Question: Tools To Find Gene Ontology Term Enrichment
27
gravatar for Biostar User
9.7 years ago by
Biostar User1.0k
Biostar User1.0k wrote:

I need to make a recommendation to people working in a wet-lab looking for an easy to use tool that does GO term enrichment determination. For those unfamiliar with the concept it means that given a list of gene names they want to find out which gene ontology terms are present in numbers that are above random chance.

There is a huge list here yet a random sampling of the tools mentioned there has lead me to many non-working sites. Other tools seem out of date or just not reliable.

What tool do you use to solve this problem?

Thanks.

gene enrichment tool • 54k views
ADD COMMENTlink modified 3.0 years ago by jin80 • written 9.7 years ago by Biostar User1.0k
4

This 2016 pre-print paper assess the impact of using obsolete Gene Enrichment tools (e.g. DAVID not being updated for years) in the current literature: http://biorxiv.org/content/early/2016/04/19/049288

ADD REPLYlink written 3.5 years ago by Giovanni M Dall'Olio26k
1

The list was updated again to this link

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by Assa Yeroslaviz1.2k

Your link to the list of geneOntology-related tools is perhaps not the best given your problem, perhaps this one is more related: http://www.geneontology.org/GO.tools.shtml#statistical

ADD REPLYlink modified 6 weeks ago by RamRS24k • written 8.0 years ago by fransua390
13
gravatar for Dave Bridges
9.7 years ago by
Dave Bridges1.3k
Ann Arbor, MI
Dave Bridges1.3k wrote:

I prefer to use DAVID ( http://david.abcc.ncifcrf.gov/ ) but id be interested to hear what other people like. There are also R packages available through Bioconductor (GOstats; http://www.bioconductor.org/packages/2.3/bioc/html/GOstats.html) that can do enrichment determination, but I am less familiar with those, and you need a good working knowlege of R to use these.

ADD COMMENTlink written 9.7 years ago by Dave Bridges1.3k
8

The annotations underlying DAVID have not been updated in six years and DAVID should no longer be used. The paper "Impact of knowledge accumulation on pathway enrichment analysis" explores some of the problems in depth. I know of publications that were rejected in part because they used DAVID.

ADD REPLYlink written 3.5 years ago by Michael Hoffman330
1

I also like DAVID.

If you're ruby users, I wrote a very basic library that allows you to query DAVID from your scripts: http://github.com/chrisamiller/davidapi

ADD REPLYlink written 9.7 years ago by Chris Miller21k
1

There is also a Bioconductor package DAVIDQuery (http://bioconductor.org/packages/release/bioc/html/DAVIDQuery.html) for accessing DAVID programmatically.

ADD REPLYlink written 9.5 years ago by Paolo230

DAVID is the one I always recommend to our wet lab biologists too. It's now been maintained well for several years, unlike many bioinformatics resources..

ADD REPLYlink written 9.7 years ago by Daniel Swan13k

A: Inconsistent numbers when using Kegg pathway analysis via DAVID?

A: Pathway Grouping with Genes

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by EagleEye6.5k
9
gravatar for Simon Cockell
9.7 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

The BiNGO plugin for Cytoscape will allow you to determine term enrichment in a Cytoscape network. It's quite a neat tool.

ADD COMMENTlink written 9.7 years ago by Simon Cockell7.3k

Tried BiNGO to calculate enrichment of a set of nodes. Excellent tool. Thanks for the suggestion

ADD REPLYlink written 9.3 years ago by Khader Shameer18k

I found BiNGO extremly handy while I was dealing with annotations of non-model organism. For future use I have documented it here, http://infoplatter.blogspot.in/2014/04/gene-ontology-go-enrichment-analysis-in.html It also allows us to save the text output, including stats, which particluary helped me in making custom barplots and pie charts of GO terms. Nice tool !!

ADD REPLYlink written 5.6 years ago by amolkolte198980
6
gravatar for brentp
9.7 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

it's very much in progress, but a colleague and I (mostly him) have been working on this for python: http://github.com/tanghaibao/goatools/

it has a command-line script to find terms that are enriched in a study group. it reports p-value for various multiple testing corrections as well as the false discovery rate.

It can also be used to plot the DAG of a particular GO term.

ADD COMMENTlink written 9.7 years ago by brentp23k
5
gravatar for Khader Shameer
9.6 years ago by
Manhattan, NY
Khader Shameer18k wrote:

I think most of the enrichment analysis tools deals with same class of statistics methods (p-value, FDR, Boneferroni etc). Defining background is a very important in such enrichment methods. To get real meaning of enrichment with respect to your experiments, you should be able to upload the background. For example, if you are looking at a set of a genes from a particular tissue, a background of that tissue give more meaningful results than a background of whole genome.

