Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
暂无分享,去创建一个
Gary D Bader | Jeff Wong | Ruth Isserlin | Jüri Reimand | Mona Meyer | Lina Wadi | Changjiang Xu | Veronique Voisin | Mike Kucera | Christian Tannus-Lopes | Asha Rostamianfar | Daniele Merico | D. Merico | Ruth Isserlin | J. Reimand | V. Voisin | Lina Wadi | Changjiang Xu | Mona Meyer | Asha Rostamianfar | Jeff Wong | Mike Kucera | Christian Tannus-Lopes
[1] Lincoln D. Stein,et al. Impact of outdated gene annotations on pathway enrichment analysis , 2016, Nature Methods.
[2] Colm O'Dushlaine,et al. INRICH: interval-based enrichment analysis for genome-wide association studies , 2012, Bioinform..
[3] J. Mesirov,et al. The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .
[4] Kenneth H. Buetow,et al. PID: the Pathway Interaction Database , 2008, Nucleic Acids Res..
[5] Matthew D. Young,et al. Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.
[6] M. Schatz,et al. Big Data: Astronomical or Genomical? , 2015, PLoS biology.
[7] Pooja Mittal,et al. A novel signaling pathway impact analysis , 2009, Bioinform..
[8] Jie Zhou,et al. RNA-seq differential expression studies: more sequence or more replication? , 2014, Bioinform..
[9] Jin Wang,et al. CePa: an R package for finding significant pathways weighted by multiple network centralities , 2013, Bioinform..
[10] Ben C. Collins,et al. Quantitative proteomics: challenges and opportunities in basic and applied research , 2017, Nature Protocols.
[11] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[12] Christophe Dessimoz,et al. Quality of Computationally Inferred Gene Ontology Annotations , 2012, PLoS Comput. Biol..
[13] Gary D. Bader,et al. Metabolic Adaptation to Chronic Inhibition of Mitochondrial Protein Synthesis in Acute Myeloid Leukemia Cells , 2013, PloS one.
[14] Gordon K Smyth,et al. Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .
[15] Kathleen Marchal,et al. Pathway and network analysis of more than 2,500 whole cancer genomes , 2018, bioRxiv.
[16] Hedi Peterson,et al. g:Profiler—a web server for functional interpretation of gene lists (2016 update) , 2016, Nucleic Acids Res..
[17] Tomé S Silva,et al. Visualization and Differential Analysis of Protein Expression Data Using R. , 2016, Methods in molecular biology.
[18] Stephen J. Guter,et al. Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders , 2014, American journal of human genetics.
[19] Daniel J. Gaffney,et al. A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.
[20] Hedi Peterson,et al. g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments , 2007, Nucleic Acids Res..
[21] M. Roizen,et al. Hallmarks of Cancer: The Next Generation , 2012 .
[22] Gary D Bader,et al. NetPath: a public resource of curated signal transduction pathways , 2010, Genome Biology.
[23] D. G. MacArthur,et al. Guidelines for investigating causality of sequence variants in human disease , 2014, Nature.
[24] Gary D Bader,et al. Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis , 2016, Clinical Epigenetics.
[25] Pornpimol Charoentong,et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..
[26] 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.
[27] Benjamin E. Gross,et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.
[28] angesichts der Corona-Pandemie,et al. UPDATE , 1973, The Lancet.
[29] Chris T. A. Evelo,et al. WikiPathways: building research communities on biological pathways , 2011, Nucleic Acids Res..
[30] Jing Wang,et al. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 , 2013, Nucleic Acids Res..
[31] Benjamin J. Raphael,et al. Mutational landscape and significance across 12 major cancer types , 2013, Nature.
[32] Thomas Lengauer,et al. Comprehensive Analysis of DNA Methylation Data with RnBeads , 2014, Nature Methods.
[33] Gary D Bader,et al. Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors. , 2016, Cell stem cell.
[34] Cory Y. McLean,et al. GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.
[35] Nuno Nunes,et al. PathVisio 3: An Extendable Pathway Analysis Toolbox , 2015, PLoS Comput. Biol..
[36] Helga Thorvaldsdóttir,et al. Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..
[37] Michael L. Creech,et al. Integration of biological networks and gene expression data using Cytoscape , 2007, Nature Protocols.
[38] P. Khatri,et al. A systems biology approach for pathway level analysis. , 2007, Genome research.
