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Gene Set (enrichr) and Gene Interaction Data for CEMiTool

Hi All!

I am really new to this field, so I hope some Bioinformatics/ Biologist may help me, even if my question probably sounds silly to you.

I want to build a Coexpression network (using CEMiTool and/ or WGCNA). I think I now understood the basic concepts and I´ve already build my network. But now I want do do functional enrichment analysis and also include gene interaction data with CEMiTool.

My problem: Where do I get the gene sets in .gmt format from and where do I get the gene interaction (protein interaction) data from? At this point I think I don´t really get the difference/ purpose of all the different databases and appraoches. In WGCNA for example, they seem to use DAVID. In CEMiTool, I´ve read about GeneMania and reactome.

My data is microarray expression data from human blood cells (monocytes), 60 humans divided into 2 sample groups. With filtering I have ~5000 input transcripts for the network in CEMiTool. Would I use the Gene Symbols of these transcripts as input for the databases, to generate the tab and gmt files?

Thank you for any help!

coexpression network functional enrichment
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updated by pedrostrusso • pedrostrusso • written by BELA • BELA

1 answer

Hi BELA, thanks for using CEMiTool!

You can get some .gmt files from the MSigDB Collections available here, including Reactome pathways. You can download several types of interaction files from a database such as STRING.

As for the format, you should make sure that both your expression file and the gmt/interaction files use the same type of identifier, or else CEMiTool will be unable to correctly identify enriched pathways, etc. If you have different identifiers, you can use a package such as biomaRt to "translate" between different identifier types.

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written by pedrostrusso • pedrostrusso

Hello Pedrostrusso I reckon you're the first author on the CEMiTool paper. Which pathways are used in the pathways.gmt file in the extdata folder of the package? Thanks

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written by KOfori • KOfori

Hi @ko2427, yes, we used Reactome pathways, however they were edited in order to fit inside the package, so we don't recommend using them.

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written by pedrostrusso • pedrostrusso

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