Hi,
I would like to know if someone has experience with GO term enrichment analysis in C. elegans for differentially expressed genes from RNA-seq data? What tools do you suggest to use?
Thanks
Best,
C.
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biomagician
Try GeneSCF, also check the advantages of using GeneSCF. It supports 'Caenorhabditis elegans' with Gene Ontology (organism code: wb) and also KEGG (organism code: cel).
Example: Gene ontology
./prepare_database -db=GO_all -org=wb
./geneSCF -m=normal -i=INPUTgene.list -t=sym -db=GO_BP -o=/ExistingOUTPUTfolder/ -org=wb --plot=yes --background=#NumberOfTotalGenesUsedForAnalysis
I will try thanks. Do you know if the Bioconductor package topGO supports C. elegans? Thanks. Best, C.
I know GeneSCF is supposed to work on Linux but do you know if it works on Mac OS?
Best, Thanks, C.
It was successfully tested with virtual emulator, MobaXterm on windows. Try on MacOS alternatives for linux gnome-terminal, http://alternativeto.net/software/gnome-terminal/?platform=mac
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You can also use ClueGO from cytoscape!