I have genes differentially expressed between two groups (case and control). I would like to annotate them by classifying them according to their biological functions.
I work on parasites of Plasmodium Falciparum type Dd2 which are divided into two groups (case and control). I carried out a Differential expression analysis with cuffdiff and CummeRbund then I annotated my genes on plasmodb.org.
Example of id genes: pfDd2_14005040
Now I would like to do a pathway analysis to see which biological pathways these genes are involved in.
StupidWolf, I resumed my annotation with the 3D7 strain of plasmoduim Falciparum then I created my geneList as you indicated but when I make the dotplot nothing is displayed
setwd("C:/cygwin64/home/DIANGO/EXCELL") library(org.Pf.plasmo.db) library(clusterProfiler) gene <- c ("PF3D7_0936800","PF3D7_1478900","PF3D7_1009700","PF3D7_0508500") geneList = keys(org.Pf.plasmo.db) enr <- enrichGO(gene,universe=geneList,OrgDb='org.Pf.plasmo.db',keyType ="SYMBOL",ont="BP") head(enr@result,readtable=TRUE) dotplot(enr)
The output gives a white rectangle
ID Description GeneRatio BgRatio pvalue GO:0006323 GO:0006323 DNA packaging 1/2 21/2615 0.01599974 GO:0071103 GO:0071103 DNA conformation change 1/2 30/2615 0.02281728 GO:0051276 GO:0051276 chromosome organization 1/2 58/2615 0.04387582 GO:0006996 GO:0006996 organelle organization 1/2 144/2615 0.10712138 GO:0016043 GO:0016043 cellular component organization 1/2 203/2615 0.14925925 GO:0006464 GO:0006464 cellular protein modification process 1/2 265/2615 0.19244223 p.adjust qvalue geneID Count GO:0006323 0.1026777 0.07205456 PF3D7_0508500 1 GO:0071103 0.1026777 0.07205456 PF3D7_0508500 1 GO:0051276 0.1316275 0.09237015 PF3D7_0508500 1 GO:0006996 0.2203602 0.15463872 PF3D7_0508500 1 GO:0016043 0.2203602 0.15463872 PF3D7_0508500 1 GO:0006464 0.2203602 0.15463872 PF3D7_1009700 1 > dotplot(enr)
Once again I need your help.