Functional and genomic context in pathway analysis of GWAS data.

[1]  D. Botstein,et al.  A genetic method for determining the order of events in a biological pathway. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[2]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[3]  中尾 光輝,et al.  KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .

[4]  Ioannis Xenarios,et al.  DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..

[5]  Gary D Bader,et al.  BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.

[6]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[7]  Hao Chen,et al.  Content-rich biological network constructed by mining PubMed abstracts , 2004, BMC Bioinformatics.

[8]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  R. Tibshirani,et al.  On testing the significance of sets of genes , 2006, math/0610667.

[10]  Kai Wang,et al.  Pathway-based approaches for analysis of genomewide association studies. , 2007, American journal of human genetics.

[11]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[12]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[13]  Jean-Pierre A. Kocher,et al.  GLOSSI: a method to assess the association of genetic loci-sets with complex diseases , 2009, BMC Bioinformatics.

[14]  Marit Holden,et al.  GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies , 2008, Bioinform..

[15]  Hong Wang,et al.  Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways , 2009, Bioinform..

[16]  Elizabeth A. Heron,et al.  The SNP ratio test: pathway analysis of genome-wide association datasets , 2009, Bioinform..

[17]  Joaquín Dopazo,et al.  Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies , 2009, Nucleic Acids Res..

[18]  David C. Wilson,et al.  Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn Disease. , 2009, American journal of human genetics.

[19]  P. Rosenberg,et al.  Pathway analysis by adaptive combination of P‐values , 2009, Genetic epidemiology.

[20]  Y. Pawitan,et al.  Strategies and issues in the detection of pathway enrichment in genome-wide association studies , 2009, Human Genetics.

[21]  M. Daly,et al.  Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions , 2009, PLoS genetics.

[22]  Kenneth H. Buetow,et al.  PID: the Pathway Interaction Database , 2008, Nucleic Acids Res..

[23]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..

[24]  Manuel A. R. Ferreira,et al.  Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. , 2009, American journal of human genetics.

[25]  J. Hirschhorn Genomewide association studies--illuminating biologic pathways. , 2009, The New England journal of medicine.

[26]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[27]  John R. Rice,et al.  SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study , 2010, Nucleic Acids Res..

[28]  Suhua Chang,et al.  i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study , 2010, Nucleic Acids Res..

[29]  Kei-Hoi Cheung,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[30]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[31]  Alfonso Valencia,et al.  TopoGSA: network topological gene set analysis , 2010, Bioinform..

[32]  X. Chen,et al.  Pathway‐based analysis for genome‐wide association studies using supervised principal components , 2010, Genetic epidemiology.

[33]  Lazaros G. Papageorgiou,et al.  Module detection in complex networks using integer optimisation , 2010, Algorithms for Molecular Biology.

[34]  M. Xiong,et al.  Genome-wide gene and pathway analysis , 2010, European Journal of Human Genetics.

[35]  Zhaoxia Yu,et al.  SNP-based pathway enrichment analysis for genome-wide association studies , 2011, BMC Bioinformatics.

[36]  Lin S. Chen,et al.  Insights into colon cancer etiology via a regularized approach to gene set analysis of GWAS data. , 2010, American journal of human genetics.

[37]  Ayellet V. Segrè,et al.  Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits , 2010, PLoS genetics.

[38]  P. Visscher,et al.  A versatile gene-based test for genome-wide association studies. , 2010, American journal of human genetics.

[39]  X. Wen,et al.  Gene, region and pathway level analyses in whole‐genome studies , 2009, Genetic epidemiology.

[40]  H. Hakonarson,et al.  Analysing biological pathways in genome-wide association studies , 2010, Nature Reviews Genetics.

[41]  P. Holmans Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits. , 2010, Advances in genetics.

[42]  Sangsoo Kim,et al.  GSA-SNP: a general approach for gene set analysis of polymorphisms , 2010, Nucleic Acids Res..

[43]  M. Daly,et al.  Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology , 2011, PLoS genetics.

[44]  Zhongming Zhao,et al.  A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia , 2011, Journal of Medical Genetics.

[45]  T. Pawson,et al.  Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor , 2011, Nature Biotechnology.

[46]  Suhua Chang,et al.  ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework , 2011, Nucleic Acids Res..

[47]  B. Franke,et al.  Integrated genome-wide association study findings: identification of a neurodevelopmental network for attention deficit hyperactivity disorder. , 2011, The American journal of psychiatry.

[48]  O. U. Sezerman,et al.  A New Methodology to Associate SNPs with Human Diseases According to Their Pathway Related Context , 2011, PloS one.

[49]  Wei Zheng,et al.  dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks , 2011, Bioinform..

[50]  Eli Upfal,et al.  Algorithms for Detecting Significantly Mutated Pathways in Cancer , 2010, RECOMB.

[51]  K. Buetow,et al.  Pathways of Distinction Analysis: A New Technique for Multi–SNP Analysis of GWAS Data , 2010, PLoS genetics.

[52]  Gary D. Bader,et al.  Pathway Commons, a web resource for biological pathway data , 2010, Nucleic Acids Res..

[53]  Johnny S. H. Kwan,et al.  GATES: a rapid and powerful gene-based association test using extended Simes procedure. , 2011, American journal of human genetics.

