPA in the rat prostate. Epigenetics (2015) 0.86
Gene position within chromosome territories correlates with their involvement in distinct rearrangement types in thyroid cancer cells. Genes Chromosomes Cancer (2009) 0.86
Deciphering gene expression program of MAP3K1 in mouse eyelid morphogenesis. Dev Biol (2012) 0.85
Surfactant-associated protein B is critical to survival in nickel-induced injury in mice. Am J Respir Cell Mol Biol (2009) 0.85
Characterization of novel non-clonal intrachromosomal rearrangements between the H4 and PTEN genes (H4/PTEN) in human thyroid cell lines and papillary thyroid cancer specimens. Mutat Res (2005) 0.85
Folliculin contributes to VHL tumor suppressing activity in renal cancer through regulation of autophagy. PLoS One (2013) 0.84
Deletion hotspots in AMACR promoter CpG island are cis-regulatory elements controlling the gene expression in the colon. PLoS Genet (2009) 0.84
Modeling variation in tumors in vivo. Proc Natl Acad Sci U S A (2005) 0.84
Expressomal approach for comprehensive analysis and visualization of ligand sensitivities of xenoestrogen responsive genes. Proc Natl Acad Sci U S A (2013) 0.84
Genomics Portals: integrative web-platform for mining genomics data. BMC Genomics (2010) 0.82
Competitive coexistence of two Pneumocystis species. Infect Genet Evol (2005) 0.81
Functional genomics of chlorine-induced acute lung injury in mice. Proc Am Thorac Soc (2010) 0.81
Nonredundant functions of alphabeta and gammadelta T cells in acrolein-induced pulmonary pathology. Toxicol Sci (2008) 0.79
Isozyme-specific abnormalities of PKC in thyroid cancer: evidence for post-transcriptional changes in PKC epsilon. J Clin Endocrinol Metab (2002) 0.79
Research resource: estrogen-driven prolactin-mediated gene-expression networks in hormone-induced prostatic intraepithelial neoplasia. Mol Endocrinol (2010) 0.79
Genomewide association analysis of respiratory syncytial virus infection in mice. J Virol (2009) 0.79
Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules. PLoS Comput Biol (2013) 0.79
Effect of lot variability on ultraviolet radiation inactivation kinetics of Cryptosporidium parvum oocysts. Environ Sci Technol (2005) 0.77
Identification of maternally regulated fetal gene networks in the placenta with a novel embryo transfer system in mice. Physiol Genomics (2011) 0.77
The role of T cells in the regulation of acrolein-induced pulmonary inflammation and epithelial-cell pathology. Res Rep Health Eff Inst (2009) 0.77
Integrative metabolome and transcriptome profiling reveals discordant energetic stress between mouse strains with differential sensitivity to acrolein-induced acute lung injury. Mol Nutr Food Res (2011) 0.76
WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results. Source Code Biol Med (2011) 0.75
Characterization of HCV NS3 Protease Variants in HCV/HIV Coinfected Patients by Ultra-deep Sequence Analysis: Relationship to Hepatic Fibrosis. J Acquir Immune Defic Syndr (2016) 0.75
Correction: IL-31-Driven Skin Remodeling Involves Epidermal Cell Proliferation and Thickening That Lead to Impaired Skin-Barrier Function. PLoS One (2017) 0.75
Issues of design and analysis in studies of gene-environment interactions. IARC Sci Publ (2004) 0.75
Mutational biases associated with potential iron-binding DNA motifs in rodent lacI and human p53 mutational databases. Mutat Res (2004) 0.75