Software and algorithm for identification of tissue-specific express genes

Question

[Shicheng Guo]

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.

Answer 1

[venu]

Not packages but these are online tools

• UCSC Gene Sorter
• BioGPS, Example result for TP53.
• Gene Investigator (Login and Installation required)
• EMBL - Expression atlas, Example result

And you can explore Human Protein Atlas, RefExA

Answer 2

[Charles Warden]

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)

Answer 3

[Antonio Camargo]

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.

Answer 4

[kousi31]

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.