Question: A database to find out which genes are expressed in which cell type of origin for human?
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gravatar for sara_wasl
10 weeks ago by
sara_wasl0
sara_wasl0 wrote:

I would like to find the different cell types that specific gene expressed on for human, is there any database provide that?

I tried Gene Expression Atlas (https://www.ebi.ac.uk/gxa/home) but I'm not sure if it's correct because I think they do some experiments and report what cells they found that specific gene is expressed on and also some genes I didn't find any such information for them.

Any help with that?

gene expression database gene • 202 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by sara_wasl0
1

In humans this may be useful: https://www.proteinatlas.org/humanproteome/cell
If cancer lines: http://amp.pharm.mssm.edu/Harmonizome/dataset/CCLE+Cell+Line+Gene+Expression+Profiles

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by genomax71k

I checked the first one, it doesn't specify the cell type of origin (which cell types they originate/first developed); they present the general cell location.

ADD REPLYlink written 10 weeks ago by sara_wasl0

And, for Mus musculus, there is the Mouse Cell Atlas

ADD REPLYlink written 10 weeks ago by Kevin Blighe48k

Thanks for that but I'm interested more on human cell

ADD REPLYlink written 10 weeks ago by sara_wasl0

Human Cell Atlas is underway, but not complete. Otherwise, I note that different groups are using custom curated lists in order to do what you want.

ADD REPLYlink written 10 weeks ago by Kevin Blighe48k

I have a look to there data here (https://prod.data.humancellatlas.org/explore/projects) because the one you shared as they stated will be discontinuing; and as you can see there is no specific data or I cannot search by gene and most of it raw data (fastq files).

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by sara_wasl0
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gravatar for Jean-Karim Heriche
10 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

The Gene Expression Atlas does have expression data by at least tissue type. It also includes the tissue data from the Human Protein Atlas. It's not that intuitive to navigate but if on the home page you select for example human as species and pancreas as biological condition, the search result is a list of experiments several of which have looked at multiple human tissues like those of the GTEx project. Clicking on one will show you a table of genes x tissues with the corresponding expression levels. For example selecting the GTEx data set, you can see that INS (insulin) is only expressed in the pancreas. If you want data by precisely defined cell types, you can have a look at the HPA tissue atlas, they have immunostaining data for cell types within tissues, e.g. check the left hand side of this page for pancreatic cell types.

ADD COMMENTlink written 10 weeks ago by Jean-Karim Heriche20k

Thanks a lot, that's kind of explained to me how things going on.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by sara_wasl0
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