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

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 co-occurrences 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 real microarray data, 221 differentially expressed genes from a microarray experiment were analyzed with CoPub Mapper, which resulted in several relevant clusters of genes with biological process and disease keywords. In addition, all genes versus keywords were hierarchical clustered to reveal a complete grouping of published genes based on co-occurrence.The CoPub Mapper program allows for quick and versatile querying of co-published genes and keywords and can be successfully used to cluster predefined groups of genes and microarray data.High throughput microarray analysis has made it possible to analyze the mRNA expression of most if not all human genes simultaneously [1,2]. The data generated from these analyses are overwhelming since hundreds of interesting differentially expressed genes can be identified in a single assay. Knowledge on expression levels of genes in different systems is useful, but does not directly answer biologically relevant questions, such as: What is the gene function? Where is the gene located within the genome? Where is the protein located within the cell? Most important is the answer to the question whether genes identified in microarray experiments have something in common, such as, are multiple genes part of a single biological pathway or proteins part of a protein complex? The public database which contains much of the relevant