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topics:bib:vilo2011a

Party- and Date hubs

Category:Data Analysis
Supervisor:Jaak Vilo
Year:2011
Abstract:Protein interaction network is a graph where protein-protein interactions are presented. Analog is a social network where human-human interactions are presented.

For proteins we can use some measured activity information (gene expression activity) that we have collected in a database and web-tool MEM http://biit.cs.ut.ee/mem/
Based on these data the goal is to analyse protein interaction network and find party- and date hubs from there.

Alternative title:
Advanced EP:PPI using MEM and other tools (GW?).

Goal: verify PPI interactions using MEM as large scale gene expression data. Identifying context-specific interactions (under certain conditions only). And identifying “date” and “party” hubs using gene expression data.

The yeast interactome exhibits organized modularity where a small proportion of proteins – the 'hubs' – interact with many partners. These hubs fall into one of two categories: 'party' hubs, which interact with most of their partners simultaneously, and 'date' hubs, which bind different partners at different locations and times.

Kemmeren, P.; van Berkum, NL.; Vilo, J.; Bijma, T.; Donders, R.; Brazma, A.; Holstege, FCP. (2002). Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Molecular Cell, 9(5), 1133 - 1143.

Adler, P.; Kolde, R.; Kull, M.; Tkachenko, A.; Peterson, H.; Reimand, J.; Vilo, J. (2009). Mining for coexpression across hundreds of datasets using novel rank aggregation and visualisation methods. Genome Biology, 10(12), R139

Han, Jing-Dong J, Bertin, Nicolas, Hao, Tong, Goldberg, Debra S, Berriz, Gabriel F, Zhang, Lan V, Dupuy, Denis, Walhout, Albertha J M, Cusick, Michael E, Roth, Frederocl P, & Vidal, Marc Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature,430, 88–93 (01 July 2004); 10.1038/nature02555

http://www.signaling-gateway.org/update/updates/200406/su-0406-4.html

Please contact Jaak Vilo vilo@ut.ee
File:vilo2011a.pdf
topics/bib/vilo2011a.txt · Last modified: 2011/10/25 12:30 by swen