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

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.

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.


'"/>

Source:BMC Bioinformatics


Page: 1

Related biology news :

1. Determining The Fate Of Cells In The Human Body
2. Stanford/Packard scientists data-mining technique strikes genetic gold
3. Mayo Clinic collaboration mining of ancient herbal text leads to potential new anti-bacterial drug
4. New nanotechnology able to examine single molecules, aiding in determining gene expression
5. Study warns deep-sea mining may pose serious threat to fragile marine ecosystems
6. Breakthrough Microarray-based Technology for the Study of Cancer
7. An entropy-based gene selection method for cancer classification using microarray data
8. Towards precise classification of cancers based on robust gene functional expression profiles
9. Robot-based system developed at Carnegie Mellon detects life in Chiles Atacama desert
10. Canada approves marijuana-based pain spray
11. Major new UNC-based drinking water study suggests pregnancy fears may be overstated
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:3/1/2017)... 1, 2017  Aware, Inc. (NASDAQ: AWRE), a leading ... Richard P. Moberg has resigned, effective March 3, ... Financial Officer and Treasurer of Aware citing a desire ... a member of the Board of Directors of Aware. ... Executive Officer and co-President, General Counsel has been named ...
(Date:2/26/2017)... DALLAS , Feb. 25, 2017  Securus ... justice technology solutions for public safety, investigation, corrections ... of Recidivism and Reentry. "Too often, ... State prisons and county jails are trying to ... of inmates and friends and family members. While significant ...
(Date:2/16/2017)... , Feb. 16, 2017  Genos, a community ... that it has received Laboratory Accreditation from the ... is presented to laboratories that meet stringent requirements ... scientifically rigorous processes. "Genos is committed ... laboratory practices. We,re honored to be receiving CAP ...
Breaking Biology News(10 mins):
(Date:3/28/2017)... ... March 28, 2017 , ... Ecovia Renewables, Inc. announced today ... grant from the National Science Foundation (NSF). Under the award , Ecovia ... of BioGel™ biopolymer materials for hygiene applications, particularly for use in the absorbent ...
(Date:3/28/2017)... and WASHINGTON , March ... service provider, GENEWIZ, will launch single-cell sequencing during the American ... Walter E. Washington Convention Center in Washington, ... researchers to perform differential gene expression of thousands of ... Experts on-hand at ...
(Date:3/28/2017)... SAN DIEGO , March 28, 2017  Viking ... focused on the development of novel therapies for metabolic ... officer, Brian Lian , Ph.D., will deliver a ... Annual NASH Investor Conference, being held April 3, ... Details for this presentation are as ...
(Date:3/28/2017)... ... March 28, 2017 , ... ... release of LabKey’s newest software solution, LabKey Biologics . Built in collaboration ... and biotech organizations, LabKey Biologics provides drug research teams tools for biological entity ...
Breaking Biology Technology: