CoPub Mapper: mining MEDLINE based on search term co-publication

Background: High throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological similarities between genes, publications from MEDLINE were identified in which pairs of gene names and combinations of gene name with specific keywords were co-mentioned. Results: MEDLINE search strings for 15,621 known genes and 3,731 keywords were generated and validated. PubMed IDs were retrieved from MEDLINE and relative probability of cooccurrences of all gene-gene and gene-keyword pairs determined. To assess gene clustering according to literature co-publication, 150 genes consisting of 8 sets with known connections (same pathway, same protein complex, or same cellular localization, etc.) were run through the program. Receiver operator characteristics (ROC) analyses showed that most gene sets were clustered much better than expected by random chance. To test grouping of genes from re...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Blaise T. F. Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman, Guido Jenster
• Keywords: Biological Process, BMCBI 2005, Expressed Genes, Keywords