Question: How Can I Compare Enriched/Depleted Go Terms Between Genelists?
9
gravatar for Aaron Statham
6.9 years ago by
Aaron Statham1.1k
Australia
Aaron Statham1.1k wrote:

So I'm analysing human ChIP-seq data, and have made genelists of genes with enrichment at their promoters in two samples - each sample has about 3000 genes enriched, with ~1500 in common. I wanted to do some gene ontology analysis to see what kinds of enriched genes I am getting, and as a GO newbie I used DAVID which is a bit clunky but OK.

So now I have a heap of tables downloaded from DAVID of the enriched GO terms (for BP & MF 1,2,3 and FAT) in each cell line - is there a framework available for comparing the two samples enrichments robustly? I'd like to explore which GO terms overlap and which differ.

Additionally, I have a second ChIP-seq set of data for these two samples, so in the future I want to split each genelist into whether this second factor is present as well, and see if that stratifies out any particular biological groupings of genes.

Any help/pointers appreciated! I've only sunk a bit of time into DAVID so I'm more than happy to try something else (if it takes refseq mrna IDs) - I'm quite intimate with the NGS side of R/Bioconductor but haven't looked at any of its GO packages.

Thanks!

gene R bioconductor annotation • 8.1k views
ADD COMMENTlink modified 6.9 years ago by Chris Evelo9.9k • written 6.9 years ago by Aaron Statham1.1k
4
gravatar for Giovanni M Dall'Olio
6.9 years ago by
London, UK
Giovanni M Dall'Olio25k wrote:

You can use babelomics, in particular their FatiGO tool

edit: have also a look at the list of third party Tools on the GeneOntology website.

ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by Giovanni M Dall'Olio25k
4
gravatar for Ian
6.9 years ago by
Ian5.0k
University of Manchester, UK
Ian5.0k wrote:

I am very 'fond' of GREAT http://great.stanford.edu/ at the moment, but have historically mostly used DAVID. GREAT's principle advantage is that it associates genes (using one of three different models) to your binding region coordinates. There is also a new function that allows you to download all information at the same time, rather than the laborious saving of each table individually.

I can see nothing wrong on performing gene ontology analysis on the gene lists you describe.

ADD COMMENTlink written 6.9 years ago by Ian5.0k
2
gravatar for Khader Shameer
6.9 years ago by
Manhattan, NY
Khader Shameer17k wrote:

FatiGo suggested by Giovanni will be a quick solution, in addition:

You may perform the GO enrichment analysis of the two sets separately and then compare the GO terms of the two sets either using visualization tools (for example REViGO) or based on comparison based on semantic similarity Ontologizer. You may use one of the standard GO annotation based enrichment calculation library for the comparison of enriched terms (topGO, GOStats).

Make sure that the tool/server that you use will help to define your own background data or already provide the platform that you are using for your analysis.

The following questions will be useful references: http://biostar.stackexchange.com/questions/1278/tools-for-visualizing-overlap-between-go-terms. http://biostar.stackexchange.com/questions/245/tools-to-find-gene-ontology-term-enrichment

ADD COMMENTlink written 6.9 years ago by Khader Shameer17k
2
gravatar for Chris Evelo
6.7 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

You could try Go_Elite, it has the advantage that it can do pruning of the GO tree. Meaning it can first calculate the significance of the higher, more detailed classes and then, in case these are found to be significant, it ca remove these from the remainder of the lower, larger level class it occurs in. This prevents that you will find classes like "metabolism" to be different without knowing what really occurs.

Edit: the GO-Elite paper has now been published. It is at: http://dx.doi.org/10.1093/bioinformatics/bts366

ADD COMMENTlink modified 5.4 years ago by Giovanni M Dall'Olio25k • written 6.7 years ago by Chris Evelo9.9k

Couldn't edit my own (old) post. Wanted to add that a GO-Elite paper has now been published. It is at: http://dx.doi.org/10.1093/bioinformatics/bts366

ADD REPLYlink written 5.4 years ago by Chris Evelo9.9k

Hi Chris, it seems that you were logged with another account (chirs.evelo lower case, instead of Chris Evelo).

ADD REPLYlink written 5.4 years ago by Giovanni M Dall'Olio25k

You might be using a different address in your 'chris.evelo' account. You could merge 'chris.evelo' into 'Chris Evelo' here.

ADD REPLYlink written 5.4 years ago by Leonor Palmeira3.6k

Thanks! I have requested that now.

ADD REPLYlink written 5.4 years ago by Chris Evelo9.9k
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