Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis

The biomedical literature is a rich source of associative information but too vast for complete manual review. We have developed an automated method of literature interrogation called "Literature Lab" that identifies and ranks associations existing in the literature between gene sets, such...

Full description

Saved in:

Bibliographic Details
Published in:	BMC genomics Vol. 8; no. 1; p. 461
Main Authors:	Febbo, Phillip G, Mulligan, Mike G, Slonina, David A, Stegmaier, Kimberly, Di Vizio, Dolores, Martinez, Paul R, Loda, Massimo, Taylor, Stephen C
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 18-12-2007 BioMed Central BMC
Subjects:	Animals Biology Breast Neoplasms - genetics Breast Neoplasms - metabolism Databases, Genetic DNA microarrays Female Humans Immunohistochemistry Male Medical literature Microarray Analysis Neoplasms - genetics Neoplasms - metabolism Pattern Recognition, Automated Prostatic Neoplasms - genetics Prostatic Neoplasms - metabolism Software United Kingdom
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	The biomedical literature is a rich source of associative information but too vast for complete manual review. We have developed an automated method of literature interrogation called "Literature Lab" that identifies and ranks associations existing in the literature between gene sets, such as those derived from microarray experiments, and curated sets of key terms (i.e. pathway names, medical subject heading (MeSH) terms, etc). Literature Lab was developed using differentially expressed gene sets from three previously published cancer experiments and tested on a fourth, novel gene set. When applied to the genesets from the published data including an in vitro experiment, an in vivo mouse experiment, and an experiment with human tumor samples, Literature Lab correctly identified known biological processes occurring within each experiment. When applied to a novel set of genes differentially expressed between locally invasive and metastatic prostate cancer, Literature Lab identified a strong association between the pathway term "FOSB" and genes with increased expression in metastatic prostate cancer. Immunohistochemistry subsequently confirmed increased nuclear FOSB staining in metastatic compared to locally invasive prostate cancers. This work demonstrates that Literature Lab can discover key biological processes by identifying meritorious associations between experimentally derived gene sets and key terms within the biomedical literature.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1471-2164 1471-2164
DOI:	10.1186/1471-2164-8-461