Gene Ontology and Gene Set Enrichment
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fromhj304 ▴ 10
@fromhj304-11588
Last seen 6.0 years ago

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!!

 

rna-seq bioinformatics gene ontology gene set enrichment go • 1.5k views
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@gordon-smyth
Last seen 50 minutes ago
WEHI, Melbourne, Australia

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.

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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 24 days ago
United States
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.
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 23 days ago
China/Guangzhou/Southern Medical Univer…

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

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