Search papers using Gene Sets
3
1
Entering edit mode
7.3 years ago
Opt ▴ 40

Hi,

I heard about a tool which lets you search for papers based on a set of genes that you input and it returns papers that have mentioned a significant set of those genes.

Does anyone know what tool this is?

Thanks

gene nlp gene-set enrichment tool • 1.3k views
ADD COMMENT
1
Entering edit mode
ADD REPLY
2
Entering edit mode
7.3 years ago
tomluec ▴ 60

In R you can do this using Org.HS.  Below is an example:

source("http://bioconductor.org/biocLite.R")
biocLite("org.Hs.eg.db")
library("org.Hs.eg.db")

# mapped_genes are all the genes that org.HS.egPMID covers (the HS refers to homosapien).  These genes are in Entrez format.

# entrez2Pmid is a list taking entrez gene ids to a vector of Pmids.  

mapped_genes <- mappedkeys(org.Hs.egPMID)
entrez2Pmid     <- as.list(org.Hs.egPMID[mapped_genes])

# now if you have an entrez gene id you can look up the relevant papers by doing

entrez2Pmid[myEntrezGene

(here is a pastebin of the code since I stink at using the biostars code formatter http://pastebin.com/JCa6L7sB)

There is a tutorial here:

http://www.bioconductor.org/packages/release/data/annotation/manuals/org.Hs.eg.db/man/org.Hs.eg.db.pdf

Also you can just use http://idconverter.bioinfo.cnio.es/IDconverter.php.  Although I've found that sometimes the results seem to be a subset of the results you get using the method outlined above.

ADD COMMENT
1
Entering edit mode
7.3 years ago
tomluec ▴ 60

Also I haven't used it much but chilibot (does anybody know of a more updated approach?) does some NLP on papers mentioning genes in a gene set to build a biological network.

http://chilibot.net/

ADD COMMENT
1
Entering edit mode
7.3 years ago
dario.garvan ▴ 490

The software is called GeneValorization and is available as a Java Web Start application.

ADD COMMENT

Login before adding your answer.

Traffic: 2062 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6