Genome Biology & Applied Bioinformatics Mehmet Tevfik DORAK, MD PhD

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Presentation transcript:

Genome Biology & Applied Bioinformatics Mehmet Tevfik DORAK, MD PhD Gene Sets Mehmet Tevfik DORAK, MD PhD

Schedule

How to Generate a Gene Set Gene Set Enrichment Analysis (GSEA) Outline How to Generate a Gene Set (NOT the nearest genes) Gene Set Enrichment Analysis (GSEA) (DAVID, GSEA, WebGestalt, ToppGene, HumanMine)

Gene Set Enrichment Possibilities Gene Ontology (GO Terms) Transcription Factor Binding Motifs miRNA targets Belonging to a Defined Group (Molecular Signatures)

DAVID Link: https://david.ncifcrf.gov/home.jsp Nature Protocol paper: http://www.ncbi.nlm.nih.gov/pubmed/19131956

DAVID Link: https://david.ncifcrf.gov/home.jsp

DAVID Link: https://david.ncifcrf.gov/home.jsp

DAVID Default options are selected. Explore other options. Link: https://david.ncifcrf.gov/home.jsp

DAVID You have done a pathway analysis. Link: https://david.ncifcrf.gov/home.jsp

GSEA Link: http://software.broadinstitute.org/gsea/index.jsp

GSEA/MSigDB Link: http://software.broadinstitute.org/gsea/msigdb/index.jsp

GSEA/MSigDB Link: http://software.broadinstitute.org/gsea/msigdb/annotate.jsp

Gene Ontology Link: http://geneontology.org

CTDbase Link: http://ctdbase.org/tools/analyzer.go (Set Analyzer)

WebGestalt Link: WebGestalt: http://bioinfo.vanderbilt.edu/webgestalt PAPER: http://nar.oxfordjournals.org/content/41/W1/W77.full

iGsea4Gwas Link: http://gsea4gwas.psych.ac.cn

HumanMine Links: HumanMine: http://www.humanmine.org/humanmine/begin.do List Analysis: http://www.humanmine.org/humanmine/bag.do

HumanMine Links: HumanMine: http://www.humanmine.org/humanmine/begin.do List Analysis: http://www.humanmine.org/humanmine/bag.do

iGsea4Gwas Links: iGsea4Gwas: http://gsea4gwas.psych.ac.cn ADDITIONAL NOTE: http://gsea4gwas.psych.ac.cn/docs/introduction.jsp PAPER: http://nar.oxfordjournals.org/content/38/suppl_2/W90.abstract

MAGENTA (MATLAB) Link: https://www.broadinstitute.org/mpg/magenta

GSEA-SNP (R) Link: https://www.nr.no/en/projects/software-genomics

Key Points - A gene set can be generated from a SNP list using the targets of each SNP’s effect - A gene set can be subject to many different types of enrichment of overlap analyses - Results of an enrichment (including pathway) analysis may help to gain insight into disease biology

… Looking forward ….. http://www.dorak.info

Course material: http://www.dorak.info/genbiol/course.html