Question: Finding genes expressed specific to tissues
0
gravatar for vishweshwaransridhar
3.9 years ago by
Singapore
vishweshwaransridhar10 wrote:

Hi All,

        I have weird requirement. Say suppose if I want to find the all the details of a gene in Arabidopsis I can just query with the gene name get the details of it, like tissue in which it is expressed etc. But now I want to find the genes that are expressed in a particular tissue during a particular condition. Like genes expressed in root during stress.

Is there any way I can find this.

Regards

Vishwesh

gene • 1.3k views
ADD COMMENTlink modified 3.9 years ago by Alex Reynolds28k • written 3.9 years ago by vishweshwaransridhar10
0
gravatar for cyril-cros
3.9 years ago by
cyril-cros890
France
cyril-cros890 wrote:

There are atlases for that, giving the transcriptome of a specific tissue (using RNASeq data). Like in this article: https://www.sciencemag.org/content/302/5652/1956.full.pdf

In your case, you want to find a RNASeq experiment looking for differential gene expression: this is bibliography work, I am not sure there is a real database for what you want.. Just googling 'arabidopsis stress differentially expressed' yields some results.

You can even find cell type specific genes if you label the cells you are interested in with GFP and do some FACS sorting.

ADD COMMENTlink written 3.9 years ago by cyril-cros890
0
gravatar for Alex Reynolds
3.9 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

As part of this paper: http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html I wrote a tool to explore RNA expression data from different tissue types here: https://expressionatlas.org/hg19

The paper may offer some ideas on how to analyze data, while the second site may offer some thoughts on how to visualize it.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Alex Reynolds28k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1659 users visited in the last hour