Pathway analysis of genomic data: concepts, methods, and prospects for future development.

[1]  Zhiping Weng,et al.  Gene set enrichment analysis: performance evaluation and usage guidelines , 2012, Briefings Bioinform..

[2]  Chloe O'Connell,et al.  Ion channels and schizophrenia: a gene set-based analytic approach to GWAS data for biological hypothesis testing , 2012, Human Genetics.

[3]  H. Kitano,et al.  Software for systems biology: from tools to integrated platforms , 2011, Nature Reviews Genetics.

[4]  M. Inouye,et al.  Genome-wide association studies and systems biology: together at last. , 2011, Trends in genetics : TIG.

[5]  Nicholas M. Pajewski,et al.  Six Degrees of Epistasis: Statistical Network Models for GWAS , 2011, Front. Gene..

[6]  Hongsheng Gui,et al.  Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn's Disease dataset , 2011, BMC Research Notes.

[7]  Jason H. Moore,et al.  Systems genetics for drug target discovery. , 2011, Trends in pharmacological sciences.

[8]  B. Vickery,et al.  An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human Tuberculosis , 2011, Pediatrics.

[9]  Ting Hu,et al.  Characterizing genetic interactions in human disease association studies using statistical epistasis networks , 2011, BMC Bioinformatics.

[10]  Karmen K. Yoder,et al.  Amyloid pathway-based candidate gene analysis of [11C]PiB-PET in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort , 2011, Brain Imaging and Behavior.

[11]  Jason H. Moore,et al.  Layers of epistasis: genome‐wide regulatory networks and network approaches to genome‐wide association studies , 2011, Wiley interdisciplinary reviews. Systems biology and medicine.

[12]  S. Eschrich,et al.  BAD Phosphorylation Determines Ovarian Cancer Chemosensitivity and Patient Survival , 2011, Clinical Cancer Research.

[13]  Simon C. Potter,et al.  Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis , 2011, Nature.

[14]  Jiali Han,et al.  Pathway Analysis for Genome-Wide Association Study of Basal Cell Carcinoma of the Skin , 2011, PloS one.

[15]  Hailiang Huang,et al.  Gene-Based Tests of Association , 2011, PLoS genetics.

[16]  Peilin Jia,et al.  Gene set analysis of genome-wide association studies: methodological issues and perspectives. , 2011, Genomics.

[17]  Osbaldo Resendis-Antonio,et al.  Proteomic patterns of cervical cancer cell lines, a network perspective , 2011, BMC Systems Biology.

[18]  T. Ochi,et al.  Abnormal networks of immune response-related molecules in bone marrow cells from patients with rheumatoid arthritis as revealed by DNA microarray analysis , 2011, Arthritis research & therapy.

[19]  Michael Wigler,et al.  Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses , 2011, Neuron.

[20]  D. Telander.  Inflammation and Age-Related Macular Degeneration (AMD) , 2011, Seminars in ophthalmology.

[21]  K. Hemminki,et al.  Consensus Pathways Implicated in Prognosis of Colorectal Cancer Identified Through Systematic Enrichment Analysis of Gene Expression Profiling Studies , 2011, PloS one.

[22]  J. Gustafsson,et al.  Estrogen receptor β induces antiinflammatory and antitumorigenic networks in colon cancer cells. , 2011, Molecular endocrinology.

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

[24]  Margaret A. Pericak-Vance,et al.  Identifying Consensus Disease Pathways in Parkinson's Disease Using an Integrative Systems Biology Approach , 2011, PloS one.

[25]  Herbert Pang,et al.  Pathway-based identification of SNPs predictive of survival , 2011, European Journal of Human Genetics.

[26]  Peilin Jia,et al.  Application of systems biology approach identifies and validates GRB2 as a risk gene for schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample , 2011, Schizophrenia Research.

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

[28]  Anbupalam Thalamuthu,et al.  Pathway-based analysis using reduced gene subsets in genome-wide association studies , 2011, BMC Bioinformatics.

[29]  Sourav Bandyopadhyay,et al.  Rewiring of Genetic Networks in Response to DNA Damage , 2010, Science.

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

[31]  Gary D Bader,et al.  Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.

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

[33]  Hsin-Chou Yang,et al.  Region-based and pathway-based QTL mapping using a p-value combination method , 2010, BMC proceedings.

[34]  Joshua M. Korn,et al.  Common Genetic Variants and Modification of Penetrance of BRCA2-Associated Breast Cancer , 2010, PLoS genetics.

[35]  B. Fridley,et al.  Self-Contained Gene-Set Analysis of Expression Data: An Evaluation of Existing and Novel Methods , 2010, PloS one.

[36]  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.

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

[38]  J. Marchini,et al.  Genotype imputation for genome-wide association studies , 2010, Nature Reviews Genetics.

