Question: Expression Databases For Human Genes
11
gravatar for Biomed
8.7 years ago by
Biomed4.5k
Bethesda, MD, USA
Biomed4.5k wrote:

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 • 13k views
ADD COMMENTlink modified 6.2 years ago by Ali R. Vahdati190 • written 8.7 years ago by Biomed4.5k
14
gravatar for Neilfws
8.7 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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

ADD COMMENTlink written 8.7 years ago by Neilfws48k
1

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...

ADD REPLYlink written 8.7 years ago by Andrew Su4.8k
7
gravatar for David Quigley
8.7 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

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

ADD COMMENTlink modified 8.7 years ago by iw9oel_ad6.0k • written 8.7 years ago by David Quigley11k
5
gravatar for Giovanni M Dall'Olio
8.7 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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

ADD COMMENTlink written 8.7 years ago by Giovanni M Dall'Olio26k
5
gravatar for Khader Shameer
8.7 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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

ADD COMMENTlink written 8.7 years ago by Khader Shameer18k
3
gravatar for Fred Fleche
8.7 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

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.

ADD COMMENTlink written 8.7 years ago by Fred Fleche4.3k
2
gravatar for Puthier
8.7 years ago by
Puthier250
Puthier250 wrote:

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]) ...

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Puthier250
2
gravatar for Larry_Parnell
8.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 8.7 years ago by Larry_Parnell16k
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