Published in BMC Genomics on March 03, 2006
WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics (2008) 18.58
Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A (2006) 6.33
Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82
Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol (2008) 4.57
A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility. Genome Res (2008) 4.33
Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol (2007) 4.06
Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
Understanding network concepts in modules. BMC Syst Biol (2007) 3.28
Is my network module preserved and reproducible? PLoS Comput Biol (2011) 2.91
A network model of a cooperative genetic landscape in brain tumors. JAMA (2009) 2.86
Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst Biol (2008) 2.51
Celsius: a community resource for Affymetrix microarray data. Genome Biol (2007) 2.38
Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol (2006) 2.36
Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. Immunity (2012) 2.16
Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics (2009) 2.15
Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics (2009) 1.77
The organization of the transcriptional network in specific neuronal classes. Mol Syst Biol (2009) 1.74
Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients. BMC Genomics (2009) 1.72
The noncoding RNA expression profile and the effect of lncRNA AK126698 on cisplatin resistance in non-small-cell lung cancer cell. PLoS One (2013) 1.65
A general co-expression network-based approach to gene expression analysis: comparison and applications. BMC Syst Biol (2010) 1.63
Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol (2009) 1.61
Comparing statistical methods for constructing large scale gene networks. PLoS One (2012) 1.49
Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics (2012) 1.47
Regulon organization of Arabidopsis. BMC Plant Biol (2008) 1.42
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Independent component analysis: mining microarray data for fundamental human gene expression modules. J Biomed Inform (2010) 1.39
Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. BMC Genomics (2010) 1.38
Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci U S A (2009) 1.31
Incorporating gene co-expression network in identification of cancer prognosis markers. BMC Bioinformatics (2010) 1.20
Molecular ecological network analyses. BMC Bioinformatics (2012) 1.19
Disease gene characterization through large-scale co-expression analysis. PLoS One (2009) 1.15
A transcriptional profile of the decidua in preeclampsia. Am J Obstet Gynecol (2011) 1.14
Growing functional modules from a seed protein via integration of protein interaction and gene expression data. BMC Bioinformatics (2007) 1.13
Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks. BMC Syst Biol (2010) 1.11
Expression-based network biology identifies alteration in key regulatory pathways of type 2 diabetes and associated risk/complications. PLoS One (2009) 1.09
Exploring the transcriptome of ciliated cells using in silico dissection of human tissues. PLoS One (2012) 1.06
Gene network effects on brain microstructure and intellectual performance identified in 472 twins. J Neurosci (2012) 1.04
Genes related to the very early stage of ConA-induced fulminant hepatitis: a gene-chip-based study in a mouse model. BMC Genomics (2010) 1.01
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Functionalization of a protosynaptic gene expression network. Proc Natl Acad Sci U S A (2012) 0.98
MicroRNA-gene expression network in murine liver during Schistosoma japonicum infection. PLoS One (2013) 0.97
Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae. Nucleic Acids Res (2008) 0.96
Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes. PLoS One (2007) 0.95
Gene networks and haloperidol-induced catalepsy. Genes Brain Behav (2011) 0.95
LncRNA and mRNA interaction study based on transcriptome profiles reveals potential core genes in the pathogenesis of human glioblastoma multiforme. J Cancer Res Clin Oncol (2014) 0.94
Genes regulated by caloric restriction have unique roles within transcriptional networks. Mech Ageing Dev (2008) 0.92
The cortical and striatal gene expression profile of 100 hz electroacupuncture treatment in 6-hydroxydopamine-induced Parkinson's disease model. Evid Based Complement Alternat Med (2012) 0.89
Long-term effects of subacute ruminal acidosis (SARA) on milk quality and hepatic gene expression in lactating goats fed a high-concentrate diet. PLoS One (2013) 0.89
Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding. BMC Genomics (2014) 0.89
Differentially expressed genes in major depression reside on the periphery of resilient gene coexpression networks. Front Neurosci (2011) 0.88
Network module detection: Affinity search technique with the multi-node topological overlap measure. BMC Res Notes (2009) 0.87
Prioritizing disease candidate genes by a gene interconnectedness-based approach. BMC Genomics (2011) 0.86
