An integrated computational proteomics method to extract protein targets for fanconi anemia studies

Jake Yue Chen, Sarah L. Pinkerton, Changyu Shen, Mu Wang

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

6 Citations (Scopus)

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.

Original languageEnglish
Title of host publicationProceedings of the ACM Symposium on Applied Computing
Pages173-179
Number of pages7
Volume1
StatePublished - 2006
Event2006 ACM Symposium on Applied Computing - Dijon, France
Duration: Apr 23 2006Apr 27 2006

Other

Other2006 ACM Symposium on Applied Computing
CountryFrance
CityDijon
Period4/23/064/27/06

Fingerprint

Proteins
Proteomics
Seed
Bioinformatics
Computational methods
Merging
Purification
Mass spectrometry
Agglomeration
Visualization

Keywords

  • Disease target
  • Fanconi anemia
  • Protein interaction network
  • Proteomics

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Chen, J. Y., Pinkerton, S. L., Shen, C., & Wang, M. (2006). An integrated computational proteomics method to extract protein targets for fanconi anemia studies. In Proceedings of the ACM Symposium on Applied Computing (Vol. 1, pp. 173-179)

An integrated computational proteomics method to extract protein targets for fanconi anemia studies. / Chen, Jake Yue; Pinkerton, Sarah L.; Shen, Changyu; Wang, Mu.

Proceedings of the ACM Symposium on Applied Computing. Vol. 1 2006. p. 173-179.

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

Chen, JY, Pinkerton, SL, Shen, C & Wang, M 2006, An integrated computational proteomics method to extract protein targets for fanconi anemia studies. in Proceedings of the ACM Symposium on Applied Computing. vol. 1, pp. 173-179, 2006 ACM Symposium on Applied Computing, Dijon, France, 4/23/06.
Chen JY, Pinkerton SL, Shen C, Wang M. An integrated computational proteomics method to extract protein targets for fanconi anemia studies. In Proceedings of the ACM Symposium on Applied Computing. Vol. 1. 2006. p. 173-179
Chen, Jake Yue ; Pinkerton, Sarah L. ; Shen, Changyu ; Wang, Mu. / An integrated computational proteomics method to extract protein targets for fanconi anemia studies. Proceedings of the ACM Symposium on Applied Computing. Vol. 1 2006. pp. 173-179
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