Finding genes expressed specific to tissues

Question

[vishweshwaransridhar]

Hi all,

I have a 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

Answer 1

[cyril-cros]

There are atlases for that, giving the transcriptome of a specific tissue (using RNASeq data). Like in this article

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.

Answer 2

[Alex Reynolds]

As part of this paper I wrote a tool to explore RNA expression data from different tissue types here

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