Published in BMC Bioinformatics on October 16, 2007
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res (2009) 7.34
Genomic expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum. Crit Care Med (2009) 3.16
Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics (2009) 3.03
The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med (2010) 3.00
Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet (2012) 2.92
Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Res (2011) 2.89
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A (2010) 2.85
PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res (2011) 2.67
Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst Biol (2008) 2.51
Atlas of gene expression in the developing kidney at microanatomic resolution. Dev Cell (2008) 2.44
Exome sequencing and systems biology converge to identify novel mutations in the L-type calcium channel, CACNA1C, linked to autosomal dominant long QT syndrome. Circ Cardiovasc Genet (2013) 1.93
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PLoS One (2011) 1.89
ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. Nucleic Acids Res (2010) 1.75
Integrating mouse anatomy and pathology ontologies into a phenotyping database: tools for data capture and training. Mamm Genome (2008) 1.62
Bioinformatics for personal genome interpretation. Brief Bioinform (2012) 1.51
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics (2010) 1.37
Loss of Rab25 promotes the development of intestinal neoplasia in mice and is associated with human colorectal adenocarcinomas. J Clin Invest (2010) 1.35
Silencing of RON receptor signaling promotes apoptosis and gemcitabine sensitivity in pancreatic cancers. Cancer Res (2010) 1.31
Gene-network analysis identifies susceptibility genes related to glycobiology in autism. PLoS One (2009) 1.23
Dissecting microregulation of a master regulatory network. BMC Genomics (2008) 1.18
GLAD4U: deriving and prioritizing gene lists from PubMed literature. BMC Genomics (2012) 1.17
PINTA: a web server for network-based gene prioritization from expression data. Nucleic Acids Res (2011) 1.16
Conserved co-expression for candidate disease gene prioritization. BMC Bioinformatics (2008) 1.15
Systems biology of the autophagy-lysosomal pathway. Autophagy (2011) 1.15
Linking genes to diseases: it's all in the data. Genome Med (2009) 1.14
In silico gene prioritization by integrating multiple data sources. PLoS One (2011) 1.10
Chapter 15: disease gene prioritization. PLoS Comput Biol (2013) 1.05
Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes. Genes Immun (2012) 1.04
Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles. Genome Med (2012) 1.01
Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization. PLoS One (2012) 0.98
Noninjurious mechanical ventilation activates a proinflammatory transcriptional program in the lung. Physiol Genomics (2009) 0.98
SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association. PLoS One (2014) 0.94
Transcriptome profiling in engrailed-2 mutant mice reveals common molecular pathways associated with autism spectrum disorders. Mol Autism (2013) 0.90
Retracted Candidate gene prioritization. Mol Genet Genomics (2012) 0.88
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. Brief Bioinform (2016) 0.86
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. Brief Funct Genomics (2011) 0.85
Use of transcriptional signatures induced in lymphoid and myeloid cell lines as an inflammatory biomarker in Type 1 diabetes. Physiol Genomics (2011) 0.85
MamPhEA: a web tool for mammalian phenotype enrichment analysis. Bioinformatics (2010) 0.85
Text mining in cancer gene and pathway prioritization. Cancer Inform (2014) 0.85
Computational tools for comparative phenomics: the role and promise of ontologies. Mamm Genome (2012) 0.85
Differential coupling of Arg- and Gly389 polymorphic forms of the beta1-adrenergic receptor leads to pathogenic cardiac gene regulatory programs. Physiol Genomics (2008) 0.84
Ethanol modulation of gene networks: implications for alcoholism. Neurobiol Dis (2011) 0.83
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. Nucleic Acids Res (2012) 0.82
A vertex similarity-based framework to discover and rank orphan disease-related genes. BMC Syst Biol (2012) 0.81
Whole transcriptome expression profiling of mouse limb tendon development by using RNA-seq. J Orthop Res (2015) 0.80
Dysfunction of the Voltage-Gated K+ Channel β2 Subunit in a Familial Case of Brugada Syndrome. J Am Heart Assoc (2016) 0.80
Whole exome sequencing identifies mutation of EDNRA involved in ACTH-independent macronodular adrenal hyperplasia. Fam Cancer (2013) 0.80
Inference of gene-phenotype associations via protein-protein interaction and orthology. PLoS One (2013) 0.79
ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context. Nucleic Acids Res (2014) 0.79
Dintor: functional annotation of genomic and proteomic data. BMC Genomics (2015) 0.79
