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.
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User 9996
2 answers
BioGPS is probably the best web interface for this purpose and includes several mouse datasets.
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.
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Interesting, what is the name of table in the UCSC db ?
Interesting, what is the name of this table in the UCSC db ?
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.
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..?