[BioC] Medline mining of microarray data (w/ synonyms and extra keyword?)

[Saurin D. Jani]

Hi Michael,

With or without microarray data, you can use a tool called GeneMesh, which mines PubMed and based on citation statistics...it will give you genes associated with diseases, therapeutics or any other key word.

GeneMesh is freely available online at:
http://proteogenomics.musc.edu/genemesh/

PubMed:
http://www.ncbi.nlm.nih.gov/pubmed?term=20359363

GeneMesh's distinct user interface (i.e., Web 2.0) allows users to explore the GeneMesh database in three different ways to find genes related to MeSH Terms:

1. With or without any data set, users can mine Genes related to a Search Term (e.g., stem cells, angiogenesis, etc.).

2. With or without any dataset, users can enter Entrez GeneID(s) and find related MeSH terms.

3. Users can upload gene expression data and perform analysis limited to a specific subcategory (e.g., cardiovascular diseases) or a broad category (e.g., Diseases), allowing for biased and unbiased analysis.


Let me know if you have any questions,
Saurin

--- On Wed, 4/14/10, Michael Imbeault <michael.imbeault at sympatico.ca> wrote:

> From: Michael Imbeault <michael.imbeault at sympatico.ca>
> Subject: [BioC] Medline mining of microarray data (w/ synonyms and extra keyword?)
> To: bioconductor at stat.math.ethz.ch
> Date: Wednesday, April 14, 2010, 9:51 AM
> Hello,
> 
> Is there a Bioconductor solution to Medline mining? Say,
> for a given set of affy identifiers, find gene names, their
> synonyms, and the pubmed count of abstracts cooccurring with
> a given keyword (such as a disease name)?
> 
> If not available in Bioconductor, is any other tool
> available for this? Searches in bioinformatic journals yield
> only old tools which (for the most part) have dead urls.
> 
> Thanks,
> Michael
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>