Article

An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies

Authors:

Sarah L. Pinkerton,

Mu WangAuthors Info & Claims

SAC '06: Proceedings of the 2006 ACM symposium on Applied computing

Pages 173 - 179

https://doi.org/10.1145/1141277.1141316

Published: 23 April 2006 Publication History

Abstract

Fanconi Anemia (FA) is a rare autosomal genetic disease with multiple birth defects and severe childhood complications for its patients. The lack of sequence homology of the entire FA Complementation Group proteins in such as FANCC, FANCG, FANCA makes them extremely difficult to characterize using conventional bioinformatics methods. In this work, we describe how to use computational methods to extract protein targets for FA, using protein interaction data set collected for FANC group C protein (FANCC). We first generated an initial set of 130 FA-interacting proteins as "FANCC seed proteins" by merging an in-house experimental set of FANCC Tandem Affinity Purification (TAP) Pulldown Proteomics data identified from Mass Spectrometry methods with publicly available human FANCC-interacting proteins. Next, we expanded the FANCC seed proteins using a nearest-neighbor method to generate a FANCC protein interaction subnetwork of 948 proteins in 903 protein interactions. We show that this network is statistically significant, with high indices of aggregation and separations. We also show a visualization of the network, support the evidence that many well-connected proteins exists in the network. Further, we developed and applied an interaction network protein scoring algorithm, which allows us to calculate a ranked list of significant FA proteins. Our result has been supporting further biological investigations of disease biologists on our team. We believe our method can be generalized to other disease biology studies with similar problems.

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Digital Library

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Cited By

Nguyen TYue ZSlominski RWelner RZhang JChen J(2022)WINNER: A network biology tool for biomolecular characterization and prioritizationFrontiers in Big Data10.3389/fdata.2022.10166065Online publication date: 4-Nov-2022
https://doi.org/10.3389/fdata.2022.1016606
Laufer VChen JLangefeld CBridges S(2017)Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic DiseasesRheumatic Disease Clinics of North America10.1016/j.rdc.2017.04.01243:3(449-466)Online publication date: Aug-2017
https://doi.org/10.1016/j.rdc.2017.04.012
Naylor SChen J(2010)Unraveling Human Complexity and Disease With Systems Biology and Personalized MedicinePersonalized Medicine10.2217/pme.10.167:3(275-289)Online publication date: 26-Apr-2010
https://doi.org/10.2217/pme.10.16

Index Terms

An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies

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cover image ACM Conferences

SAC '06: Proceedings of the 2006 ACM symposium on Applied computing

April 2006

1967 pages

ISBN:1595931082

DOI:10.1145/1141277

Conference Chair:
Hisham M. Haddad
Kennesaw State University, Kennesaw, Georgia

Copyright © 2006 ACM.

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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Published: 23 April 2006

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April 23 - 27, 2006

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Cited By

Nguyen TYue ZSlominski RWelner RZhang JChen J(2022)WINNER: A network biology tool for biomolecular characterization and prioritizationFrontiers in Big Data10.3389/fdata.2022.10166065Online publication date: 4-Nov-2022
https://doi.org/10.3389/fdata.2022.1016606
Laufer VChen JLangefeld CBridges S(2017)Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic DiseasesRheumatic Disease Clinics of North America10.1016/j.rdc.2017.04.01243:3(449-466)Online publication date: Aug-2017
https://doi.org/10.1016/j.rdc.2017.04.012
Naylor SChen J(2010)Unraveling Human Complexity and Disease With Systems Biology and Personalized MedicinePersonalized Medicine10.2217/pme.10.167:3(275-289)Online publication date: 26-Apr-2010
https://doi.org/10.2217/pme.10.16

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