Mining alzheimer disease relevant proteins from integrated protein interactome data

Jake Yub Chen, Changyu Shen, Andrey Y. Sivachenko

Research output: Chapter in Book/Report/Conference proceedingConference contribution

117 Citations (Scopus)

Abstract

Huge unrealized post-genome opportunities remain in the understanding of detailed molecular mechanisms for Alzheimer Disease (AD), In this work, we developed a computational method to rank-order AD-related proteins, based on an initial list of ADrelaled genes and public human protein interaction data. In this method, we first collected an initial seed list of 65 AD-related genes from the OMIM database and mapped them to 70 AD seed proteins. We then expanded the seed proteins to an enriched AD set of 765 proteins using protein interactions from the Online Predicated Human Interaction Database (OPHID). We showed that the expanded AD-related proteins form a highly connected and statistically significant protein interaction sub-network. We further analyzed the sub-network to develop an algorithm, which can be used to automatically score and rank-order each protein for its biological relevance to AD pathways(s). Our results show that functionally relevant AD proteins were consistently ranked at the top: among the top 20 of 765 expanded AD proteins, 19 proteins are confirmed to belong to the original 70 AD seed protein set. Our method represents a novel use of protein interaction network data for Alzheimer disease studies and may be generalized for other disease areas in the future.

Original languageEnglish
Title of host publicationProceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006
Pages367-378
Number of pages12
StatePublished - 2006
Event11th Pacific Symposium on Biocomputing 2006, PSB 2006 - Maui, HI, United States
Duration: Jan 3 2006Jan 7 2006

Other

Other11th Pacific Symposium on Biocomputing 2006, PSB 2006
CountryUnited States
CityMaui, HI
Period1/3/061/7/06

Fingerprint

Alzheimer Disease
Proteins
Protein Interaction Maps
Seeds
Seed
Genes
Databases
Genetic Databases
Computational methods
Genome

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)

Cite this

Chen, J. Y., Shen, C., & Sivachenko, A. Y. (2006). Mining alzheimer disease relevant proteins from integrated protein interactome data. In Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006 (pp. 367-378)

Mining alzheimer disease relevant proteins from integrated protein interactome data. / Chen, Jake Yub; Shen, Changyu; Sivachenko, Andrey Y.

Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. 2006. p. 367-378.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chen, JY, Shen, C & Sivachenko, AY 2006, Mining alzheimer disease relevant proteins from integrated protein interactome data. in Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. pp. 367-378, 11th Pacific Symposium on Biocomputing 2006, PSB 2006, Maui, HI, United States, 1/3/06.
Chen JY, Shen C, Sivachenko AY. Mining alzheimer disease relevant proteins from integrated protein interactome data. In Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. 2006. p. 367-378
Chen, Jake Yub ; Shen, Changyu ; Sivachenko, Andrey Y. / Mining alzheimer disease relevant proteins from integrated protein interactome data. Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. 2006. pp. 367-378
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