PubGene - a new tool for supervised analysis of gene expression data
eivind.hovig at labmed.uio.no
Mon Apr 30 15:24:25 EST 2001
The NTNU University in Trondheim and the Norwegian Radium Hospital in
Oslo are pleased to present free worl wide web access to PubGene
(http://www.pubgene.org). PubGene is a collection of tools, including
modules for supervised analysis of gene expression data based on the
information contained in MEDLINE (http://www.nlm.nih.gov) .
For documentation and reference, please see http://genetics.nature.com/
(Jenssen, T.-K., Laegreid, A., Komorowski, J., Hovig, E.: A literature
network of human genes for high-throughput gene-expression analysis.
p.21-28. Nature Genetics. May 2001).
The complete MEDLINE titles and abstracts are indexed for the occurrence
of all instances of human gene names and literature aliases, and mapped
to their correct primary gene symbols, as defined by the HUGO
nomenclature committee. All pairs of primary gene symbols are indexed to
create a network of genes based on their literature associations. This
approach opens the path for a whole new range of tools for the
biologist, and for gene expression analysis in particular. The web site
is a work in progress, and content may increase with time.
Among the more prominent features at present are:
* Gene network browsing: view the literature neighbors of any human gene
having MEDLINE recorded publications
* Gene subnet viewing: identify and view the literature interactions
between your own selection of genes
* Explore relevant MeSH terms for your gene(s) of interest
* Explore gene ontology terms for your gene(s) of interest
* Find the MEDLINE references most relevant for your selected set of
genes (without boolean searches)
* Do complete gene expression analysis on your own data. The result will
indicate which literature gene clusters are most significantly affected.
For further information or questions regarding this web site please
contact: ehovig at radium.uio.no or tkj at idi.ntnu.no
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