Recurrent Rare Genomic Copy Number Variants and Bicuspid Aortic Valve Are Enriched in Early Onset Thoracic Aortic Aneurysms and Dissections. PLoS One (2016) 0.78
Alzheimer disease: An interactome of many diseases. Ann Indian Acad Neurol (2014) 0.78
Exome Sequencing of Normal and Isogenic Transformed Human Colonic Epithelial Cells (HCECs) Reveals Novel Genes Potentially Involved in the Early Stages of Colorectal Tumorigenesis. BMC Genomics (2015) 0.78
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. Int Rev Neurobiol (2012) 0.77
Prioritization of candidate genes for attention deficit hyperactivity disorder by computational analysis of multiple data sources. Protein Cell (2012) 0.77
Integrated pathway clusters with coherent biological themes for target prioritisation. PLoS One (2014) 0.77
Prediction of novel genes associated with negative regulators of toll-like receptors-induced inflammation based on endotoxin tolerance. Inflammation (2012) 0.77
Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq. PLoS One (2016) 0.76
Transcriptional profile of SH-SY5Y human neuroblastoma cells transfected by Toxoplasma rhoptry protein 16. Mol Med Rep (2016) 0.75
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes. PLoS One (2016) 0.75
RecRWR: a recursive random walk method for improved identification of diseases. Biomed Res Int (2015) 0.75
Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways. Int J Mol Sci (2016) 0.75
Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold. BMC Bioinformatics (2016) 0.75
A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects. PLoS Comput Biol (2016) 0.75
Elucidation of MRAS-mediated Noonan syndrome with cardiac hypertrophy. JCI Insight (2017) 0.75
Gene Prioritization for Imaging Genetics Studies Using Gene Ontology and a Stratified False Discovery Rate Approach. Front Neuroinform (2016) 0.75
Autosomal and X chromosome structural variants are associated with congenital heart defects in Turner syndrome: The NHLBI GenTAC registry. Am J Med Genet A (2016) 0.75
Comorbidity of bipolar disorder with substance abuse: selection of prioritized genes for translational research. Summit on Translat Bioinforma (2009) 0.75
Applying Systems Biology Methodology To Identify Genetic Factors Possibly Associated with Recovery after Traumatic Brain Injury. J Neurotrauma (2017) 0.75
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (2004) 26.64
The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res (2004) 25.99
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05
BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res (2003) 18.75
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res (2005) 17.58
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet (2002) 14.69
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res (2004) 12.19
Human protein reference database--2006 update. Nucleic Acids Res (2006) 12.16
The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol (2004) 11.18
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res (2005) 9.05
The PROSITE database. Nucleic Acids Res (2006) 8.11
The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res (2005) 7.66
Gene prioritization through genomic data fusion. Nat Biotechnol (2006) 7.48
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87
The modular nature of genetic diseases. Clin Genet (2007) 4.06
A similarity-based method for genome-wide prediction of disease-relevant human genes. Bioinformatics (2002) 3.04
Speeding disease gene discovery by sequence based candidate prioritization. BMC Bioinformatics (2005) 2.99
SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics (2006) 2.96
POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol (2003) 2.93
Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res (2005) 2.46
Disruption of Abcc6 in the mouse: novel insight in the pathogenesis of pseudoxanthoma elasticum. Hum Mol Genet (2005) 2.36
Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res (2006) 2.30
Mutation of the gene encoding the ROR2 tyrosine kinase causes autosomal recessive Robinow syndrome. Nat Genet (2000) 2.03
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res (2006) 1.95
Loss-of-function mutations in the EGF-CFC gene CFC1 are associated with human left-right laterality defects. Nat Genet (2000) 1.92
Conserved requirement for EGF-CFC genes in vertebrate left-right axis formation. Genes Dev (1999) 1.74
Fuzzy measures on the Gene Ontology for gene product similarity. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.67
Disease gene discovery through integrative genomics. Annu Rev Genomics Hum Genet (2005) 1.51
Murine genetic models of human disease. Curr Opin Genet Dev (1994) 0.99
Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol (2002) 16.75
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res (2009) 7.34
Eotaxin-3 and a uniquely conserved gene-expression profile in eosinophilic esophagitis. J Clin Invest (2006) 5.48
Genetic manipulation of periostin expression reveals a role in cardiac hypertrophy and ventricular remodeling. Circ Res (2007) 4.53
An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. Genome Biol (2003) 4.49
Cardiac-specific deletion of Gata4 reveals its requirement for hypertrophy, compensation, and myocyte viability. Circ Res (2006) 4.41
ApoE and clusterin cooperatively suppress Abeta levels and deposition: evidence that ApoE regulates extracellular Abeta metabolism in vivo. Neuron (2004) 4.21
Blockade of chronic type I interferon signaling to control persistent LCMV infection. Science (2013) 4.14
Pattern of sequence variation across 213 environmental response genes. Genome Res (2004) 3.93
The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor. Cell (2012) 3.91
Genome-level expression profiles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome. Physiol Genomics (2007) 3.37
Activation of IKKalpha target genes depends on recognition of specific kappaB binding sites by RelB:p52 dimers. EMBO J (2004) 3.32
Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics (2009) 3.03
Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol (2007) 2.70
Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res (2002) 2.60
Clusterin promotes amyloid plaque formation and is critical for neuritic toxicity in a mouse model of Alzheimer's disease. Proc Natl Acad Sci U S A (2002) 2.58
Genome-level longitudinal expression of signaling pathways and gene networks in pediatric septic shock. Mol Med (2007) 2.58
GUDMAP: the genitourinary developmental molecular anatomy project. J Am Soc Nephrol (2008) 2.45
Atlas of gene expression in the developing kidney at microanatomic resolution. Dev Cell (2008) 2.44
Genetic induction of proinflammatory immunity in children with biliary atresia. Lancet (2002) 2.44
Gene expression signature for biliary atresia and a role for interleukin-8 in pathogenesis of experimental disease. Hepatology (2014) 2.20
The GUDMAP database--an online resource for genitourinary research. Development (2011) 2.20
Evaluation of myc E-box phylogenetic footprints in glycolytic genes by chromatin immunoprecipitation assays. Mol Cell Biol (2004) 2.19
The retinoblastoma tumor suppressor modifies the therapeutic response of breast cancer. J Clin Invest (2006) 2.18
The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Dev Biol (2011) 2.16
Altered gene expression profiles in nasal respiratory epithelium reflect stable versus acute childhood asthma. J Allergy Clin Immunol (2005) 2.16
Cardiomyocyte GATA4 functions as a stress-responsive regulator of angiogenesis in the murine heart. J Clin Invest (2007) 2.12
Mitochondrial death protein Nix is induced in cardiac hypertrophy and triggers apoptotic cardiomyopathy. Nat Med (2002) 2.05
Identification of IFRD1 as a modifier gene for cystic fibrosis lung disease. Nature (2009) 2.05
Independent and overlapping transcriptional activation during liver development and regeneration in mice. Hepatology (2002) 2.02
MicroRNA-21 limits in vivo immune response-mediated activation of the IL-12/IFN-gamma pathway, Th1 polarization, and the severity of delayed-type hypersensitivity. J Immunol (2011) 2.00
Myocyte enhancer factors 2A and 2C induce dilated cardiomyopathy in transgenic mice. J Biol Chem (2006) 1.92
Caveolin-1-/- null mammary stromal fibroblasts share characteristics with human breast cancer-associated fibroblasts. Am J Pathol (2009) 1.87
Unrestrained erythroblast development in Nix-/- mice reveals a mechanism for apoptotic modulation of erythropoiesis. Proc Natl Acad Sci U S A (2007) 1.86
A catalogue of gene expression in the developing kidney. Kidney Int (2003) 1.83
MEK inhibition exhibits efficacy in human and mouse neurofibromatosis tumors. J Clin Invest (2012) 1.83
Analysis of early nephron patterning reveals a role for distal RV proliferation in fusion to the ureteric tip via a cap mesenchyme-derived connecting segment. Dev Biol (2009) 1.83
Large-scale molecular comparison of human schwann cells to malignant peripheral nerve sheath tumor cell lines and tissues. Cancer Res (2006) 1.80
Human breast cancer-associated fibroblasts (CAFs) show caveolin-1 downregulation and RB tumor suppressor functional inactivation: Implications for the response to hormonal therapy. Cancer Biol Ther (2008) 1.79
MicroRNA signature in patients with eosinophilic esophagitis, reversibility with glucocorticoids, and assessment as disease biomarkers. J Allergy Clin Immunol (2012) 1.79
ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. Nucleic Acids Res (2010) 1.75
Hypoxia induces chondrocyte-specific gene expression in mesenchymal cells in association with transcriptional activation of Sox9. Bone (2005) 1.68
Wnt/beta-catenin signaling is required for development of the exocrine pancreas. BMC Dev Biol (2007) 1.68
Synergistic effects of the GATA-4-mediated miR-144/451 cluster in protection against simulated ischemia/reperfusion-induced cardiomyocyte death. J Mol Cell Cardiol (2010) 1.66
