Expression Databases For Human Genes
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13.6 years ago
Biomed 5.0k

I would like to see in which human tissues a gene (list of genes) are expressed. What would be the best+most complete resource/web site/database for this purpose?

gene • 15k views
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13.6 years ago
Neilfws 49k

BioGPS is very good for this. Enter a gene symbol, click search. The first item displayed is a plot of expression in different tissues.

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I'll also add that in addition to providing the Gene Atlas expression data that Neil describes above, BioGPS is meant to serve as a marketplace for gene-centric data via the "plugin library". So after you search for your gene of interest, look for the "Add a plugin" box in the upper right and type "expression". You'll find pretty much all the resources listed below plus a few more...

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13.6 years ago

For a complementary view from the protein side of things, see proteinatlas.org. This is a beautiful site that organizes information about where proteins are expressed, as quantified by antibody staining. For an example, see their entry on Hras. You can drill down to see the actual stains for any given sample, e.g. this stain of Hras in the colon

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13.6 years ago

For a list of databases and a nice interface to them, have a look at the UCSC Gene Sorter

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13.6 years ago

In addition to the resources suggested here, you may also take a look at "Expression" tab in HPRD / Human Proteinpedia. The reason to check in HPRD is the data is manually curated from literature and you can get a reference.

For example: see SOD1 at HPRD / Proteinpedia

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13.5 years ago

You can have a look at the Gene Expression Atlas hosted b EMBL-EBI. [?]You can enter you gene(s) of interest, the organism and the conditions of the experiments.[?] You should be able to customize the results if you try to use the Gene Expression Atlas REST APIs. It can return you a result either in XML or JSON format.

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13.5 years ago
Puthier ▴ 250

I would also recommend:

GeneSapiens.org (human)

ImmGen (human and mouse)

BloodExpress (mouse)

Finally, you can also use GEO Profiles using operators in the search field (with the preview/Index tab):

(BCL2[Gene Symbol]) AND (30[Min Value Rank]) ...

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13.5 years ago

I'll provide an answer that I have given in the past - BLAST search against an EST database. There are more tissues that served as sources for the cDNA libraries than you'll find in many if not all of the databases listed above. (These are excellent choices for one approach - I'm offering another). Look to see from which tissue the library was made, from which the clones were sequenced to give the BLAST hit(s) you observe.

At the same time, you may want to consider RNAseq data. There is not so much readily available compared to other data types and databases, but you should think about ways to identify expression of a given gene by looking at this ever increasing data type.

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