Biclustering of time series microarray data

Jia Meng; Yufei Huang

doi:10.1007/978-1-61779-400-1_6

Biclustering of time series microarray data

Jia Meng, Yufei Huang^*

^*Corresponding author for this work

Research output: Chapter in Book or Report/Conference proceeding › Chapter › peer-review

2 Citations (Scopus)

Abstract

Clustering is a popular data exploration technique widely used in microarray data analysis. In this chapter, we review ideas and algorithms of bicluster and its applications in time series microarray analysis. We introduce first the concept and importance of biclustering and its different variations. We then focus our discussion on the popular iterative signature algorithm (ISA) for searching biclusters in microarray dataset. Next, we discuss in detail the enrichment constraint time-dependent ISA (ECTDISA) for identifying biologically meaningful temporal transcription modules from time series microarray dataset. In the end, we provide an example of ECTDISA application to time series microarray data of Kaposi's Sarcoma-associated Herpesvirus (KSHV) infection.

Original language	English
Title of host publication	Next Generation Microarray Bioinformatics
Subtitle of host publication	Methods and Protocols
Editors	Junbai Wang, Tianhai Tian, Aik Choon Tan
Pages	87-100
Number of pages	14
DOIs	https://doi.org/10.1007/978-1-61779-400-1_6
Publication status	Published - 2012
Externally published	Yes

Publication series

Name	Methods in Molecular Biology
Volume	802
ISSN (Print)	1064-3745

Keywords

Bicluster
Clustering
Enrichment constrained
Iterative signature algorithm
Microarray
Temporal module
Time dependent
Time series

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10.1007/978-1-61779-400-1_6

Cite this

Meng, J., & Huang, Y. (2012). Biclustering of time series microarray data. In J. Wang, T. Tian, & A. C. Tan (Eds.), Next Generation Microarray Bioinformatics: Methods and Protocols (pp. 87-100). (Methods in Molecular Biology; Vol. 802). https://doi.org/10.1007/978-1-61779-400-1_6

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abstract = "Clustering is a popular data exploration technique widely used in microarray data analysis. In this chapter, we review ideas and algorithms of bicluster and its applications in time series microarray analysis. We introduce first the concept and importance of biclustering and its different variations. We then focus our discussion on the popular iterative signature algorithm (ISA) for searching biclusters in microarray dataset. Next, we discuss in detail the enrichment constraint time-dependent ISA (ECTDISA) for identifying biologically meaningful temporal transcription modules from time series microarray dataset. In the end, we provide an example of ECTDISA application to time series microarray data of Kaposi's Sarcoma-associated Herpesvirus (KSHV) infection.",

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KW - Iterative signature algorithm

KW - Microarray

KW - Temporal module

KW - Time dependent

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Biclustering of time series microarray data

Abstract

Publication series

Keywords

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