Literature mining based on gene annotation
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.
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natasha.sernova
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GR
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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
I would suggest also to search for RNA-seq, since
transcriptomemight not always be exactly written there.