Ⅱ 1.4 atsushi_doi@cell-innovator.com 812-8582 3-1-1 8 806 http://www.cell-innovator.com
BioGPS Connectivity Map The Cancer Genome Atlas (TCGA); cbioportal GO DAVID, GSEA WCGNA
BioGPS http://biogps.org/ GEO http://www.ncbi.nlm.nih.gov/geo/ NGS Connectivity Map https://www.broadinstitute.org/cmap/ The Cancer Genome Atlas http://cancergenome.nih.gov mrna, SNP, CNV, etc.
BioGPS
BioGPS GEO BioGPS (GSE1133) (GSE10246)
Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/geo/ NCBI ArrayExpress
Connectivity Map up down ProbeSetID (Affymetrix GeneChip Human Genome U133A Array) ( BioMart
results details foldchange
CEL data matrix 6100
Connectivity Map 1 1300 HL60, MCF7, PC3, SKMEL5, ssmcf7 TCGA
The Cancer Genome Atlas (TCGA) mrna, SNP, CNV cbioportal Acute Myeloid Leukemia [LAML], Adrenocortical carcinoma [ACC], Bladder Urothelial Carcinoma [BLCA], Brain Lower Grade Glioma [LGG] 34
cbioportal TCGA http://www.cbioportal.org
cbioportal: (1) Mutated Genes
cbioportal: (2)
cbioportal: Co-Expression Co-Expression
cbioportal: Survival
cbioportal: Network NCI_Nature (Pathway Intraction Database), HPRD, REACTOME, DrugBank
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(circos, chord diagram)
, t-
stem cell ES BioGPS stem cell ES liver, heart 180 GO stem cell
(functional analysis): GO, DAVID, GSEA (biological function) GO 2 The Database for Annotation, Visualization and Integrated Discovery (DAVID) Gene Set Enrichment Analysis (GSEA)
GO Gene Ontology Gene Ontology (GO) 1 Myc GO DNA binding, E-box binding, RNA polymerase II core promoter proximal region sequence-specific DNA binding, core promoter proximal region sequence-specific DNA binding, double-stranded DNA binding, protein binding, protein complex binding, protein dimerization activity, protein heterodimerization activity, etc.
(DAG) GO http://geneontology.org
GO GO kinase ->
GO GO apoptosis GO apoptotic process apoptosis GO:0001071 nucleic acid binding transcription factor activity GO:0006351 transcription, DNAtemplated metastasis
GO inflammatory response GO inflammatory response negative regulation positive regulation negative, positive
The Database for Annotation, Visualization and Integrated Discovery (DAVID) DAVID GO ID https://david.ncifcrf.gov
DAVID 1 1 GO p-value Enrichment Score Enrichment Score > 1.3
Gene Set Enrichment Analysis (GSEA) GSEA DAVID Enrichment Score MSigDB http://www.broadinstitute.org/gsea/ index.jsp
Gene Set GO metastasis EMT MSigDB GO GO
*MSigDB
GSEA Enrichment Score n DAVID up, down up, down *GSEA GO up down
KEGG GO DAVID GSEA KEGG http://www.genome.jp/kegg/ pathway.html
GO GSEA up, down up, down
> > NGS > Weighted correlation network analysis (WGCNA)
WCGNA, DAVID Prudencio et al., Nat. Neurosci. 2015 Aug;18(8): 1175-82. RNA-Seq DAVID
http://array.cell-innovator.com
URL BioGPS - http://biogps.org/ GEO - http://www.ncbi.nlm.nih.gov/geo/ Connectivity Map - https://www.broadinstitute.org/cmap/ TCGA - https://www.broadinstitute.org/cmap/ cbioportal - http://www.cbioportal.org DAVID - https://david.ncifcrf.gov GSEA - http://www.broadinstitute.org/gsea/index.jsp KEGG - http://www.genome.jp/kegg/pathway.html WCGNA - http://labs.genetics.ucla.edu/horvath/coexpressionnetwork/ Rpackages/WGCNA/