Question: Tools For Visualizing Overlap Between Go Terms
17
gravatar for Michael Kuhn
8.9 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

Some sibling GO categories are highly correlated. Is there any tool / webserver that would take a list of GO terms and show me a matrix of the fraction of shared genes in a particular species? Or at least a Venn diagramm for two or three GO terms?

For example, almost 1000 human genes are annotated as "cell cycle", but the sum of the node counts is much higher. I'd like to see which categories are overlapping with each other.

gene visualization • 15k views
ADD COMMENTlink modified 8.9 years ago by Obi Griffith17k • written 8.9 years ago by Michael Kuhn5.0k
9
gravatar for Leszek
8.2 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

Hi there,

Recently I have tried REViGO and I strongly recommend it. What it does is simply collapsing GO with semantic similarity. It visualise it together with nice colouring according to p-valuse (or other metric) assigned to each GO.

Some more info:

REViGO is a web server that can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds.

ADD COMMENTlink modified 7 months ago by RamRS21k • written 8.2 years ago by Leszek4.0k

I just checked REViGO (I didn't know it existed) and I have to say it looks very promising. I should definitely take a deeper look at it when I have some time

ADD REPLYlink written 8.2 years ago by Pablo Pareja1.6k

Definitely have to go through REViGO sounds promising

ADD REPLYlink written 8.2 years ago by Thaman3.2k

I tried REViGO with about 4k GO IDs, and made it collapsed with Http error 500 ……

ADD REPLYlink written 7.1 years ago by Casual90

I think, the max limit is 500.

ADD REPLYlink written 6.5 years ago by Sukhdeep Singh9.7k

the limit is 350 terms

ADD REPLYlink written 23 months ago by Gema Sanz70
8
gravatar for Mary
8.4 years ago by
Mary11k
Boston MA area
Mary11k wrote:

@Charles B. --thanks for BioVenn. @niallhaslam --thanks for the other one. I have added them to a list of Venn tools I've started here:

I ♥ Venns

There are a couple of other Venn tools over there. People here might like the Cytoscape one http://www.dishevelled.org/venn-cytoscape-plugin I haven't tried it for GO terms, but in the Cytoscape framework I would imagine it is possible.

ADD COMMENTlink written 8.4 years ago by Mary11k
7
gravatar for Khader Shameer
8.9 years ago by
Manhattan, NY
Khader Shameer18k wrote:

You could try semantic similarity calculation in Ontologizer using 'Similarity' option . For a set of genes, Ontologizer generates NxN matrix with all genes in your list and can be visualized as a matrix with semantic similarity score of the two genes based on GO terms.

ADD COMMENTlink written 8.9 years ago by Khader Shameer18k
5
gravatar for Niallhaslam
8.4 years ago by
Niallhaslam2.2k
Dublin
Niallhaslam2.2k wrote:

Hi Michael,

I've used this before for the visualisation of multiple lists of terms/ids. http://www.pangloss.com/seidel/Protocols/venn.cgi

However, if you want to go above 3 terms then you will need something more complicated. I'm currently working on something that will allow the visualisation of the overlap (with the correct spacial ratios) of 4 or more terms. If you are interested in this shoot me a mail. I'm defo interested in getting some example datasets that people need to analyse. I can send you on a poster with an example if you want.

ADD COMMENTlink written 8.4 years ago by Niallhaslam2.2k

This tool is not working well when using GO terms.

ADD REPLYlink written 5.5 years ago by biotech520
5
gravatar for Doron
8.2 years ago by
Doron50
Doron50 wrote:

GOrilla is a GO-enrichment analysis tool we developed exactly to answer this kind of question. Following calculation of enrichment of GO terms, it will display the results mapped to on the GO hierarchy tree, so you can clearly see all the overlaps and relationships.

ADD COMMENTlink modified 7 months ago by RamRS21k • written 8.2 years ago by Doron50
4
gravatar for Charles B.
8.4 years ago by
Charles B.160
Rennes
Charles B.160 wrote:

You can obtain a list of genes annotated by a GO terms for a selected species from [?]AMIGO[?]. It finds all genes annotated directly or implicitly (following the true path rule). If it yields more genes than it can display, you can obtain genes list in RDF-XML or tab-delimited gene association format.

When you have your lists, you can use a tool to generate a Venn diagram, like niallhaslam said. I prefer to use Biovenn which displays circles of proportional size to the sets which they represent. You can generate the figure at SVG format, which support characters drag & drop.

ADD COMMENTlink modified 7 months ago by RamRS21k • written 8.4 years ago by Charles B.160
4
gravatar for Obi Griffith
7.2 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

@niallhaslam -- Have you checked out VennMaster? This is the best tool I've found for visualizing overlap between 4 or more term lists. It is simple and works well but has a very limited set of options for customizing and often requires edits in external image editing software to produce a final publication ready imate. I would definitely be interested to see what you come up with as this is a problem not well solved so far (IMO). Venny is really good for 4 term lists (or less) but doesn't meet your criteria for "correct spacial ratios". This topic has been covered pretty well in another post.

ADD COMMENTlink written 7.2 years ago by Obi Griffith17k
3
gravatar for Iain
7.8 years ago by
Iain260
Iain260 wrote:

I would recommend using the Enrichment map plugin for Cytoscape.

It can be downloaded from http://baderlab.org/Software/EnrichmentMap

Some example use cases are shown here: http://baderlab.org/Software/EnrichmentMap/Description

The plug-in generates a network view of a functional enrichment analysis, where nodes represent enriched terms and the edges between the nodes represent how similar the terms are (based on how many genes are in common between them). Interestingly, it is also possible to generate a network view comparing the results of two different enrichment analysis.

ADD COMMENTlink written 7.8 years ago by Iain260
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