Selecting biologically informative genes in co-expression networks with a centrality score. Biol Direct (2014) 0.84
Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks. BMC Genomics (2012) 0.84
Building gene co-expression networks using transcriptomics data for systems biology investigations: Comparison of methods using microarray data. Bioinformation (2012) 0.84
Systems genetics analysis of mouse chondrocyte differentiation. J Bone Miner Res (2011) 0.84
The effects of network neighbours on protein evolution. PLoS One (2011) 0.83
Associations between HIV and human pathways revealed by protein-protein interactions and correlated gene expression profiles. PLoS One (2012) 0.83
Cell cycle control, DNA damage repair, and apoptosis-related pathways control pre-ameloblasts differentiation during tooth development. BMC Genomics (2015) 0.82
Global profiling of signaling networks: study of breast cancer stem cells and potential regulation. Oncologist (2011) 0.82
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. BMC Syst Biol (2013) 0.81
Discovery of core biotic stress responsive genes in Arabidopsis by weighted gene co-expression network analysis. PLoS One (2015) 0.81
Learning from Co-expression Networks: Possibilities and Challenges. Front Plant Sci (2016) 0.81
Enhancing the functional content of eukaryotic protein interaction networks. PLoS One (2014) 0.81
The complexity of gene expression dynamics revealed by permutation entropy. BMC Bioinformatics (2010) 0.81
A null model for pearson coexpression networks. PLoS One (2015) 0.80
Systematic identification of cell-wall related genes in Populus based on analysis of functional modules in co-expression network. PLoS One (2014) 0.80
Microarray analysis of Long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori Infection. BMC Med Genomics (2015) 0.80
Functional analysis of prognostic gene expression network genes in metastatic breast cancer models. PLoS One (2014) 0.79
Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria. BMC Genomics (2013) 0.79
Discovery of consensus gene signature and intermodular connectivity defining self-renewal of human embryonic stem cells. Stem Cells (2014) 0.79
CorSig: a general framework for estimating statistical significance of correlation and its application to gene co-expression analysis. PLoS One (2013) 0.78
Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy. Neurobiol Dis (2015) 0.78
Regulatory network structure as a dominant determinant of transcription factor evolutionary rate. PLoS Comput Biol (2012) 0.78
Comparison of long noncoding RNA and mRNA expression profiles in mesenchymal stem cells derived from human periodontal ligament and bone marrow. Biomed Res Int (2014) 0.78
Placental gene-expression profiles of intrahepatic cholestasis of pregnancy reveal involvement of multiple molecular pathways in blood vessel formation and inflammation. BMC Med Genomics (2014) 0.78
Identification of a fungi-specific lineage of protein kinases closely related to tyrosine kinases. PLoS One (2014) 0.78
A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways. Front Genet (2016) 0.77
MINER: exploratory analysis of gene interaction networks by machine learning from expression data. BMC Genomics (2009) 0.77
Differential network analyses of Alzheimer's disease identify early events in Alzheimer's disease pathology. Int J Alzheimers Dis (2014) 0.77
Transcriptomic analysis of the effects of Toll-like receptor 4 and its ligands on the gene expression network of hepatic stellate cells. Fibrogenesis Tissue Repair (2016) 0.77
Module-based association analysis for omics data with network structure. PLoS One (2015) 0.77
Variable Levels of Long Noncoding RNA Expression in DNA Mismatch Repair-Proficient Early-Stage Colon Cancer. Dig Dis Sci (2017) 0.76
Cluster and propensity based approximation of a network. BMC Syst Biol (2013) 0.76
Aberrant expression of long noncoding RNAs in chronic thromboembolic pulmonary hypertension. Mol Med Rep (2014) 0.76
Systems genetics of environmental response in the mature wheat embryo. Genetics (2013) 0.76
Reconstruction of composite regulator-target splicing networks from high-throughput transcriptome data. BMC Genomics (2015) 0.76
Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken. PLoS One (2017) 0.76
Adaptive responses by mouse fetus to a maternal HLE diet by downregulating SREBP1: a microarray- and bio-analytic-based study. J Lipid Res (2013) 0.76
Networks' Characteristics Matter for Systems Biology. Netw Sci (Camb Univ Press) (2014) 0.76
Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma. BMC Med Genomics (2015) 0.76
Differential Regulatory Analysis Based on Coexpression Network in Cancer Research. Biomed Res Int (2016) 0.75
High hydrostatic pressure activates transcription factors involved in Saccharomyces cerevisiae stress tolerance. Curr Pharm Biotechnol (2012) 0.75
A systematic analysis of human lipocalin family and its expression in esophageal carcinoma. Sci Rep (2015) 0.75
