Question

Getting gene ID's from camera results

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AB ▴ 110

@ab-8975

Last seen 19 months ago

United States

Hi,

I have used camera (limma package) to do a gene set enrichment analysis with a gene set from MSigDB. I was wondering if there is any way I could use the results from camera to get the genes belonging to that list.

NGenes Correlation Direction PValue FDR
HALLMARK_E2F_TARGETS 201 -0.0047718432 Up 0.01676313 0.5229967
HALLMARK_PI3K_AKT_MTOR_SIGNALING 96 -0.0074777132 Down 0.03990746 0.5229967
HALLMARK_IL6_JAK_STAT3_SIGNALING 68 -0.0109702506 Down 0.04448435 0.5229967
HALLMARK_INTERFERON_ALPHA_RESPONSE 62 -0.0131317542 Down 0.04721300 0.5229967

For instance, HALLMARK_E2F_TARGETS has 201 genes. How can I find out which genes from my input gene identifiers belong to this list ?

Thanks

limma camera • 1.7k views

ADD COMMENT • link updated 8.0 years ago by phil.chapman ▴ 150 • written 8.0 years ago by AB ▴ 110

score 2 · Answer 1 · 2016-05-09

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Aaron Lun ★ 28k

@alun

Last seen 13 minutes ago

The city by the bay

Well, you don't really need the results from CAMERA, because your gene sets are already defined. Assuming your list of index vectors is indices and your matrix y has the gene IDs as the row names , you could do:

rownames(y)[indices$HALLMARK_E2F_TARGETS]

If that doesn't work, you'll have to give some more details about the inputs you're using to run camera.

ADD COMMENT • link 8.0 years ago Aaron Lun ★ 28k

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That did work. Thank you very much. But is there anyway to do it without knowing the indices ?

I have a shiny interface that loads up the precomputed camera results from an Rdata and I need the interface to display the gene list when each row is clicked on. I have the gene set and the camera results but not the indices.

ADD REPLY • link 8.0 years ago AB ▴ 110

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You had to know the indices to do the camera analysis in the first place. If you want to re-access to them in the future, can you not simply store them in the RData file together with the camera output?

Obviously you can't list the genes in a set without knowing the indices because the indices define which genes are in the set.

ADD REPLY • link 8.0 years ago Gordon Smyth 50k

score 0 · Answer 2 · 2016-05-09

Since these are MSigDB gene set collections you could just use the .gmt files directly or one of a number of bioconductor packages that can process these for you. I use the piano package quite a lot which has a loadGSC function, so having downloaded, for example, the hallmarks .gmt file (h.all.v5.0.symbols.gmt) from http://software.broadinstitute.org/gsea/msigdb you can just do:

library(piano)
my_gsc <- loadGSC('h.all.v5.0.symbols.gmt')
my_gsc
my_gsc$gsc[1:5]
my_gsc$gsc[['HALLMARK_E2F_TARGETS']]