Question: Software and algorithm for identification of tissue-specific express genes
0
gravatar for Shicheng Guo
3.5 years ago by
Shicheng Guo7.7k
Shicheng Guo7.7k wrote:

Hi All,

Is there any atlas for the software, package or algorithm to identify tissue-specific express genes?

For example: ROKU: a novel method for identification of tissue-specific genes.

Thanks.

ADD COMMENTlink modified 3 months ago by kousi310 • written 3.5 years ago by Shicheng Guo7.7k
3
gravatar for venu
3.5 years ago by
venu6.2k
Germany
venu6.2k wrote:

Not packages but these are online tools

And you can explore Human Protein Atlas, RefExA

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by venu6.2k
2
gravatar for Charles Warden
3.5 years ago by
Charles Warden7.2k
Duarte, CA
Charles Warden7.2k wrote:

In order for an algorithm to be useful, you would need a large dataset covering many different tissues. So, I would focus on databases designed to cover multiple tissues:

TiGER has an easy to use web interface: http://bioinfo.wilmer.jhu.edu/tiger/

Other than that, +1 for the recommendation to use the EMBL Expression Atlas (which includes RNA-Seq datasets like the Illumina Body Map)

ADD COMMENTlink written 3.5 years ago by Charles Warden7.2k
0
gravatar for elsoja
3 months ago by
elsoja30
elsoja30 wrote:

If you're looking for a database of expression patterns, including tissue-specificity, you can take a look at PaGenBase. In case you want to identify tissue-specific genes in your own data, you can use tspex, a tool that I've developed. It offers a variety of tissue-specificity metrics, including ROKU.

ADD COMMENTlink written 3 months ago by elsoja30
0
gravatar for kousi31
3 months ago by
kousi310
kousi310 wrote:

To identify tissue-specific expression you may check out these two links. link_1 link_2 I haven't tried them yet. But I am planning to. I'm also interested to know, if there are any suggestions from other members.

ADD COMMENTlink modified 3 months ago • written 3 months ago by kousi310
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