GO dataset for s. pombe

Parharn · 09-16-2014, 03:57 AM

Hi,
I am willing to do GO analysis on my RNA-seq data from S. pombe organism. As far as I understood "gageData" package doesn't hold the data set for S. pombe. So I could find the data set on www.pombase.org, this link. But I don't know how to load this data set into my analysis. I am following this workflow, section 4. Please help me with loading the GO dataset into above mentioned workflow.

Thanks a lot!

GenoMax · 09-16-2014, 02:17 PM

You had asked a similar question back in June (http://seqanswers.com/forums/showthread.php?t=44116). Did the suggestions given there not work?

Parharn · 09-17-2014, 01:38 AM

No this one is different! The answer to the transcriptDB post helped a lot. This one is GO annotations! Aren't them different?
I have another post with more detailed information here (https://www.biostars.org/p/112790/) if that can help to elucidate my question.

bigmw · 09-17-2014, 09:43 AM

What you want to do is to read in and process the annotation data into a list. Each element of this list is a gene set. You can download and unzip the data from the link you provide under linux shell:

Code:

curl -O ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.pombase.gz
gunzip gene_association.pombase.gz

Then read and process the data in R like:
pombgo=read.delim("gene_association.pombase", sep="\t", head=F, skip=44)
go=split(as.character(pombgo[,2]), pombgo[,5])
here "go" is a gene set list you can use in your gage analysis.

Parharn · 09-18-2014, 08:23 AM

Thanks a lot!

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09-16-2014, 03:57 AM	#1
Parharn Member Location: Sweden Join Date: Jul 2013 Posts: 84	GO dataset for s. pombe Hi, I am willing to do GO analysis on my RNA-seq data from S. pombe organism. As far as I understood "gageData" package doesn't hold the data set for S. pombe. So I could find the data set on www.pombase.org, this link. But I don't know how to load this data set into my analysis. I am following this workflow, section 4. Please help me with loading the GO dataset into above mentioned workflow. Thanks a lot! Last edited by Parharn; 09-16-2014 at 06:49 AM.

09-17-2014, 01:38 AM	#3
Parharn Member Location: Sweden Join Date: Jul 2013 Posts: 84	No this one is different! The answer to the transcriptDB post helped a lot. This one is GO annotations! Aren't them different? I have another post with more detailed information here (https://www.biostars.org/p/112790/) if that can help to elucidate my question. Last edited by Parharn; 09-17-2014 at 01:49 AM.

09-17-2014, 09:43 AM	#4
bigmw Senior Member Location: US Join Date: Aug 2013 Posts: 123	What you want to do is to read in and process the annotation data into a list. Each element of this list is a gene set. You can download and unzip the data from the link you provide under linux shell: Code: curl -O ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.pombase.gz gunzip gene_association.pombase.gz Then read and process the data in R like: pombgo=read.delim("gene_association.pombase", sep="\t", head=F, skip=44) go=split(as.character(pombgo[,2]), pombgo[,5]) here "go" is a gene set list you can use in your gage analysis.

09-16-2014, 02:17 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	You had asked a similar question back in June (http://seqanswers.com/forums/showthread.php?t=44116). Did the suggestions given there not work?

09-18-2014, 08:23 AM	#5
Parharn Member Location: Sweden Join Date: Jul 2013 Posts: 84	Thanks a lot!