Genome-wide gene and pathway analysis.

Analysing biological pathways in genome-wide association studies. Nat Rev Genet (2010) 6.63

Pathway analysis of genomic data: concepts, methods, and prospects for future development. Trends Genet (2012) 1.86

Gene set analysis of genome-wide association studies: methodological issues and perspectives. Genomics (2011) 1.76

Gene set analysis of SNP data: benefits, challenges, and future directions. Eur J Hum Genet (2011) 1.73

Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways. Age (Dordr) (2011) 1.26

Insights into pancreatic cancer etiology from pathway analysis of genome-wide association study data. PLoS One (2012) 1.19

Functional and genomic context in pathway analysis of GWAS data. Trends Genet (2014) 1.18

The oxytocin receptor gene (OXTR) is associated with autism spectrum disorder: a meta-analysis. Mol Psychiatry (2014) 1.18

Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PLoS Genet (2013) 1.14

Discovery and Replication of Gene Influences on Brain Structure Using LASSO Regression. Front Neurosci (2012) 1.10

Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies. Genet Epidemiol (2011) 1.06

Pathway-based analysis using reduced gene subsets in genome-wide association studies. BMC Bioinformatics (2011) 1.02

Genome-wide pathway analysis of memory impairment in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort implicates gene candidates, canonical pathways, and networks. Brain Imaging Behav (2012) 1.00

Comparison of pathway analysis approaches using lung cancer GWAS data sets. PLoS One (2012) 1.00

Genome-wide gene-environment interaction analysis for asbestos exposure in lung cancer susceptibility. Carcinogenesis (2012) 0.99

Integration of biological networks and pathways with genetic association studies. Hum Genet (2012) 0.92

Integrative pathway analysis of a genome-wide association study of (V)O(2max) response to exercise training. J Appl Physiol (1985) (2013) 0.91

Using genetically informed, randomized prevention trials to test etiological hypotheses about child and adolescent drug use and psychopathology. Am J Public Health (2013) 0.91

Genome-wide pathway association studies of multiple correlated quantitative phenotypes using principle component analyses. PLoS One (2012) 0.90

Pathway-based analysis of primary biliary cirrhosis genome-wide association studies. Genes Immun (2013) 0.90

Pathway-based approaches for sequencing-based genome-wide association studies. Genet Epidemiol (2013) 0.90

Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps. Stat Appl Genet Mol Biol (2012) 0.87

Pathway-based analysis tools for complex diseases: a review. Genomics Proteomics Bioinformatics (2014) 0.87

Measles contributes to rheumatoid arthritis: evidence from pathway and network analyses of genome-wide association studies. PLoS One (2013) 0.86

Unraveling genetic origin of aging-related traits: evolving concepts. Rejuvenation Res (2013) 0.86

An integrative genomics approach to biomarker discovery in breast cancer. Cancer Inform (2011) 0.86

Oesophageal squamous cell carcinoma in high-risk Chinese populations: Possible role for vascular epithelial growth factor A. Eur J Cancer (2014) 0.84

Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies. Pharmacogenomics (2012) 0.84

Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives. BioData Min (2013) 0.83

Gene-based Higher Criticism methods for large-scale exonic single-nucleotide polymorphism data. BMC Proc (2011) 0.82

A model of early human embryonic stem cell differentiation reveals inter- and intracellular changes on transition to squamous epithelium. Stem Cells Dev (2011) 0.81

A PLSPM-based test statistic for detecting gene-gene co-association in genome-wide association study with case-control design. PLoS One (2013) 0.81

Gene-based multiple trait analysis for exome sequencing data. BMC Proc (2011) 0.80

Predicting disease-related subnetworks for type 1 diabetes using a new network activity score. OMICS (2012) 0.80

A goodness-of-fit association test for whole genome sequencing data. BMC Proc (2014) 0.80

Gene-environment interactions and obesity: recent developments and future directions. BMC Med Genomics (2015) 0.79

How far from the SNP may the causative genes be? Nucleic Acids Res (2016) 0.79

Genome-wide interrogation reveals hundreds of long intergenic noncoding RNAs that associate with cardiometabolic traits. Hum Mol Genet (2016) 0.79