[39] Y. Benjamini,et al. More powerful procedures for multiple significance testing. , 1990, Statistics in medicine.
[40] Martin Kuiper,et al. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..
[41] Davide Heller,et al. STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..
[42] P. Laird. Principles and challenges of genome-wide DNA methylation analysis , 2010, Nature Reviews Genetics.
[43] Gary D Bader,et al. Integrated analysis of proteome, phosphotyrosine‐proteome, tyrosine‐kinome, and tyrosine‐phosphatome in acute myeloid leukemia , 2017, Proteomics.
[44] Hui Yang,et al. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR , 2015, Nature Protocols.
[45] Gary D. Bader,et al. Pathguide: a Pathway Resource List , 2005, Nucleic Acids Res..
[46] Atul J. Butte,et al. Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges , 2012, PLoS Comput. Biol..
[47] Minoru Kanehisa,et al. KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..
[48] Gary D Bader,et al. Functional impact of global rare copy number variation in autism spectrum disorders , 2010, Nature.
[49] J. Mesirov,et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.
[50] E. Lander. Initial impact of the sequencing of the human genome , 2011, Nature.
[51] G. Smyth,et al. Camera: a competitive gene set test accounting for inter-gene correlation , 2012, Nucleic acids research.
[52] Susumu Goto,et al. KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..
[53] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[54] Gary D Bader,et al. Computational approaches to identify functional genetic variants in cancer genomes , 2013, Nature Methods.
[55] K. Dolinski,et al. Use and misuse of the gene ontology annotations , 2008, Nature Reviews Genetics.
[56] Gary D Bader,et al. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy , 2014, Nature.
[57] Charity W. Law,et al. voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.
[58] Sandrine Dudoit,et al. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.
[59] Peter D. Karp,et al. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases , 2007, Nucleic Acids Res..
[60] Gary D Bader,et al. Metabolomic profiling in liver of adiponectin-knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action. , 2015, The Biochemical journal.
[61] Peter Bühlmann,et al. Analyzing gene expression data in terms of gene sets: methodological issues , 2007, Bioinform..
[62] C. Mason,et al. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data , 2013, Genome Biology.
[63] V. Bansal,et al. Statistical analysis strategies for association studies involving rare variants , 2010, Nature Reviews Genetics.
[64] Sara Ballouz,et al. Using predictive specificity to determine when gene set analysis is biologically meaningful , 2016, bioRxiv.
[65] Jing Chen,et al. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization , 2009, Nucleic Acids Res..
[66] Michael P. Schroeder,et al. IntOGen-mutations identifies cancer drivers across tumor types , 2013, Nature Methods.
[67] Martin Krzywinski,et al. Points of significance: Power and sample size , 2013, Nature Methods.
[68] Gary D Bader,et al. Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion , 2012, Cell stem cell.
[69] Israel Steinfeld,et al. BMC Bioinformatics BioMed Central , 2008 .
[70] K. Cibulskis,et al. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. , 2012, The Journal of clinical investigation.
[71] Gary D Bader,et al. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.
[72] Benjamin J. Raphael,et al. Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.
[73] Davis J. McCarthy,et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor , 2013, Nature Protocols.
[74] Joshua M. Korn,et al. Accurately Assessing the Risk of Schizophrenia Conferred by Rare Copy-Number Variation Affecting Genes with Brain Function , 2010, PLoS genetics.
[75] Jun Ma,et al. THINK Back: KNowledge-based Interpretation of High Throughput data , 2012, BMC Bioinformatics.
[76] Andrew D. Rouillard,et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..
[77] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[78] Gary D Bader,et al. Pathway and network analysis of cancer genomes , 2015, Nature Methods.
[79] Brad T. Sherman,et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.
[80] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[81] H. Ji,et al. A network-based gene-weighting approach for pathway analysis , 2011, Cell Research.
[82] Matthew E. Ritchie,et al. limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.
[83] W. Huber,et al. Differential expression analysis for sequence count data , 2010 .
[84] Henning Hermjakob,et al. The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..
[85] Anushya Muruganujan,et al. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees , 2012, Nucleic Acids Res..
[86] G. Church,et al. Systematic determination of genetic network architecture , 1999, Nature Genetics.
[87] Alfonso Valencia,et al. EnrichNet: network-based gene set enrichment analysis , 2012, Bioinform..
[88] Gary D. Bader,et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function , 2010, Nucleic Acids Res..