Clonality analysis after retroviral-mediated gene transfer to CD34+ cells from the cord blood of ADA-deficient SCID neonates. Nat Med (2003) 1.65
MiR-223 deficiency increases eosinophil progenitor proliferation. J Immunol (2013) 1.60
Transcriptional profiles of intestinal tumors in Apc(Min) mice are unique from those of embryonic intestine and identify novel gene targets dysregulated in human colorectal tumors. Cancer Res (2005) 1.58
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Res (2006) 1.58
Calcium influx is sufficient to induce muscular dystrophy through a TRPC-dependent mechanism. Proc Natl Acad Sci U S A (2009) 1.58
Subtype-specific peripheral blood gene expression profiles in recent-onset juvenile idiopathic arthritis. Arthritis Rheum (2009) 1.56
Unbiased analysis of RB-mediated transcriptional repression identifies novel targets and distinctions from E2F action. Cancer Res (2002) 1.55
Transcript signatures in experimental asthma: identification of STAT6-dependent and -independent pathways. J Immunol (2004) 1.54
Genes that confer the identity of the renin cell. J Am Soc Nephrol (2011) 1.52
Genetic variants in SCN5A promoter are associated with arrhythmia phenotype severity in patients with heterozygous loss-of-function mutation. Heart Rhythm (2012) 1.51
Prolonged exposure to reduced levels of androgen accelerates prostate cancer progression in Nkx3.1; Pten mutant mice. Cancer Res (2007) 1.51
Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease. Inflamm Bowel Dis (2008) 1.46
High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays. BMC Biotechnol (2010) 1.45
A thrombospondin-dependent pathway for a protective ER stress response. Cell (2012) 1.45
Activator protein-1 transcription factors are associated with progression and recurrence of prostate cancer. Cancer Res (2008) 1.42
Integrative genomic analyses of neurofibromatosis tumours identify SOX9 as a biomarker and survival gene. EMBO Mol Med (2009) 1.41
Subtype distribution of lymphomas in Southwest China: analysis of 6,382 cases using WHO classification in a single institution. Diagn Pathol (2011) 1.38
Genomic responses of the brain to ischemic stroke, intracerebral haemorrhage, kainate seizures, hypoglycemia, and hypoxia. Eur J Neurosci (2002) 1.37
Credentialing a preclinical mouse model of alveolar rhabdomyosarcoma. Cancer Res (2009) 1.37
Overexpression of Stat3C in pulmonary epithelium protects against hyperoxic lung injury. J Immunol (2005) 1.37
Drug repositioning for orphan diseases. Brief Bioinform (2011) 1.37
RB loss abrogates cell cycle control and genome integrity to promote liver tumorigenesis. Gastroenterology (2007) 1.36
Novel resequencing chip customized to diagnose mutations in patients with inherited syndromes of intrahepatic cholestasis. Gastroenterology (2006) 1.35
Loss of Rab25 promotes the development of intestinal neoplasia in mice and is associated with human colorectal adenocarcinomas. J Clin Invest (2010) 1.35
Functional evolution of the p53 regulatory network through its target response elements. Proc Natl Acad Sci U S A (2008) 1.34
Intestinal macrophage/epithelial cell-derived CCL11/eotaxin-1 mediates eosinophil recruitment and function in pediatric ulcerative colitis. J Immunol (2008) 1.33
The transcription factor GATA-6 regulates pathological cardiac hypertrophy. Circ Res (2010) 1.32
Identification of human nephron progenitors capable of generation of kidney structures and functional repair of chronic renal disease. EMBO Mol Med (2013) 1.32
Genomics of the periinfarction cortex after focal cerebral ischemia. J Cereb Blood Flow Metab (2003) 1.32
Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome--clozapine-induced agranulocytosis as a case study. PLoS Comput Biol (2011) 1.26
Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system. BMC Genomics (2004) 1.25
Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus. Proc Natl Acad Sci U S A (2010) 1.23
Serine 105 phosphorylation of transcription factor GATA4 is necessary for stress-induced cardiac hypertrophy in vivo. Proc Natl Acad Sci U S A (2011) 1.23
mTOR inhibitors synergize on regression, reversal of gene expression, and autophagy in hepatocellular carcinoma. Sci Transl Med (2012) 1.21
In vitro and in vivo near-infrared photothermal therapy of cancer using polypyrrole organic nanoparticles. Adv Mater (2012) 1.21
The SWI/SNF ATPase Brm is a gatekeeper of proliferative control in prostate cancer. Cancer Res (2008) 1.21
Shared gene expression profiles in developing heart valves and osteoblast progenitor cells. Physiol Genomics (2008) 1.21
Essential requirement of apolipoprotein J (clusterin) signaling for IkappaB expression and regulation of NF-kappaB activity. J Biol Chem (2003) 1.20
Dynamic interaction between T cell-mediated beta-cell damage and beta-cell repair in the run up to autoimmune diabetes of the NOD mouse. Physiol Genomics (2005) 1.19