[54]  Xi Chen,et al.  An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies , 2011, Bioinform..

[55]  Judy H. Cho,et al.  Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association Studies , 2011, PLoS genetics.

[56]  J. Sutcliffe,et al.  Genetic analysis of biological pathway data through genomic randomization , 2011, Human Genetics.

[57]  B. Fridley,et al.  Gene set analysis of SNP data: benefits, challenges, and future directions , 2011, European Journal of Human Genetics.

[58]  Ralf Herwig,et al.  ConsensusPathDB: toward a more complete picture of cell biology , 2010, Nucleic Acids Res..

[59]  G. Smyth,et al.  Camera: a competitive gene set test accounting for inter-gene correlation , 2012, Nucleic acids research.

[60]  Alfonso Valencia,et al.  EnrichNet: network-based gene set enrichment analysis , 2012, Bioinform..

[61]  Livia Perfetto,et al.  MINT, the molecular interaction database: 2012 update , 2011, Nucleic Acids Res..

[62]  Robert Kofler,et al.  Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies , 2012, Bioinform..

[63]  Johnny S. H. Kwan,et al.  HYST: a hybrid set-based test for genome-wide association studies, with application to protein-protein interaction-based association analysis. , 2012, American journal of human genetics.

[64]  B. Fridley,et al.  Use of the gamma method for self-contained gene-set analysis of SNP data , 2011, European Journal of Human Genetics.

[65]  Jun Ma,et al.  THINK Back: KNowledge-based Interpretation of High Throughput data , 2012, BMC Bioinformatics.

[66]  Daniel L. Koller,et al.  Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture , 2012, Nature Genetics.

[67]  Colm O'Dushlaine,et al.  INRICH: interval-based enrichment analysis for genome-wide association studies , 2012, Bioinform..

[68]  Atul J. Butte,et al.  Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges , 2012, PLoS Comput. Biol..

[69]  Jason H. Moore,et al.  Pathway analysis of genomic data: concepts, methods, and prospects for future development. , 2012, Trends in genetics : TIG.

[70]  N. Hastie,et al.  Uncovering Networks from Genome-Wide Association Studies via Circular Genomic Permutation , 2012, G3: Genes | Genomes | Genetics.

[71]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[72]  Jianmin Wu,et al.  PINA v2.0: mining interactome modules , 2011, Nucleic Acids Res..

[73]  Jin Wang,et al.  Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes , 2012, BMC Systems Biology.

[74]  Hiromitsu Araki,et al.  GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis , 2012, FEBS open bio.

[75]  Zhaoxia Yu,et al.  A pathway analysis method for genome‐wide association studies , 2012, Statistics in medicine.

[76]  Andrew E. Jaffe,et al.  Gene set bagging for estimating the probability a statistically significant result will replicate , 2013, BMC Bioinformatics.

[77]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[78]  M. Stephens,et al.  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 , 2013, PLoS genetics.

[79]  I. Nookaew,et al.  Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods , 2013, Nucleic acids research.

[80]  Michal Ziv-Ukelson,et al.  A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks , 2013, Bioinform..

[81]  Jin Wang,et al.  CePa: an R package for finding significant pathways weighted by multiple network centralities , 2013, Bioinform..

[82]  Cristina Mitrea,et al.  Methods and approaches in the topology-based analysis of biological pathways , 2013, Front. Physiol..

[83]  A. Zell,et al.  Integrative Pathway-Based Approach for Genome-Wide Association Studies: Identification of New Pathways for Rheumatoid Arthritis and Type 1 Diabetes , 2013, PloS one.

[84]  Wei Keat Lim,et al.  Assembling cell context-specific gene sets: a case in cardiomyopathy , 2013, J. Integr. Bioinform..

[85]  Y. Teo,et al.  Pathways-Driven Sparse Regression Identifies Pathways and Genes Associated with High-Density Lipoprotein Cholesterol in Two Asian Cohorts , 2013, PLoS genetics.

[86]  Jing Wang,et al.  WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 , 2013, Nucleic Acids Res..

[87]  O. Andreassen,et al.  All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs , 2013, PLoS genetics.

[88]  Margaret A. Pericak-Vance,et al.  Pathway-PDT: a flexible pathway analysis tool for nuclear families , 2013, BMC Bioinformatics.

[89]  S. Drăghici,et al.  Analysis and correction of crosstalk effects in pathway analysis , 2013, Genome research.

[90]  John D. Storey,et al.  Gene set bagging for estimating replicability of gene set analyses , 2013, 1301.3933.

[91]  E. C. Schirmer,et al.  Tissue specificity in the nuclear envelope supports its functional complexity , 2013, Nucleus.

[92]  Marina Evangelou,et al.  Two novel pathway analysis methods based on a hierarchical model , 2013, Bioinform..

[93]  Jason H. Moore,et al.  A System‐Level Pathway‐Phenotype Association Analysis Using Synthetic Feature Random Forest , 2014, Genetic epidemiology.

[94]  Organization to promote biomarker development. , 2014, Journal of nuclear medicine : official publication, Society of Nuclear Medicine.

[95]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[96]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.