Literature mining based on gene annotation
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5.0 years ago
RT ▴ 360

Dear All,

I was wondering if it is possible to mine the published studies for a species based on their gene annotation. For example, if I want all the transcriptome studies for human transcription factors. Is it possible to make this kind of queries on some database?

Currently I am making the following search in GEO:

(transcription factors and transcriptome) AND "Homo sapiens"[porgn:__txid9606]

Wondering if there is any better way to do this?

Thanks.

data-mining annotations • 1.3k views
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Look here, for example:

http://www.bioguo.org/AnimalTFDB/help.php

or here

http://pazar.info/

I usually don't use GEO, sorry

Try NCBI www.ncbi.nlm.nih.gov) with your query. I have done it (without tax id) and got the following :

https://www.ncbi.nlm.nih.gov/gquery/?term=%28transcription+factors+and+transcriptome%29+AND+%22Homo+sapiens%22+

This is data from 13 databases including GEO by the way...

You can also look at this article:

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

http://nar.oxfordjournals.org/content/44/D1/D116.full.pdf

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I would suggest also to search for RNA-seq, since transcriptome might not always be exactly written there.

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