Compare sets of GO enrichments

Question

[grant.hovhannisyan]

Hi Biostars,

Imagine I have done two different experiments and obtained a list of differentially expressed genes from both of them. Then for each list of genes I can do GO enrichment analysis. Is there a software to compare the two (or more) sets of GO terms to find overlaps and differences?

Thanks

Answer 1

[Gjain]

You may want to look at the R package RRHO

• The RRHO algorithm allows for the comparison of two gene expression signatures
• Each signature is processed as a ranked list based on expression differences between two classes of samples
• The signatures can be input either as raw expression data and sample and class labels, or as a preranked gene list

Link: http://systems.crump.ucla.edu/rankrank/rankranksimple.php

Manuscript: http://nar.oxfordjournals.org/content/38/17/e169

Answer 2

[Zhilong Jia]

Visualization of profile comparison section from Bioconductor package clusterProfiler. See Figure below. x-axis, X2 and X3 (or more) can be your two (or more) sets of DEGs, y-axis can be GO.

[perlasalbert]

Do you have any example of the input needed for this kind of analysis??

[brianj.park]

You need a data frame in which the columns correspond to a list of gene identifiers. Check the vignette for clusterProfiler, specifically chapter 11.

https://yulab-smu.github.io/clusterProfiler-book/chapter11.html

[janetscully]

Hi! In this latter graph, the y-axis represents a kind of "summarized" list of molecular functions. Do you know where can I find the main list? or if there is an "official" one? I found something called FunCat (Functional classification Catalog of proteins) but it seems in disuse (https://omictools.com/funcat-tool). I don't have Blast2Go access so I can make use of some level of GO-terms annotation. When using GOslim annotation, molecular functions still seem very broad (i.e. I want a wider classification). I have a list of proteins gathered from many many papers I'm studying, so I would like to have the "big picture". Could you help me with this, please?? Thank you so much!

[brianj.park]

Do you mean you want a database of gene sets? Above graph is using Gene Ontology (GO) database to associate related genes by their function (i.e., BP, MF, CC). http://geneontology.org/

You may also use KEGG which is divided into 7 broad categories of biochemical processes: https://www.genome.jp/kegg/

Other databases for function analysis include Reactome (https://reactome.org/), MSigDB (https://www.gsea-msigdb.org/gsea/msigdb) ...

Answer 3

[Jean-Karim Heriche]

For 2 or 3 lists, you can use Venn Diagrams. Alternatively, you may want to try the R package UpSetR. Links to tutorials are also available on the GitHub page.

[grant.hovhannisyan]

Thanks, I will try it out.

Answer 4

[cfuzo]

Dear, You can use Toppcluster for comparison between two or more set of genes. It is available at https://toppcluster.cchmc.org/. Regards,

[Zhilong Jia]

Interesting. but not runnable now. Running with sample data resulted in the error as below.

HTTP Status 500 - Internal Server Error
type Exception report

messageInternal Server Error

descriptionThe server encountered an internal error that prevented it from fulfilling this request.

exception

org.apache.jasper.JasperException: java.lang.NullPointerException
root cause

java.lang.NullPointerException
note The full stack traces of the exception and its root causes are available in the GlassFish Server Open Source Edition 4.1 logs.