Question

Retrieving Gene Expression Profiles For A Set Of Genes From All Tissues?

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13.2 years ago

User 9996 ▴ 840

I am trying to get gene expression values for a set of genes (e.g. identified by Ensembl gene IDs or gene names) from a large set of mouse tissues/cell types. Is there a way to do this programmatically from Python, or alternatively, using a web interface where the input is a set of genes?

I simply want to get their expression by microarray (or even RNA-Seq) from a big enough collection of tissues in mouse -- it's not particularly important what the platform is. UCSC offers a table that comes close to this, but it does not give gene IDs associated with each gene in the microarray. Ensembl BioMart gives a list of experiment IDs but no expression values.

Any ideas on how to do this either from Python or using a web interface would be great. thanks.

microarray geo next-gen sequencing gene • 4.3k views

ADD COMMENT • link updated 9.3 years ago by nvijay.1991 • 0 • written 13.2 years ago by User 9996 ▴ 840

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Interesting, what is the name of this table in the UCSC db ?

ADD REPLY • link 13.2 years ago by Pierre Lindenbaum 161k

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I'd guess it's the Affy Exon Tissues table and/or one of the GNF tables: http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=187313313&clade=mammal&org=Mouse&db=mm9&hgta_group=regulation.

ADD REPLY • link updated 4.6 years ago by Ram 43k • written 13.2 years ago by Neilfws 49k

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Interesting, what is the name of table in the UCSC db ?

ADD REPLY • link 13.2 years ago by Pierre Lindenbaum 161k

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In similar way,how can i retrieve the information for differential expression analysis for protein accession id's generated through itraq ms/ms method.and how can we achieve the confidence of obtained id's/intensity values..?

ADD REPLY • link 9.3 years ago by nvijay.1991 • 0

score 4 · Answer 1 · 2011-02-25

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13.2 years ago

Neilfws 49k

BioGPS is probably the best web interface for this purpose and includes several mouse datasets.

ADD COMMENT • link 13.2 years ago by Neilfws 49k

Ram · Answer 2 · 2011-02-25

UCSC Gene Sorter could do this too.

Go to the website
Then choose mouse.
Then choose one of the expression sets (maybe try them all).
Go to the "filter" and you can enter a list of genes in.
Go back to the "configure" button and choose something besides "selected" tissues, which is a subset of the available tissues.
You get a graphical table, but you can output the list subsequently to text with values with the text button.

It's a limited set of experiments. But might do what you want. And with the IDs you could link back to the array IDs with the table browser.