Scheduled Seminars on 3/27/2012

Erik L. L. Sonnhammer at 11:00  Edit  Reschedule  Delete
Affiliation: Stockholm Bioinformatics Centre and Department of Biochemistry and Biophysics, Stockholm University
Host: Michael Galperin

Comparative interactomics with FunCoup
Background. No single experimental method can discover all connections in the interactome. A computational approach can help by integrating data from multiple, often unrelated, proteomics and genomics pipelines. Reconstructing global networks of functional coupling (FC) faces the challenges of scale and heterogeneity—how to efficiently integrate huge amounts of diverse data from multiple organisms, yet ensuring high accuracy.

Results. We present FunCoup, a database that maintains and visualizes global gene/protein networks of functional coupling that have been constructed by Bayesian integration of diverse high-throughput data. FunCoup achieves high coverage by orthology-based integration of data sources from different model organisms and from different platforms. We here present release 2.0 in which the data sources have been updated and the methodology has been refined. It contains a new data type Genetic Interaction, and three new species: chicken, dog and zebra fish. The networks for worm, human, mouse, rat, Ciona, fly, Arabidopsis, and yeast have been updated.

Conclusions. As FunCoup extensively transfers functional coupling information between species, the new input datasets have considerably improved both coverage and quality of the networks. The number of high-confidence network links has increased dramatically. For instance, the human network has more than eight times as many links above confidence 0.5 as the previous release. http://FunCoup.sbc.su.se provides on-line facilities for network analysis. New for release 2.0 is improved analysis of network conservation between species. I will explain how to do comparative interactomics on the FunCoup website.

Refs for FunCoup:
http://www.ncbi.nlm.nih.gov/pubmed/22110034
http://www.ncbi.nlm.nih.gov/pubmed/19246318
http://www.ncbi.nlm.nih.gov/pubmed/18445606
http://www.ncbi.nlm.nih.gov/pubmed/20463971
I will also very briefly mention two new standards for orthology data exchange, see SeqXML.org and OrthoXML.org.

Schedule Another Seminar on 3/27/2012