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Protein complex prediction via bottleneck-based graph partitioning

Published: 29 October 2012 Publication History

Abstract

Detecting protein complexes is one of essential and fundamental tasks in understanding various biological functions or processes. Therefore, precise identification of protein complexes is indispensible. For more precise detection of protein complexes, we propose a novel data structure which employs bottleneck proteins as partitioning points for detecting the protein complexes. The partitioning process allows overlapping between resulting protein complexes. We applied our algorithm to several PPI (Protein-Protein Interaction) networks of Saccharomyces cerevisiae and Homo sapiens, and validated our results using public databases of protein complexes. Our algorithm resulted in overlapping protein complexes with significantly improved F1 score, which comes from higher precision.

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Cited By

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  • (2013)Improved method for protein complex detection using bottleneck proteinsBMC Medical Informatics and Decision Making10.1186/1472-6947-13-S1-S513:S1Online publication date: 5-Apr-2013
  • (2012)DTMBIO 2012Proceedings of the 21st ACM international conference on Information and knowledge management10.1145/2396761.2398758(2766-2767)Online publication date: 29-Oct-2012

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cover image ACM Conferences
DTMBIO '12: Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics
October 2012
92 pages
ISBN:9781450317160
DOI:10.1145/2390068
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Publication History

Published: 29 October 2012

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Author Tags

  1. bottleneck protein
  2. network clustering
  3. protein complex detection
  4. protein-protein interaction

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Cited By

View all
  • (2013)Improved method for protein complex detection using bottleneck proteinsBMC Medical Informatics and Decision Making10.1186/1472-6947-13-S1-S513:S1Online publication date: 5-Apr-2013
  • (2012)DTMBIO 2012Proceedings of the 21st ACM international conference on Information and knowledge management10.1145/2396761.2398758(2766-2767)Online publication date: 29-Oct-2012

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