Pathway analysis with next-generation sequencing data. Eur J Hum Genet (2014) 0.78

Pathway-based association analysis of two genome-wide screening data identifies rheumatoid arthritis-related pathways. Genes Immun (2014) 0.78

Integrative genomic analysis for the discovery of biomarkers in prostate cancer. Biomark Insights (2014) 0.78

Prioritizing biological pathways by recognizing context in time-series gene expression data. BMC Bioinformatics (2016) 0.77

Comprehensive assessment and network analysis of the emerging genetic susceptibility landscape of prostate cancer. Cancer Inform (2013) 0.77

Genome-wide association study of perioperative myocardial infarction after coronary artery bypass surgery. BMJ Open (2015) 0.77

META-GSA: Combining Findings from Gene-Set Analyses across Several Genome-Wide Association Studies. PLoS One (2015) 0.77

A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci. PLoS One (2016) 0.76

Trade-offs in the effects of the apolipoprotein E polymorphism on risks of diseases of the heart, cancer, and neurodegenerative disorders: insights on mechanisms from the Long Life Family Study. Rejuvenation Res (2015) 0.76

Embracing Integrative Multiomics Approaches. Int J Genomics (2016) 0.76

Gene set analysis: A step-by-step guide. Am J Med Genet B Neuropsychiatr Genet (2015) 0.76

Association between putative functional variants in the PSMB9 gene and risk of melanoma--re-analysis of published melanoma genome-wide association studies. Pigment Cell Melanoma Res (2013) 0.76

Unravelling genes and pathways implicated in working memory of schizophrenia in Han Chinese. Int J Mol Sci (2015) 0.75

Whole-genome pathway analysis on 132,497 individuals identifies novel gene-sets associated with body mass index. PLoS One (2014) 0.75

Multiple linear combination (MLC) regression tests for common variants adapted to linkage disequilibrium structure. Genet Epidemiol (2016) 0.75

Single-nucleotide polymorphisms associated with skin naphthyl-keratin adduct levels in workers exposed to naphthalene. Environ Health Perspect (2012) 0.75

Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development. Genes Cancer (2016) 0.75

Gene-set meta-analysis of lung cancer identifies pathway related to systemic lupus erythematosus. PLoS One (2017) 0.75

Supervised categorical principal component analysis for genome-wide association analyses. BMC Genomics (2014) 0.75

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95

Finding the missing heritability of complex diseases. Nature (2009) 67.95

KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res (1999) 40.62

Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet (2007) 12.27

TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. N Engl J Med (2007) 12.24

Mapping complex disease loci in whole-genome association studies. Nature (2004) 7.31

The future of association studies: gene-based analysis and replication. Am J Hum Genet (2004) 5.44

Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet (2009) 4.79

Network medicine--from obesity to the "diseasome". N Engl J Med (2007) 3.83

Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci U S A (2008) 3.37

Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57. Nat Genet (2008) 3.06

Nutritional biochemistry: A new redox-cofactor vitamin for mammals. Nature (2003) 2.97

Robust estimation of the false discovery rate. Bioinformatics (2006) 2.87

Complement and coagulation: strangers or partners in crime? Trends Immunol (2007) 2.48

Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis (2007) 2.22

Environmental health and genomics: visions and implications. Nat Rev Genet (2000) 2.05

From genotype to phenotype: systems biology meets natural variation. Science (2008) 1.93

Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes. J Lipid Res (2006) 1.69

The p38 mitogen-activated protein kinase (MAPK) pathway in rheumatoid arthritis. Ann Rheum Dis (2007) 1.63

An allograft inflammatory factor 1 (AIF1) single nucleotide polymorphism (SNP) is associated with anticentromere antibody positive systemic sclerosis. Rheumatology (Oxford) (2007) 1.63

B lymphocyte stimulator regulates adaptive immune responses by directly promoting dendritic cell maturation. J Immunol (2008) 1.21

Mechanisms of disease: genetics of rheumatoid arthritis--ethnic differences in disease-associated genes. Nat Clin Pract Rheumatol (2007) 1.19

Antigen-dependent B-cell development. Curr Opin Immunol (2002) 1.14

Injection of LPS causes transient suppression of biological clock genes in rats. J Surg Res (2008) 1.11

