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Question: Gene Ontology and Gene Set Enrichment
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gravatar for fromhj304
2.1 years ago by
fromhj30410
fromhj30410 wrote:

Hi all, I'm right now working with a RNA-seq raw count data file (in .txt format). It's a matrix of ~50,000 genes (row) and 8 samples (column).

My assignment is to get differential gene ontology and gene set enrichment. But I'm not really sure what it means by that. I'm trying to use R for this task, and when I googled for gene ontology analysis in R, there are several packages that are designed to get GO and GSE. But, if I'm starting with a raw count data file, which package do you recommend for this task?

Also, if one wants to see gene ontology, what exactly they mean by that (probably like an example of ideal results)?

I'm really new to bioinformatics and R, so please explain from the scratch.

Thanks a lot!!

 

ADD COMMENTlink modified 2.0 years ago by Guangchuang Yu1.0k • written 2.1 years ago by fromhj30410
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gravatar for Gordon Smyth
2.1 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

Here is a complete analysis workflow for an RNA-seq dataset:

https://f1000research.com/articles/5-1438

This example analysis includes both gene ontology and gene set enrichment analyses as well as two different types of MA plots.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Gordon Smyth35k
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gravatar for Luo Weijun
2.0 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
You may use the RNA-Seq Data Pathway and Gene-set Analysis Workflows with GAGE/Pathview: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf It is a full workflow from preparation, reads counting, data preprocessing, gene set test, to pathway visualization in about 40 lines of codes. The same workflow can be used for GO analysis or other types of gene set analysis too. We also describe joint workflows, i.e. to do gene-level analysis using one of the major RNA-Seq analysis tools.
ADD COMMENTlink written 2.0 years ago by Luo Weijun1.4k
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gravatar for Guangchuang Yu
2.0 years ago by
Guangchuang Yu1.0k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.0k wrote:

maybe you can follow this workflow: https://github.com/twbattaglia/RNAseq-workflow

ADD COMMENTlink written 2.0 years ago by Guangchuang Yu1.0k
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