KEGG gene sets enriched in colorectal lesions.Marine PessonAlain VolantArnaud UguenKilian TrilletPierre de la GrangeMarc AubryMélanie DaoulasMichel RobaszkiewiczGerald Le GacAlain Morel
#View(msigdbr_collections())#查看msigdbr包中所有的基因集unique(genesets$gs_subcat)# 有多个数据库来源的基因集可选,这里选用KEGGgenesets<-subset(genesets,gs_subcat=="CP:KEGG",select=c("gs_name","gene_symbol"))unique(genesets$gs_name)#查看有多少条通路(186个) 但是这里面的kegg只有186个基因...
get_gmt_for_gsva <- function(all_gene_sets){ gs=split(all_gene_sets$gene_symbol,all_gene_sets$gs_name) gs = lapply(gs, unique) head(gs) gsc <- GeneSetCollection(mapply(function(geneIds, keggId) { GeneSet(geneIds, geneIdType=EntrezIdentifier(), collectionType=KEGGCollection(keggId),...
Functional KEGG categories enriched within gene sets.Travis J. WilesJ. Paul NortonColin W. RussellBrian K. DalleyKael F. FischerMatthew A. Mulvey
Create a list of gene sets based on KEGG pathways termsCamille TerfveXin Wang
Perform Gene Set Enrichment Analysis (GSEA) of Gene Ontologies (GO) and Kegg gene sets.Evarist Planet
GSEA Se-deficient and low-Se most significant KEGG gene sets.doi:10.1371/journal.pone.0232160.s008Rachel M. TaylorKristelle M. MendozaJ. AbrahanteK. ReedR. SundePLOS ONEPLOS ONE
Create a list of gene sets based on KEGG pathways terms.Evarist Planet
Generate up-to-date KEGG pathway gene setsWeijun Luo
Overlap of the top10 gene sets enriched by 6 different gene-ranking methods on four datasets for the C2CP, C2KEGG and C5 gene datasets.Zhilong, JiaXiang, ZhangNaiyang, GuanXiaochen, BoMichael, R. BarnesZhigang, Luo