Bystander B cells rapidly acquire antigen receptors from activated B cells by membrane transfer. Proc Natl Acad Sci U S A (2008) 1.07

Aberrant MHC class II expression in mouse joints leads to arthritis with extraarticular manifestations similar to rheumatoid arthritis. Proc Natl Acad Sci U S A (2006) 0.95

Differential regulation of interleukin 5-stimulated signaling pathways by dynamin. J Biol Chem (2006) 0.92

HLA-DQB1 CAR1/CAR2, TNFa IR2/IR4 and CTLA-4 polymorphisms in Tunisian patients with rheumatoid arthritis and Sjögren's syndrome. Rheumatology (Oxford) (2001) 0.92

Genomic rearrangements on VCAM1, SELE, APEG1and AIF1 loci in atherosclerosis. J Cell Mol Med (2005) 0.89

Association of MICA polymorphism with rheumatoid arthritis patients in Koreans. Hum Immunol (2003) 0.88

Microsatellite polymorphism of the MICA gene and susceptibility to rheumatoid arthritis. Clin Exp Rheumatol (2001) 0.84

HLA-DPB1*0301 is a major risk factor for rheumatoid factor-negative adult rheumatoid arthritis. Arthritis Rheum (1991) 0.84

A role for the complement system in rheumatoid arthritis. Curr Pharm Des (2005) 0.83

Enhanced expression of the cytoskeleton-associated proteins paxillin and focal adhesion kinase in glomerular immune injury. J Lab Clin Med (1999) 0.82

An endogenous retroviral long terminal repeat at the HLA-DQB1 gene locus confers susceptibility to rheumatoid arthritis. Hum Immunol (1999) 0.82

Cell-cell communication by endocannabinoids during immune surveillance of the central nervous system. Results Probl Cell Differ (2006) 0.80

HLA-DPB1*0201 is associated with particular clinical features of rheumatoid arthritis. Rev Rhum Engl Ed (1995) 0.80

Cell adhesion molecules in inflammation and immunity: relevance to periodontal diseases. Crit Rev Oral Biol Med (1994) 0.80

Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med (2013) 24.88

Specific recruitment of regulatory T cells in ovarian carcinoma fosters immune privilege and predicts reduced survival. Nat Med (2004) 22.96

A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet (2004) 13.71

TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. N Engl J Med (2007) 12.24

Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet (2010) 9.90

STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med (2007) 9.80

Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet (2008) 7.36

Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet (2008) 7.07

Functional variants of OCTN cation transporter genes are associated with Crohn disease. Nat Genet (2004) 5.83

A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am J Hum Genet (2009) 5.62

Common 5p15.33 and 6p21.33 variants influence lung cancer risk. Nat Genet (2008) 5.43

Refining the complex rheumatoid arthritis phenotype based on specificity of the HLA-DRB1 shared epitope for antibodies to citrullinated proteins. Arthritis Rheum (2005) 5.18

Telomere dysfunction: a potential cancer predisposition factor. J Natl Cancer Inst (2003) 5.09

High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat Genet (2012) 4.46

A risk model for prediction of lung cancer. J Natl Cancer Inst (2007) 4.25

PTPN22 genetic variation: evidence for multiple variants associated with rheumatoid arthritis. Am J Hum Genet (2005) 3.95

Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD. PLoS Genet (2010) 3.91

Test for interaction between two unlinked loci. Am J Hum Genet (2006) 3.88

Ignoring linkage disequilibrium among tightly linked markers induces false-positive evidence of linkage for affected sib pair analysis. Am J Hum Genet (2004) 3.83

Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell (2013) 3.81

Characterization of BRCA1 and BRCA2 mutations in a large United States sample. J Clin Oncol (2006) 3.73

Screening the genome for rheumatoid arthritis susceptibility genes: a replication study and combined analysis of 512 multicase families. Arthritis Rheum (2003) 3.73

Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants. N Engl J Med (2009) 3.70

The CHRNA5-A3 region on chromosome 15q24-25.1 is a risk factor both for nicotine dependence and for lung cancer. J Natl Cancer Inst (2008) 3.67

Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nat Genet (2009) 3.52

Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol Microbiol (2003) 3.26

Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with Behçet's disease. Nat Genet (2010) 3.24

Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. J Natl Cancer Inst (2010) 3.18

Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. Nat Genet (2010) 3.15

Clinical and pathologic characteristics of patients with BRCA-positive and BRCA-negative breast cancer. J Clin Oncol (2008) 3.09

Gene and pathway-based second-wave analysis of genome-wide association studies. Eur J Hum Genet (2010) 3.03

Genome-wide association study in alopecia areata implicates both innate and adaptive immunity. Nature (2010) 2.85

Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer. Nat Genet (2009) 2.76

Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. Cancer Res (2009) 2.63

Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus. Nat Genet (2010) 2.61

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev (2011) 2.53

Germline p53 mutations in a cohort with childhood sarcoma: sex differences in cancer risk. Am J Hum Genet (2003) 2.52

Dissecting the genetic complexity of the association between human leukocyte antigens and rheumatoid arthritis. Am J Hum Genet (2002) 2.47

DNA repair capacity in peripheral lymphocytes predicts survival of patients with non-small-cell lung cancer treated with first-line platinum-based chemotherapy. J Clin Oncol (2011) 2.34

Genome-wide association study identifies three new melanoma susceptibility loci. Nat Genet (2011) 2.29

Bias in estimates of quantitative-trait-locus effect in genome scans: demonstration of the phenomenon and a method-of-moments procedure for reducing bias. Am J Hum Genet (2002) 2.25

Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Am J Hum Genet (2006) 2.22

Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis. Arthritis Rheum (2013) 2.17

Mitochondrial DNA content: its genetic heritability and association with renal cell carcinoma. J Natl Cancer Inst (2008) 2.17

Genetic variants on 15q25.1, smoking, and lung cancer: an assessment of mediation and interaction. Am J Epidemiol (2012) 2.16

Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. J Natl Cancer Inst (2008) 2.15

Extension of variance components approach to incorporate temporal trends and longitudinal pedigree data analysis. Genet Epidemiol (2002) 2.14

Genetic susceptibility to lung cancer: the role of DNA damage and repair. Cancer Epidemiol Biomarkers Prev (2003) 2.09

Underestimation of risk of a BRCA1 or BRCA2 mutation in women with high-grade serous ovarian cancer by BRCAPRO: a multi-institution study. J Clin Oncol (2014) 2.05

An expanded risk prediction model for lung cancer. Cancer Prev Res (Phila) (2008) 2.05

Clustering of disease features within 512 multicase rheumatoid arthritis families. Arthritis Rheum (2004) 2.00

Relationship between CYP2A6 and CHRNA5-CHRNA3-CHRNB4 variation and smoking behaviors and lung cancer risk. J Natl Cancer Inst (2011) 1.97

Validity of models for predicting BRCA1 and BRCA2 mutations. Ann Intern Med (2007) 1.94

The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol Biol Evol (2003) 1.93

EGFR-T790M is a rare lung cancer susceptibility allele with enhanced kinase activity. Cancer Res (2007) 1.91

Short leukocyte telomere length predicts risk of diabetes in american indians: the strong heart family study. Diabetes (2013) 1.91

Association studies for next-generation sequencing. Genome Res (2011) 1.89

Inherited variation at chromosome 12p13.33, including RAD52, influences the risk of squamous cell lung carcinoma. Cancer Discov (2011) 1.87

Forward-time simulations of human populations with complex diseases. PLoS Genet (2007) 1.87

A genome-wide association study identifies a locus on chromosome 14q21 as a predictor of leukocyte telomere length and as a marker of susceptibility for bladder cancer. Cancer Prev Res (Phila) (2011) 1.86

Fine mapping of chromosome 6q23-25 region in familial lung cancer families reveals RGS17 as a likely candidate gene. Clin Cancer Res (2009) 1.83

The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature (2013) 1.82

A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry. Nat Genet (2013) 1.82

Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy. PLoS Genet (2011) 1.80

Meta-analysis of the prognostic value of circulating tumor cells in breast cancer. Clin Cancer Res (2012) 1.79

Association of the lymphoid tyrosine phosphatase R620W variant with rheumatoid arthritis, but not Crohn's disease, in Canadian populations. Arthritis Rheum (2005) 1.79

