[BioC] Packages for GO and KEGG analysis on RNAseq data

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Fri Sep 12 20:05:40 CEST 2014

Dear Nicolas,

You are welcome to try getEnrichedGo and getEnrichedPath in ChIPpeakAnno

Best regards,


On 9/12/14 1:54 PM, "Merienne Nicolas" <Nicolas.Merienne at chuv.ch> wrote:

> Dear all,
> We are two biologists (so very new in bioinformatic field...) working with
> RNAseq data and having little "troubles" with pathways analysis. We performed
> mRNA sequencing on 4 distinct cell populations to compare their
> transcriptional profile (platform Illumina HiSeq 2000). Row reads were mapped
> using TopHat and differential analysis was performed with edgeR+voom+limma
> packages. Our final output is a table (.txt file) for each contrast containing
> our 16058 expressed genes with respective log fold change, expression values
> (normalized) and adjusted p-values. We wish to perform pathway enrichment
> analysis (first GO for a global level and KEGG for a more precise analysis) to
> determine which pathways are enriched/depleted in specific cell population
> compared to the others in order to infer cell-type specific functional
> signatures. However, we have difficulties to find an optimal method to do
> this. We tried several packages (e.g gage, goseq) and web-based softwares (e.g
> GeneGO, AmiGO) and found different outputs (sometimes opposite results). What
> could be the more "validated" method/package for these analysis? In addition,
> we found differences considering the input data (raw reads, log FC, a list of
> differentially expressed genes�) and finally we don't understand what should
> be the input data for the analysis (we think that it is dependent of the
> package/method used�). So, does anyone of you experiences with GO/KEGG for
> RNAseq and maybe help us to use a good quantification method please?
> Thank you very much for your help.
> Best,
> Nicolas
> [[alternative HTML version deleted]]
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