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:6/22/2016)... , June 22, 2016   Acuant ... and verification solutions, has partnered with RightCrowd ... solutions for Visitor Management, Self-Service Kiosks and ... products that add functional enhancements to existing ... corporations and venues with an automated ID ...
(Date:6/15/2016)... June 15, 2016 Transparency ... titled "Gesture Recognition Market by Application Market - Global Industry Analysis ... 2024". According to the report, the  global gesture recognition ... 2015 and is estimated to grow at a ... by 2024.  Increasing application of gesture ...
(Date:6/2/2016)... , June 2, 2016 The ... has awarded the 44 million US Dollar project, for ... Embossed Vehicle Plates including Personalization, Enrolment, and IT Infrastructure ... leader in the production and implementation of Identity Management Solutions. ... January, however Decatur was selected for ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... ... 2016 , ... Parallel 6 , the leading software as a service ... Virtual Patient Encounter CONSULT module which enables both audio and video telemedicine communication ... , Using the CONSULT module, patients and physicians can schedule a face to face ...
(Date:6/27/2016)... , ... June 27, 2016 , ... ... for Amgen, will join the faculty of the University of North Carolina ... professor of strategy and entrepreneurship at UNC Kenan-Flagler, with a focus on the ...
(Date:6/27/2016)... June 27, 2016   Ginkgo Bioworks , a ... engineering, was today awarded as one of the ... the world,s most innovative companies. Ginkgo Bioworks is ... the real world in the nutrition, health and ... directly with customers including Fortune 500 companies to ...
(Date:6/24/2016)... SAN DIEGO , June 24, 2016 /PRNewswire/ ... that more sensitively detects cancers susceptible to PARP ... individual circulating tumor cells (CTCs). The new test ... of HRD-targeted therapeutics in multiple cancer types. ... therapies targeting DNA damage response pathways, including PARP, ...
Breaking Biology Technology: