MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.
MeSHer uses a simple statistical approach to identify biological concepts in the form of Medical Subject Headings (MeSH terms) obtained from the PubMed database that are significantly overrepresented within the identified gene set relative to those associated with the overall collection of genes on the underlying DNA microarray platform. As a demonstration, we apply this approach to gene lists acquired from a published study of the effects of angiotensin II (Ang II) treatment on cardiac gene expression and demonstrate that this approach can aid in the interpretation of the resulting 'significant' gene set.


BACKGROUND
The software is available at http://www.tm4.org.


BACKGROUND
Results from the analysis of significant genes from the published Ang II study.
Djebbari
Amira
A
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
Karamycheva
Svetlana
S
Howe
Eleanor
E
Quackenbush
John
J
D001185:Artificial Intelligence; D001695:Biology / Q000379:methods; D003628:Database Management Systems; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D046650:Medical Subject Headings; D008957:Models, Genetic; D015233:Models, Statistical; D009323:Natural Language Processing; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods; D039781:PubMed; D012984:Software; D018875:Vocabulary, Controlled