Question: Compare sets of GO enrichments
0
gravatar for grant.hovhannisyan
2.8 years ago by
grant.hovhannisyan2.0k wrote:

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

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ADD COMMENTlink modified 2.7 years ago by Zhilong Jia1.6k • written 2.8 years ago by grant.hovhannisyan2.0k
3
gravatar for Gjain
2.7 years ago by
Gjain5.5k
Bengaluru, India
Gjain5.5k wrote:

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

enter image description here

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Gjain5.5k
3
gravatar for Zhilong Jia
2.7 years ago by
Zhilong Jia1.6k
London
Zhilong Jia1.6k wrote:

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. enter image description here

ADD COMMENTlink written 2.7 years ago by Zhilong Jia1.6k

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

ADD REPLYlink written 10 months ago by perlasalbert0

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

ADD REPLYlink written 9 months ago by brianj.park50

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!

ADD REPLYlink written 9 months ago by janetscully0

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) ...

ADD REPLYlink written 9 months ago by brianj.park50
2
gravatar for Jean-Karim Heriche
2.8 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche24k wrote:

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.

ADD COMMENTlink written 2.8 years ago by Jean-Karim Heriche24k

Thanks, I will try it out.

ADD REPLYlink written 2.8 years ago by grant.hovhannisyan2.0k
1
gravatar for cfuzo
2.7 years ago by
cfuzo10
cfuzo10 wrote:

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

ADD COMMENTlink written 2.7 years ago by cfuzo10

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.
ADD REPLYlink written 2.7 years ago by Zhilong Jia1.6k
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