Tool to analysis GO term enrichment in C. elegans

Question

[biomagician]

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.

[Lila M]

You can also use ClueGO from cytoscape!

Answer 1

[EagleEye]

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

[biomagician]

I will try thanks. Do you know if the Bioconductor package topGO supports C. elegans? Thanks. Best, C.

[biomagician]

I know GeneSCF is supposed to work on Linux but do you know if it works on Mac OS?

Best, Thanks, C.

[EagleEye]

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