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CLARM: An integrative approach for functional modules discovery
CLARM: An integrative approach for functional modules discovery
Type
Conference Paper
Authors
Salem, Saeed M.
Alroobi, Rami
Banitaan, Shadi
Seridi, Loqmane
Brewer, James E.
Aljarah, Ibrahim
KAUST Department
Applied Mathematics and Computational Science Program
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Date
2011
Abstract
Functional module discovery aims to find well-connected subnetworks which can serve as candidate protein complexes. Advances in High-throughput proteomic technologies have enabled the collection of large amount of interaction data as well as gene expression data. We propose, CLARM, a clustering algorithm that integrates gene expression profiles and protein protein interaction network for biological modules discovery. The main premise is that by enriching the interaction network by adding interactions between genes which are highly co-expressed over a wide range of biological and environmental conditions, we can improve the quality of the discovered modules. Protein protein interactions, known protein complexes, and gene expression profiles for diverse environmental conditions from the yeast Saccharomyces cerevisiae were used for evaluate the biological significance of the reported modules. Our experiments show that the CLARM approach is competitive to wellestablished module discovery methods. Copyright © 2011 ACM.
Citation
Salem, S., Seridi, L., Alroobi, R., Brewer, J., Banitaan, S., & Aljarah, I. (2011). CLARM. Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB ’11. doi:10.1145/2147805.2147917
Publisher
Association for Computing Machinery (ACM)
Journal
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11
Conference/Event Name
2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011
DOI
10.1145/2147805.2147917
Permanent link to this record
http://hdl.handle.net/10754/564351
Collections
Conference Papers
Applied Mathematics and Computational Science Program
Computer Science Program
Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
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