Identification of yeast cell cycle transcription factors using dynamic system model

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

Abstract

To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs) that regulate the expression of cell cycle-regulated genes. We developed a method to identify cell cycle TFs in yeast by integrating current ChIP-chip, mutant, transcription factor binding site (TFBS), and cell cycle gene expression data. We identified 17 cell cycle TFs, 12 of which are known cell cycle TFs, while the remaining five (Ash1, Rlm1, Ste12, Stp1, Tec1) are putative novel cell cycle TFs. Several lines of evidence are provided to verify our predictions. Besides, a high confidence TF-gene regulatory matrix is derived as a byproduct of our method. Moreover, we show that our method performs better than four existing methods for identifying yeast cell cycle TFs. Finally, an application of our method to different cell cycle gene expression datasets suggests that our method is robust.

Original languageEnglish
Title of host publication2010 IEEE Workshop on Signal Processing Systems, SiPS 2010 - Proceedings
Pages210-215
Number of pages6
DOIs
Publication statusPublished - 2010 Dec 27
Event2010 IEEE Workshop on Signal Processing Systems, SiPS 2010 - San Francisco, CA, United States
Duration: 2010 Oct 62010 Oct 8

Publication series

NameIEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation
ISSN (Print)1520-6130

Other

Other2010 IEEE Workshop on Signal Processing Systems, SiPS 2010
CountryUnited States
CitySan Francisco, CA
Period10-10-0610-10-08

Fingerprint

Transcription factors
Cell Cycle
Transcription Factor
Yeast
Dynamic Systems
Dynamical systems
Cells
Model
Gene expression
Chip
Genes
Gene
Binding sites
Gene Expression Data
Mutant
Gene Expression
Confidence
Byproducts
Verify

All Science Journal Classification (ASJC) codes

  • Electrical and Electronic Engineering
  • Signal Processing
  • Applied Mathematics
  • Hardware and Architecture

Cite this

Wu, W-S. (2010). Identification of yeast cell cycle transcription factors using dynamic system model. In 2010 IEEE Workshop on Signal Processing Systems, SiPS 2010 - Proceedings (pp. 210-215). [5624789] (IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation). https://doi.org/10.1109/SIPS.2010.5624789
Wu, Wei-Sheng. / Identification of yeast cell cycle transcription factors using dynamic system model. 2010 IEEE Workshop on Signal Processing Systems, SiPS 2010 - Proceedings. 2010. pp. 210-215 (IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation).
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Wu, W-S 2010, Identification of yeast cell cycle transcription factors using dynamic system model. in 2010 IEEE Workshop on Signal Processing Systems, SiPS 2010 - Proceedings., 5624789, IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation, pp. 210-215, 2010 IEEE Workshop on Signal Processing Systems, SiPS 2010, San Francisco, CA, United States, 10-10-06. https://doi.org/10.1109/SIPS.2010.5624789

Identification of yeast cell cycle transcription factors using dynamic system model. / Wu, Wei-Sheng.

2010 IEEE Workshop on Signal Processing Systems, SiPS 2010 - Proceedings. 2010. p. 210-215 5624789 (IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation).

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

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Wu W-S. Identification of yeast cell cycle transcription factors using dynamic system model. In 2010 IEEE Workshop on Signal Processing Systems, SiPS 2010 - Proceedings. 2010. p. 210-215. 5624789. (IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation). https://doi.org/10.1109/SIPS.2010.5624789