Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies

Yuriy L. Orlov; Mikael Huss; Roy Joseph; Han Xu; Vinsensius B. Vega; Yew K. Lee; Wee S. Goh; Jane S. Thomsen; Edwin Cheung; Neil D. Clarke; Huck H. Ng

doi:10.1145/1531780.1531784

Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies

Yuriy L. Orlov, Mikael Huss, Roy Joseph, Han Xu, Vinsensius B. Vega, Yew K. Lee, Wee S. Goh, Jane S. Thomsen, Edwin Cheung, Neil D. Clarke, Huck H. Ng

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

2 Scopus citations

Abstract

Genome-wide identification of transcription factor binding sites and gene regulatory elements is an important problem of computational genomics. Advances in high-throughput sequencing technologies combined with chromatin immunoprecipitation, such as ChIP-on-chip, ChIP-seq and ChIPPET (Paired-End diTag) allow us to map transcription factor binding sites (TFBS) and analyze mechanisms of gene regulation on the level of the entire genome. Examples include Oct4, Sox2, Nanog and 10 other transcription factors in mouse, and p53, c-Myc, ER, FoxA1 in human. Clustering of multiple binding sites by different TF reveals potential enhancer regions in mammalian genome. We discuss here statistical analysis of data mapping quality, sensitivity and specificity issues of the ChIP-seq TFBS sets and downstream gene expression analysis.

Original language	English (US)
Title of host publication	Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009
Publisher	Association for Computing Machinery, Inc
Pages	11-18
Number of pages	8
ISBN (Electronic)	9781605585567
DOIs	https://doi.org/10.1145/1531780.1531784
State	Published - May 18 2009
Externally published	Yes
Event	1st Workshop on Breaking Frontiers of Computational Biology, CompBio 2009 - Ischia, Italy Duration: May 18 2009 → May 20 2009

Publication series

Name	Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009

Other

Other	1st Workshop on Breaking Frontiers of Computational Biology, CompBio 2009
Country/Territory	Italy
City	Ischia
Period	5/18/09 → 5/20/09

Keywords

ChIP-seq
Gene expression regulation
Genome-wide statistics
Transcription factor binding sites

ASJC Scopus subject areas

Developmental Biology
Biomedical Engineering
Health Informatics

Access to Document

10.1145/1531780.1531784

Cite this

Orlov, Y. L., Huss, M., Joseph, R., Xu, H., Vega, V. B., Lee, Y. K., Goh, W. S., Thomsen, J. S., Cheung, E., Clarke, N. D., & Ng, H. H. (2009). Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies. In Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009 (pp. 11-18). (Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009). Association for Computing Machinery, Inc. https://doi.org/10.1145/1531780.1531784

Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies. / Orlov, Yuriy L.; Huss, Mikael; Joseph, Roy et al.
Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009. Association for Computing Machinery, Inc, 2009. p. 11-18 (Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009).

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

Orlov, YL, Huss, M, Joseph, R, Xu, H, Vega, VB, Lee, YK, Goh, WS, Thomsen, JS, Cheung, E, Clarke, ND & Ng, HH 2009, Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies. in Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009. Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009, Association for Computing Machinery, Inc, pp. 11-18, 1st Workshop on Breaking Frontiers of Computational Biology, CompBio 2009, Ischia, Italy, 5/18/09. https://doi.org/10.1145/1531780.1531784

Orlov YL, Huss M, Joseph R, Xu H, Vega VB, Lee YK et al. Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies. In Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009. Association for Computing Machinery, Inc. 2009. p. 11-18. (Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009). doi: 10.1145/1531780.1531784

Orlov, Yuriy L. ; Huss, Mikael ; Joseph, Roy et al. / Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies. Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009. Association for Computing Machinery, Inc, 2009. pp. 11-18 (Computing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009).

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AU - Xu, Han

AU - Vega, Vinsensius B.

AU - Lee, Yew K.

AU - Goh, Wee S.

AU - Thomsen, Jane S.

AU - Cheung, Edwin

AU - Clarke, Neil D.

AU - Ng, Huck H.

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AB - Genome-wide identification of transcription factor binding sites and gene regulatory elements is an important problem of computational genomics. Advances in high-throughput sequencing technologies combined with chromatin immunoprecipitation, such as ChIP-on-chip, ChIP-seq and ChIPPET (Paired-End diTag) allow us to map transcription factor binding sites (TFBS) and analyze mechanisms of gene regulation on the level of the entire genome. Examples include Oct4, Sox2, Nanog and 10 other transcription factors in mouse, and p53, c-Myc, ER, FoxA1 in human. Clustering of multiple binding sites by different TF reveals potential enhancer regions in mammalian genome. We discuss here statistical analysis of data mapping quality, sensitivity and specificity issues of the ChIP-seq TFBS sets and downstream gene expression analysis.

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Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies

Abstract

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Keywords

ASJC Scopus subject areas

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