A time-series biclustering algorithm for revealing co-regulated genes

Ya Zhang, Hongyuan Zha, Chao Hisen Chu

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

41 Citations (Scopus)

Abstract

Although existing bicluster algorithms claimed to be able to discover co-regulated genes under a subset of given experiment conditions, they ignore the inherent sequential relationship between crucial time points and thus are not applicable to analyze time-series gene expression data. A simple and effective deletion-based algorithm, using the mean squared residue score as a measure, was developed to bicluster time-series gene expression data. While enforcing a threshold value for the score, the algorithm alternately eliminates genes and time points according to their correlation to the bicluster. To ensure the time locality, only the starting and ending points in the time interval are eligible for deletion. As a result, the number of genes and the length of time interval are simultaneously maximized. Our experimental results shown that the proposed method is capable of identifying co-regulated genes characterized by partial time-course data that previous methods failed to discover.

Original languageEnglish (US)
Title of host publicationProceedings ITCC 2005 - International Conference on Information Technology
Subtitle of host publicationCoding and Computing
EditorsH. Selvaraj, P.K. Srimani
Pages32-37
Number of pages6
StatePublished - Sep 22 2005
EventITCC 2005 - International Conference on Information Technology: Coding and Computing - Las Vegas, NV, United States
Duration: Apr 4 2005Apr 6 2005

Publication series

NameInternational Conference on Information Technology: Coding and Computing, ITCC
Volume1

Other

OtherITCC 2005 - International Conference on Information Technology: Coding and Computing
CountryUnited States
CityLas Vegas, NV
Period4/4/054/6/05

Fingerprint

Time series
Genes
Gene expression
Experiments

All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

Zhang, Y., Zha, H., & Chu, C. H. (2005). A time-series biclustering algorithm for revealing co-regulated genes. In H. Selvaraj, & P. K. Srimani (Eds.), Proceedings ITCC 2005 - International Conference on Information Technology: Coding and Computing (pp. 32-37). (International Conference on Information Technology: Coding and Computing, ITCC; Vol. 1).
Zhang, Ya ; Zha, Hongyuan ; Chu, Chao Hisen. / A time-series biclustering algorithm for revealing co-regulated genes. Proceedings ITCC 2005 - International Conference on Information Technology: Coding and Computing. editor / H. Selvaraj ; P.K. Srimani. 2005. pp. 32-37 (International Conference on Information Technology: Coding and Computing, ITCC).
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abstract = "Although existing bicluster algorithms claimed to be able to discover co-regulated genes under a subset of given experiment conditions, they ignore the inherent sequential relationship between crucial time points and thus are not applicable to analyze time-series gene expression data. A simple and effective deletion-based algorithm, using the mean squared residue score as a measure, was developed to bicluster time-series gene expression data. While enforcing a threshold value for the score, the algorithm alternately eliminates genes and time points according to their correlation to the bicluster. To ensure the time locality, only the starting and ending points in the time interval are eligible for deletion. As a result, the number of genes and the length of time interval are simultaneously maximized. Our experimental results shown that the proposed method is capable of identifying co-regulated genes characterized by partial time-course data that previous methods failed to discover.",
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Zhang, Y, Zha, H & Chu, CH 2005, A time-series biclustering algorithm for revealing co-regulated genes. in H Selvaraj & PK Srimani (eds), Proceedings ITCC 2005 - International Conference on Information Technology: Coding and Computing. International Conference on Information Technology: Coding and Computing, ITCC, vol. 1, pp. 32-37, ITCC 2005 - International Conference on Information Technology: Coding and Computing, Las Vegas, NV, United States, 4/4/05.

A time-series biclustering algorithm for revealing co-regulated genes. / Zhang, Ya; Zha, Hongyuan; Chu, Chao Hisen.

Proceedings ITCC 2005 - International Conference on Information Technology: Coding and Computing. ed. / H. Selvaraj; P.K. Srimani. 2005. p. 32-37 (International Conference on Information Technology: Coding and Computing, ITCC; Vol. 1).

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

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Zhang Y, Zha H, Chu CH. A time-series biclustering algorithm for revealing co-regulated genes. In Selvaraj H, Srimani PK, editors, Proceedings ITCC 2005 - International Conference on Information Technology: Coding and Computing. 2005. p. 32-37. (International Conference on Information Technology: Coding and Computing, ITCC).