Gene and gene function table

akitrav · 07-31-2014, 07:13 AM

Hi,

I am looking for a two column table that has genes and their functions by their side. Any suggestions how i can get that?

Thanks!

V

GenoMax · 07-31-2014, 07:30 AM

For which organism?

akitrav · 07-31-2014, 11:20 AM

Homo sapiens

GenoMax · 07-31-2014, 12:31 PM

Two options:

1. Get this file: http://geneontology.org/gene-associa...a_ref_human.gz You will need to parse out the columns you want from this file. Should be possible using unix commands (post if you need help) or use perl/python.

2. Visit: http://www.proteinatlas.org/ Hit "search" (leave field blank). This will list all proteins. Choose "show/hide columns" and then select "protein class" (that is the closest to the function category). You can download the results as a tabbed file.

Richard Finney · 07-31-2014, 01:22 PM

They still don't know what (most? , many?) Human genes do, so don't think any current list will be the real truth about the function of a gene.

Note that there will be a bias to the "what's been studied" in any "gene set to function" analysis. Lots of genes are associated with neuron development and cancer (because brain studies and cancer research get lots of attention). Such genes of course, may have other functions.

akitrav · 08-01-2014, 08:26 AM

Well I am looking for something like the Summary text (This gene encodes a blabla) from this NCBI record

http://www.ncbi.nlm.nih.gov/gene/673

Any suggestions on how I can create a database or find one?

V

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07-31-2014, 07:13 AM	#1
akitrav Junior Member Location: New york Join Date: Jul 2014 Posts: 5	Gene and gene function table Hi, I am looking for a two column table that has genes and their functions by their side. Any suggestions how i can get that? Thanks! V

07-31-2014, 01:22 PM	#5
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	They still don't know what (most? , many?) Human genes do, so don't think any current list will be the real truth about the function of a gene. Note that there will be a bias to the "what's been studied" in any "gene set to function" analysis. Lots of genes are associated with neuron development and cancer (because brain studies and cancer research get lots of attention). Such genes of course, may have other functions. Last edited by Richard Finney; 07-31-2014 at 01:25 PM.

07-31-2014, 07:30 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,088	For which organism?

07-31-2014, 11:20 AM	#3
akitrav Junior Member Location: New york Join Date: Jul 2014 Posts: 5	Homo sapiens

07-31-2014, 12:31 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,088	Two options: 1. Get this file: http://geneontology.org/gene-associa...a_ref_human.gz You will need to parse out the columns you want from this file. Should be possible using unix commands (post if you need help) or use perl/python. 2. Visit: http://www.proteinatlas.org/ Hit "search" (leave field blank). This will list all proteins. Choose "show/hide columns" and then select "protein class" (that is the closest to the function category). You can download the results as a tabbed file.

08-01-2014, 08:26 AM	#6
akitrav Junior Member Location: New york Join Date: Jul 2014 Posts: 5	Well I am looking for something like the Summary text (This gene encodes a blabla) from this NCBI record http://www.ncbi.nlm.nih.gov/gene/673 Any suggestions on how I can create a database or find one? V