Question

Pathview & topGO

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cabezasdelafuented ▴ 10

@cabezasdelafuented-11338

Last seen 6.8 years ago

Hello,

I'm using my results of a Differential Gene Expression from RNAseq data using DESeq2 as input data for both Pathview and topGO. I manage to get similar results for both but I am interested to know if i can use the results from one package as the input to the other (e.g. use the GO obtained from topGO to construct a KEGG pathway with pathview).

This question comes for the fact that topGO is used for microarray data and when i want to obtain the list of genes that are significant in one of the GO terms I can't do it using the printGenes function, as I'm not using a chip library (I use a custom annotation that are my Ensembl gene IDs). I am also interested in the showGroupDensity function of topGO.

So, is there any way to perform a topGO analysis and then construct the pathway with pathwview using the data from topGO?

Many thanks,

Dan

R GO topGO pathview • 1.8k views

ADD COMMENT • link updated 7.7 years ago by Luo Weijun ★ 1.6k • written 7.7 years ago by cabezasdelafuented ▴ 10

score 0 · Answer 1 · 2016-08-25

I assume you are talking about gage/pathview workflow, where gage does the pathway-level analysis, and pathview do the visualization. Gage does work on KEGG pathways, GO and other types of gene set data, it also provides visualization options like heatmap, scatter plot etc. Pathview does not construct any pathway, but rather it maps, integrate sand visualizes your data onto existing KEGG pathways. For more info, please check the documentation of pathview: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf http://bioconductor.org/packages/release/bioc/html/gage.html http://bioconductor.org/packages/release/bioc/html/pathview.html