Dresden 2006 – scientific programme

Parts | Days | Selection | Search | Downloads | Help

AKB: Biologische Physik

AKB 16: Biological Networks

AKB 16.2: Talk

Wednesday, March 29, 2006, 14:30–14:45, ZEU 255

Locating overlapping dense subgraphs in gene association networks and identifying novel functional units among these groups — •Illes J. Farkas, Gergely Palla, Imre Derenyi, and Tamas Vicsek — Biol. Phys. Res. Group of HAS and Dept. of Biol. Phys., Eotvos Univ., H-1117 Budapest, Pazmany P. stny. 1A, Hungary

The identification of the groups of proteins performing the diverse tasks in a cell is crucial to our understanding of cellular networks. In the yeast, S. cerevisiae, known physically interacting groups of proteins (complexes) strongly overlap. The total number of proteins in them by far underestimates their total size (from Refs. [1,2] the ratio is 2750/8932 and 1355/2676), thus, all functional groups of proteins, both physically interacting and other, are likely to share many of their members with other groups. However, most current community search methods exclude overlaps. With the aim to discover both novel functions of individual proteins and novel functional units in gene association networks we combine (i) a search for overlapping dense subgraphs based on the Clique Percolation Method (CPM) [3,4], which explicitly allows overlaps among the groups, and (ii) the verification and characterization of the identified groups of nodes (genes) by annotation tools listing known functions [5].

[1] Guldener, U., et.al. Nucl. Acids Res. 33, D364-368 (2005).

[2] Gavin, A. C., et.al. Nature 415, 141-147 (2002).

[3] Derenyi, I., et.al. Phys. Rev. Lett. 94, 160202 (2005).

[4] Palla, G., et.al. Nature 435, 814-818 (2005),
http://angel.elte.hu/clustering .

[5] The Gene Ontology Consortium. Nature Genetics 25, 25-29 (2000).