Discovery of Ca2+-relevant and differentiation-associated genes downregulated in esophageal squamous cell carcinoma using cDNA microarray. Oncogene (2004) 1.77

Influence of common genetic variation on lung cancer risk: meta-analysis of 14 900 cases and 29 485 controls. Hum Mol Genet (2012) 1.77

Genome-wide meta-analysis for rheumatoid arthritis. Hum Genet (2006) 1.75

IGF1 gene polymorphism and risk for hereditary nonpolyposis colorectal cancer. J Natl Cancer Inst (2006) 1.70

Several regions in the major histocompatibility complex confer risk for anti-CCP-antibody positive rheumatoid arthritis, independent of the DRB1 locus. Mol Med (2008) 1.69

Lung cancer risk in germline p53 mutation carriers: association between an inherited cancer predisposition, cigarette smoking, and cancer risk. Hum Genet (2003) 1.68

An analysis of DNA repair as a determinant of survival in patients with non-small-cell lung cancer. J Natl Cancer Inst (2002) 1.65

An entropy-based genome-wide transmission/disequilibrium test. Hum Genet (2007) 1.65

Family-based association studies for next-generation sequencing. Am J Hum Genet (2012) 1.65

Variants at IRF5-TNPO3, 17q12-21 and MMEL1 are associated with primary biliary cirrhosis. Nat Genet (2010) 1.62

Present Y chromosomes reveal the ancestry of Emperor CAO Cao of 1800 years ago. J Hum Genet (2011) 1.61

CARD15 and HLA DRB1 alleles influence susceptibility and disease localization in Crohn's disease. Am J Gastroenterol (2004) 1.57

p53 Genotypes and Haplotypes Associated With Lung Cancer Susceptibility and Ethnicity. J Natl Cancer Inst (2002) 1.56

Mediating effects of smoking and chronic obstructive pulmonary disease on the relation between the CHRNA5-A3 genetic locus and lung cancer risk. Cancer (2010) 1.55

Genetic variations in radiation and chemotherapy drug action pathways predict clinical outcomes in esophageal cancer. J Clin Oncol (2006) 1.55

Possible genomic imprinting of three human obesity-related genetic loci. Am J Hum Genet (2005) 1.54

Henoch-Schönlein purpura with hypocomplementemia. Pediatr Nephrol (2012) 1.54

A large-scale rheumatoid arthritis genetic study identifies association at chromosome 9q33.2. PLoS Genet (2008) 1.53

Association analyses identify multiple new lung cancer susceptibility loci and their interactions with smoking in the Chinese population. Nat Genet (2012) 1.49

Racial differences in the association between SNPs on 15q25.1, smoking behavior, and risk of non-small cell lung cancer. J Thorac Oncol (2009) 1.49

An entropy-based statistic for genomewide association studies. Am J Hum Genet (2005) 1.47

Unique mitochondrial genome architecture in unicellular relatives of animals. Proc Natl Acad Sci U S A (2003) 1.47

Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genet Epidemiol (2011) 1.47

High prevalence of preinvasive lesions adjacent to BRCA1/2-associated breast cancers. Cancer Prev Res (Phila) (2009) 1.47

Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3. Nat Genet (2011) 1.46

Cytokine receptor CXCR4 mediates estrogen-independent tumorigenesis, metastasis, and resistance to endocrine therapy in human breast cancer. Cancer Res (2010) 1.45

Meta-analyses of colorectal cancer risk factors. Cancer Causes Control (2013) 1.42

Repair of UV light-induced DNA damage and risk of cutaneous malignant melanoma. J Natl Cancer Inst (2003) 1.42

Association between testing for human immunodeficiency virus and changes in risk behaviors among injecting drug users in southern China. Sex Transm Dis (2009) 1.41

Psychological impact of genetic testing for hereditary nonpolyposis colorectal cancer. J Clin Oncol (2005) 1.41

Smoking, DNA repair capacity and risk of nonsmall cell lung cancer. Int J Cancer (2003) 1.39

An oncogenic isoform of HER2 associated with locally disseminated breast cancer and trastuzumab resistance. Mol Cancer Ther (2009) 1.39