[39]  Li Shen,et al.  Genetic pathway‐based hierarchical clustering analysis of older adults with cognitive complaints and amnestic mild cognitive impairment using clinical and neuroimaging phenotypes , 2010, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[40]  Judy H. Cho,et al.  Pathway analysis comparison using Crohn's disease genome wide association studies , 2010, BMC Medical Genomics.

[41]  Simon Heath,et al.  Implication of the immune system in Alzheimer's disease: evidence from genome-wide pathway analysis. , 2010, Journal of Alzheimer's disease : JAD.

[42]  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.

[43]  Sterling Thomas,et al.  A survey of current software for network analysis in molecular biology , 2010, Human Genomics.

[44]  Peter Kraft,et al.  Pathway analysis of breast cancer genome-wide association study highlights three pathways and one canonical signaling cascade. , 2010, Cancer research.

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

[46]  Mark Newman,et al.  Networks: An Introduction , 2010 .

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

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

[49]  Xia Yang,et al.  Integrating pathway analysis and genetics of gene expression for genome-wide association studies. , 2010, American journal of human genetics.

[50]  Jing Cao,et al.  GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach , 2010, Bioinform..

[51]  N. Cox,et al.  Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS , 2010, PLoS genetics.

[52]  K. Lange,et al.  Prioritizing GWAS results: A review of statistical methods and recommendations for their application. , 2010, American journal of human genetics.

[53]  D. Hadley,et al.  Inference of disease associations with unmeasured genetic variants by combining results from genome-wide association studies with linkage disequilibrium patterns in a reference data set , 2009, BMC proceedings.

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

[55]  C. Hoggart,et al.  Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases , 2009, PloS one.

[56]  John M. Hancock,et al.  The functional annotation of mammalian genomes: the challenge of phenotyping. , 2009, Annual review of genetics.

[57]  E. Schadt.  Molecular networks as sensors and drivers of common human diseases , 2009, Nature.

[58]  Annarita D'Addabbo,et al.  Comparative study of gene set enrichment methods , 2009, BMC Bioinformatics.

[59]  Ivan P. Gorlov,et al.  GWAS Meets Microarray: Are the Results of Genome-Wide Association Studies and Gene-Expression Profiling Consistent? Prostate Cancer as an Example , 2009, PloS one.

[60]  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.

[61]  C. Wijmenga,et al.  Using genome‐wide pathway analysis to unravel the etiology of complex diseases , 2009, Genetic epidemiology.

[62]  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..

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

[64]  P. Portin.  The elusive concept of the gene. , 2009, Hereditas.

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

[66]  Ting Wang,et al.  The UCSC Cancer Genomics Browser , 2009, Nature Methods.

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

[68]  F. McMahon,et al.  Convergent functional genomics of genome‐wide association data for bipolar disorder: Comprehensive identification of candidate genes, pathways and mechanisms , 2009, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[69]  N. Craddock,et al.  Gene-wide analyses of genome-wide association data sets: evidence for multiple common risk alleles for schizophrenia and bipolar disorder and for overlap in genetic risk , 2009, Molecular Psychiatry.

[70]  M. McCarthy,et al.  Interrogating Type 2 Diabetes Genome-Wide Association Data Using a Biological Pathway-Based Approach , 2009, Diabetes.

[71]  Jason H. Moore,et al.  Pathways-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission , 2009, Human Genetics.

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

[73]  K. Dolinski,et al.  Use and misuse of the gene ontology annotations , 2008, Nature Reviews Genetics.

[74]  Winnie S. Liang,et al.  Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons , 2008, Proceedings of the National Academy of Sciences.

[75]  D. Stephan,et al.  A survey of genetic human cortical gene expression , 2007, Nature Genetics.

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

[77]  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.

[78]  N. Price,et al.  Biochemical and statistical network models for systems biology. , 2007, Current opinion in biotechnology.

[79]  T. Gingeras,et al.  Genome-wide transcription and the implications for genomic organization , 2007, Nature Reviews Genetics.

[80]  Peter Bühlmann,et al.  Analyzing gene expression data in terms of gene sets: methodological issues , 2007, Bioinform..

[81]  Gary D. Bader,et al.  Pathguide: a Pathway Resource List , 2005, Nucleic Acids Res..

[82]  J. Mesirov,et al.  From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005 .

[83]  Emily Dimmer,et al.  An evaluation of GO annotation retrieval for BioCreAtIvE and GOA , 2005, BMC Bioinformatics.

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

[85]  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.

[86]  A. Minagar,et al.  Genetic variation influences glutamate concentrations in brains of patients with multiple sclerosis , 2011 .

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

[88]  Momiao Xiong,et al.  Gene and pathway-based second-wave analysis of genome-wide association studies , 2010, European Journal of Human Genetics.

[89]  C. Sabatti.  Avoiding false discoveries in association studies. , 2007, Methods in molecular biology.

[90]  D. Blacker,et al.  Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database , 2007, Nature Genetics.

[91]  D. Volsky,et al.  PAGE: Parametric Analysis of Gene Set Enrichment , 2005, BMC Bioinformatics.

[92]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .