PathFindR: Running Reactome for Mouse

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3.1 years ago

OST ▴ 10

Hello!

I want to kindly ask how can we run Reactome for run_pathfindR for mouse (Mus musculus) genes?

Thank you!

PathFindR • 945 views

ADD COMMENT • link updated 3.1 years ago by Pratik ★ 1.1k • written 3.1 years ago by OST ▴ 10

1

Entering edit mode

Hello,

I have never used PathFindR, but from looking at the tutorial here: Enrichment Analysis, Clustering and Scoring with pathfindR

It looks like you need to provide the output of an RNA-seq comparison generated from DESeq2 or other DGE analysis package (EdgeR?). Check out the tutorial I linked above...

If you can see... the input for PathFindR looks something like this:

head(RA_input)

  Gene.symbol    logFC  adj.P.Val
1     FAM110A -0.69394 3.4087e-06
2      RNASE2  1.35350 1.0085e-05
3      S100A8  1.54483 3.4664e-05
4      S100A9  1.02809 2.2626e-04
5      TEX261 -0.32360 2.2626e-04
6    ARHGAP17 -0.69193 2.7081e-04

This would be the standard output of DESeq2 (except that logFC would be log2FC). Maybe someone else could chime in here as well, with regard to using LogFC or Log2FC?

ADD REPLY • link 3.1 years ago by Pratik ★ 1.1k

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