Functional divergence and convergence between the transcript network and gene network in lung adenocarcinoma. Onco Targets Ther (2016) 0.75
Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer. PLoS One (2016) 0.75
Co-Expression Network Models Suggest that Stress Increases Tolerance to Mutations. Sci Rep (2015) 0.75
Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart. PLoS One (2016) 0.75
Altered gene transcription in human cells treated with Ludox® silica nanoparticles. Int J Environ Res Public Health (2014) 0.75
Paradigm of Time-sequence Development of the Intestine of Suckling Piglets with Microarray. Asian-Australas J Anim Sci (2012) 0.75
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Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
Lethality and centrality in protein networks. Nature (2001) 29.64
Error and attack tolerance of complex networks Nature (2000) 27.90
The large-scale organization of metabolic networks. Nature (2000) 27.57
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Global mapping of the yeast genetic interaction network. Science (2004) 21.34
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A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol (2005) 17.23
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet (2001) 7.16
Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell (2001) 6.39
Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A (2004) 5.10
Similarities and differences in genome-wide expression data of six organisms. PLoS Biol (2003) 4.75
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The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep (2004) 2.75
Predicting gene function by conserved co-expression. Trends Genet (2003) 2.56
Genomics. Microarrays--guilt by association. Science (2003) 1.76
Wrestling with pleiotropy: genomic and topological analysis of the yeast gene expression network. Bioessays (2002) 1.58
Estimating coarse gene network structure from large-scale gene perturbation data. Genome Res (2002) 1.38
Fractal-small-world dichotomy in real-world networks. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 1.31
An exponential core in the heart of the yeast protein interaction network. Mol Biol Evol (2004) 1.31
Building and analysing genome-wide gene disruption networks. Bioinformatics (2002) 1.24
Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations. J Am Chem Soc (2003) 1.23
Genome-wide atlas of gene expression in the adult mouse brain. Nature (2006) 28.02
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78
Genetics of gene expression and its effect on disease. Nature (2008) 21.35
Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science (2008) 20.68
Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet (2008) 20.38
Mapping the genetic architecture of gene expression in human liver. PLoS Biol (2008) 19.44
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation. Nature (2010) 18.69
WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics (2008) 18.58
A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol (2005) 17.23
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13
Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N Engl J Med (2005) 15.42
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
High-throughput oncogene mutation profiling in human cancer. Nat Genet (2007) 12.68
Variations in DNA elucidate molecular networks that cause disease. Nature (2008) 12.04
Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature (2011) 10.16
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res (2011) 7.84
Gene expression profiling of gliomas strongly predicts survival. Cancer Res (2004) 7.79
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics (2007) 7.72
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Role of the murine reprogramming factors in the induction of pluripotency. Cell (2009) 7.46
Linkage, association, and gene-expression analyses identify CNTNAP2 as an autism-susceptibility gene. Am J Hum Genet (2008) 7.13
Loss of tumor suppressor PTEN function increases B7-H1 expression and immunoresistance in glioma. Nat Med (2006) 7.10
Global histone modification patterns predict risk of prostate cancer recurrence. Nature (2005) 7.03
Functional organization of the transcriptome in human brain. Nat Neurosci (2008) 7.02
Pathological α-synuclein transmission initiates Parkinson-like neurodegeneration in nontransgenic mice. Science (2012) 6.66
Clinical features of the initial cases of 2009 pandemic influenza A (H1N1) virus infection in China. N Engl J Med (2009) 6.45
American College of Rheumatology/European League Against Rheumatism provisional definition of remission in rheumatoid arthritis for clinical trials. Arthritis Rheum (2011) 6.28
Synapse loss and microglial activation precede tangles in a P301S tauopathy mouse model. Neuron (2007) 6.07
Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet (2006) 5.82
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet (2008) 5.80
Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A (2006) 5.69
Differential sensitivity of melanoma cell lines with BRAFV600E mutation to the specific Raf inhibitor PLX4032. J Transl Med (2010) 5.57
PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics (2004) 5.55
Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med (2008) 5.54
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics (2011) 5.45
DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med (2011) 4.98
Melanoma whole-exome sequencing identifies (V600E)B-RAF amplification-mediated acquired B-RAF inhibitor resistance. Nat Commun (2012) 4.94
Neuronal alpha-synucleinopathy with severe movement disorder in mice expressing A53T human alpha-synuclein. Neuron (2002) 4.77
Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain. PLoS Med (2006) 4.63
LKB1 inactivation dictates therapeutic response of non-small cell lung cancer to the metabolism drug phenformin. Cancer Cell (2013) 4.58
Phase II study of bevacizumab plus temozolomide during and after radiation therapy for patients with newly diagnosed glioblastoma multiforme. J Clin Oncol (2010) 4.23
American College of Rheumatology/European League against Rheumatism provisional definition of remission in rheumatoid arthritis for clinical trials. Ann Rheum Dis (2011) 4.15
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Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics (2007) 3.83
Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene (2003) 3.83
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Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes. PLoS Genet (2010) 3.75
Increasing prevalence of knee pain and symptomatic knee osteoarthritis: survey and cohort data. Ann Intern Med (2011) 3.65
Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm Genome (2007) 3.59
Epigenetic predictor of age. PLoS One (2011) 3.46
A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet (2010) 3.42
Distinct transcription profiles of primary and secondary glioblastoma subgroups. Cancer Res (2006) 3.41
Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology (2008) 3.38
Analysis of the phosphatidylinositol 3'-kinase signaling pathway in glioblastoma patients in vivo. Cancer Res (2003) 3.36
Dendritic cell vaccination in glioblastoma patients induces systemic and intracranial T-cell responses modulated by the local central nervous system tumor microenvironment. Clin Cancer Res (2005) 3.35
Mammalian target of rapamycin inhibition promotes response to epidermal growth factor receptor kinase inhibitors in PTEN-deficient and PTEN-intact glioblastoma cells. Cancer Res (2006) 3.31
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Carbonic anhydrase IX is an independent predictor of survival in advanced renal clear cell carcinoma: implications for prognosis and therapy. Clin Cancer Res (2003) 3.25
Distinct α-synuclein strains differentially promote tau inclusions in neurons. Cell (2013) 3.24
Evidence for sequenced molecular evolution of IDH1 mutant glioblastoma from a distinct cell of origin. J Clin Oncol (2011) 3.23
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Gene expression profiling identifies molecular subtypes of gliomas. Oncogene (2003) 3.13
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature (2013) 3.06
Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biol (2012) 3.05
Gene expression profile correlates with T-cell infiltration and relative survival in glioblastoma patients vaccinated with dendritic cell immunotherapy. Clin Cancer Res (2010) 3.05
Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc Natl Acad Sci U S A (2006) 3.03
Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis. Science (2004) 3.01
A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res (2011) 3.00
U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet (2010) 2.99
Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet (2009) 2.97
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Synthetic tau fibrils mediate transmission of neurofibrillary tangles in a transgenic mouse model of Alzheimer's-like tauopathy. J Neurosci (2013) 2.90
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell (2013) 2.87
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc Natl Acad Sci U S A (2010) 2.85
Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci U S A (2010) 2.81
Oncogenic EGFR signaling activates an mTORC2-NF-κB pathway that promotes chemotherapy resistance. Cancer Discov (2011) 2.77
Proteasomal and genetic inactivation of the NF1 tumor suppressor in gliomagenesis. Cancer Cell (2009) 2.73
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Retracted Mutations in CLCN2 encoding a voltage-gated chloride channel are associated with idiopathic generalized epilepsies. Nat Genet (2003) 2.70
Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol (2010) 2.61
Differential sensitivity of glioma- versus lung cancer-specific EGFR mutations to EGFR kinase inhibitors. Cancer Discov (2012) 2.61