ADD COMMENTlink written 9.6 years ago by Khader Shameer18k
1

hi Khader Shameer,

yeah i read a paper in which they did the Gene Ontology Term Enrichment analysis exactly like u said here. and i wanna analyse my data in that way ( significantly differentially regulated transcripts Enrichment analysis against unchanged background transcripts ). my data is RNQ-seq, so how could i make regulation level unchanged transcripts set as a background analyse Ontology Term Enrichment? what kind of approach or tool should i use there? would u give me some suggestions?

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Kurban170
3
gravatar for Giovanni M Dall'Olio
9.7 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

You can try one of the tools at babelomics, in particular FatiGO; or as an alternative, you can use the same AmiGO Term Enrichment tool.

However, be careful when using GeneOntology: it is a very active and supported project, so they make big enhancements between two releases. If you look at thei bug tracker, there are at least 8-10 changes to geneontology terms every day. So, annotate the version and date of GeneOntology if you want your experiment to be reproducible.

ADD COMMENTlink written 9.7 years ago by Giovanni M Dall'Olio26k
3
gravatar for Allpowerde
9.7 years ago by
Allpowerde1.2k
Allpowerde1.2k wrote:

Another option is GONOME (http://gonome.imb.uq.edu.au/), which finds the over- and under-represented GO terms for a given set of genomic positions.

ADD COMMENTlink written 9.7 years ago by Allpowerde1.2k
3
gravatar for Madelaine Gogol
9.6 years ago by
Madelaine Gogol5.1k
Kansas City
Madelaine Gogol5.1k wrote:

GOrilla makes nice pictures.

ADD COMMENTlink written 9.6 years ago by Madelaine Gogol5.1k
3
gravatar for Stew
9.6 years ago by
Stew1.4k
Cambridge
Stew1.4k wrote:

David is a great place to start. I also like GeneTrail, which can do GSEA analysis as well as standard enrichment on a gene list. Out of the web world I really like ClueGO and to a lesser degree BInGO in Cytoscape.

In case they were ever useful I put up some slides from a short course I give on functional analysis using web tools and Cytoscape.

ADD COMMENTlink written 9.6 years ago by Stew1.4k
3
gravatar for Dejian
8.9 years ago by
Dejian1.3k
United States
Dejian1.3k wrote:

WEGO is a convenient tool to plot the enriched GO items. http://wego.genomics.org.cn/cgi-bin/wego/index.pl

ADD COMMENTlink written 8.9 years ago by Dejian1.3k
3
gravatar for boczniak767
8.0 years ago by
boczniak767680
Poland
boczniak767680 wrote:

WebStart version of Ontologizer will be perfect. If you provide association and OBO files to your wet-lab colleagues they easily could use this program.

ADD COMMENTlink written 8.0 years ago by boczniak767680
2

+1 for ontologizer. It's easy to download and use as part of a pipeline since it's just a java program.

ADD REPLYlink written 8.0 years ago by Damian Kao15k
2
gravatar for Ian Simpson
9.6 years ago by
Ian Simpson930
Edinburgh
Ian Simpson930 wrote:

Like several of the others I also recommend DAVID to wet lab biologists. It is well maintained, but you should check the version on the particular species annotation(s) they are currently using as it it sometimes not the latest.

They use a variant of the Fisher exact statistic for their p-value calculations called the EASE score which they wrote up in a paper a few years back http://www.ncbi.nlm.nih.gov/pubmed/14519205 which is more conservative that the standard.

ADD COMMENTlink written 9.6 years ago by Ian Simpson930

Just to echo other comments (note my original response was 6 years ago !). Don't use DAVID. We don't.

ADD REPLYlink written 3.5 years ago by Ian Simpson930
2
gravatar for fransua
8.0 years ago by
fransua390
Spain
fransua390 wrote:

another one here:

http://www.blast2go.com/b2ghome

userfriendly and complete, with many tools regarding to visualization import/export and statistical tests. free version is sufficient for almost every work

ADD COMMENTlink written 8.0 years ago by fransua390
2
gravatar for Surya Saha
3.5 years ago by
Surya Saha260
NY
Surya Saha260 wrote:

Just wanted to add a note that DAVID has not been updated since 2010 so should not be used. See preprint for more detailed discussion.

ADD COMMENTlink written 3.5 years ago by Surya Saha260
0
gravatar for jin
3.0 years ago by
jin80
jin80 wrote:

For plants, you can try PlantRegMap, which integrated GO annotation for 132 plant species and perform enrichment analysis.

ADD COMMENTlink written 3.0 years ago by jin80
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