Discovering coherent value bicliques in genetic interaction data

Gowtham Atluri; Jeremy Bellay; Gaurav Pandey; Chad Myers; Vipin Kumar

Discovering coherent value bicliques in genetic interaction data

Gowtham Atluri, Jeremy Bellay, Gaurav Pandey, Chad Myers, Vipin Kumar

Computer Science and Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

6 Scopus citations

Abstract

Genetic Interaction (GI) data provides a means for exploring the structure and function of pathways in a cell. Coherent value bicliques (submatrices) in GI data represents functionally similar gene modules or protein complexes. However, no systematic approach has been proposed for exhaustively enumerating all coherent value submatrices in such data sets, which is the problem addressed in this paper. Using a monotonic range measure to capture the coherence of values in a submatrix of an input data matrix, we propose a two-step Apriori-based algorithm for discovering all nearly constant value submatrices, referred to as Range Constrained Blocks. By systematic evaluation on an extensive genetic interaction data set, we show that the coherent value submatrices represent groups of genes that are functionally related than the submatrices with diverse values. We also show that our approach can exhaustively find all the submatrices with a range less than a given threshold, while the other competing approaches can not find all such submatrices.

Original language	English (US)
Title of host publication	Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
Publisher	Association for Computing Machinery
Pages	125-132
Number of pages	8
ISBN (Electronic)	9781605583020
State	Published - 2010
Event	9th International Workshop on Data Mining in Bioinformatics, BIOKDD 2010, Held in Conjunction with 16th ACM SIGKDD Conference on Knowledge Discovery and Data Mining - Washington, United States Duration: Jul 25 2010 → Jul 28 2010

Publication series

Name	Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

Other

Other	9th International Workshop on Data Mining in Bioinformatics, BIOKDD 2010, Held in Conjunction with 16th ACM SIGKDD Conference on Knowledge Discovery and Data Mining
Country/Territory	United States
City	Washington
Period	7/25/10 → 7/28/10

Bibliographical note

Publisher Copyright:
Copyright © 2010 ACM.

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Atluri, G., Bellay, J., Pandey, G., Myers, C., & Kumar, V. (2010). Discovering coherent value bicliques in genetic interaction data. In Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (pp. 125-132). (Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining). Association for Computing Machinery.

Discovering coherent value bicliques in genetic interaction data. / Atluri, Gowtham; Bellay, Jeremy; Pandey, Gaurav et al.
Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery, 2010. p. 125-132 (Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Atluri, G, Bellay, J, Pandey, G, Myers, C & Kumar, V 2010, Discovering coherent value bicliques in genetic interaction data. in Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Association for Computing Machinery, pp. 125-132, 9th International Workshop on Data Mining in Bioinformatics, BIOKDD 2010, Held in Conjunction with 16th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Washington, United States, 7/25/10.

Atluri, Gowtham ; Bellay, Jeremy ; Pandey, Gaurav et al. / Discovering coherent value bicliques in genetic interaction data. Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery, 2010. pp. 125-132 (Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining).

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ER -

Discovering coherent value bicliques in genetic interaction data

Abstract

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