Functional and genomic context in pathway analysis of GWAS data.
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J. Nigg | S. McWeeney | M. Mooney | B. Wilmot | Beth Wilmot
[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.