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

<p>Abstract</p> <p>Background</p> <p>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).</p> <p>Results</p> <p>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 <it>in vitro </it>experiment, an <it>in vivo </it>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.</p> <p>Conclusion</p> <p>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.</p

Multidisciplinary approach of early breast cancer: The biology applied to radiation oncology

Early breast cancer treatment is based on a multimodality approach with the application of clinical and histological prognostic factors to determine locoregional and systemic treatments. The entire scientific community is strongly involved in the management of this disease: radiologists for screening and early diagnosis, gynecologists, surgical oncologists and radiation oncologists for locoregional treatment, pathologists and biologists for personalized characterization, genetic counselors for BRCA mutation history and medical oncologists for systemic therapies

Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis-1

<p><b>Copyright information:</b></p><p>Taken from "Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis"</p><p>http://www.biomedcentral.com/1471-2164/8/461</p><p>BMC Genomics 2007;8():461-461.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2244637.</p><p></p> treatment in the prostates of transgenic MPAKT mice. B) Association of pathway terms (Squares) with the 64 genes (circles) associated with RAD001 treatment of MPAKT mice. Size of square indicates confidence of associations, thickness of connecting line correlates with the number of abstracts linking any pair of term and gene. C) Protein lysates prepared from the VP of individual MPAKT and WT mice either treated with RAD001 (+) or with placebo (-) for 48 hours were immunoblotted with anti-Hif1α and anti-tubulin as indicated. Lower panel shows the densitometric ratio of Hif1α and tubulin

Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis-4

<p><b>Copyright information:</b></p><p>Taken from "Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis"</p><p>http://www.biomedcentral.com/1471-2164/8/461</p><p>BMC Genomics 2007;8():461-461.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2244637.</p><p></p> Heat map of the top 100 genes with increased expression in HL60 cells treated with ATRA compared to untreated HL60 cells (Red – high normalized expression, Blue – low normalized expression). C) Percentage of cells positive for nitro blue tetrazolium (NBT) reduction (Mean +/- St dev). D) Literature Lab ranking, association scores, and confidence calls for cell physiology, metabolism, and pathway terms (Association score is the log of the product of frequency (logPF))