Finding functional promoter motifs by computational methods: A word of caution

Rajesh Chowdhary; Limsoon Wong; Vladimir B. Bajic

doi:10.1504/IJBRA.2006.010605

Finding functional promoter motifs by computational methods: A word of caution

Rajesh Chowdhary, Limsoon Wong, Vladimir B. Bajic^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

The standard practice in the analysis of promoters is to select promoter regions of convenient length. This may lead to false results when searching for Transcription Factor Binding Sites (TFBSs), since the sequences may contain coding segments. In such cases, motif detection may single out motifs from the coding regions. The mapping of TFBSs to promoters may result in a misleading picture of 'promoter' content. We illustrate these issues using the example of histones H2A and H2B and show how such analysis could be misleading if care is not exercised to eliminate coding regions from the presumed promoter sequences.

Original language	English (US)
Pages (from-to)	282-288
Number of pages	7
Journal	International Journal of Bioinformatics Research and Applications
Volume	2
Issue number	3
DOIs	https://doi.org/10.1504/IJBRA.2006.010605
State	Published - 2006
Externally published	Yes

Keywords

Motifs
Promoter
Transcription Factor Binding Sites (TFBSs)
Transcription Start Sites (TSSs)
Translation Initiation Sites (TIS)

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Clinical Biochemistry
Health Information Management

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title = "Finding functional promoter motifs by computational methods: A word of caution",

abstract = "The standard practice in the analysis of promoters is to select promoter regions of convenient length. This may lead to false results when searching for Transcription Factor Binding Sites (TFBSs), since the sequences may contain coding segments. In such cases, motif detection may single out motifs from the coding regions. The mapping of TFBSs to promoters may result in a misleading picture of 'promoter' content. We illustrate these issues using the example of histones H2A and H2B and show how such analysis could be misleading if care is not exercised to eliminate coding regions from the presumed promoter sequences.",

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AU - Wong, Limsoon

AU - Bajic, Vladimir B.

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N2 - The standard practice in the analysis of promoters is to select promoter regions of convenient length. This may lead to false results when searching for Transcription Factor Binding Sites (TFBSs), since the sequences may contain coding segments. In such cases, motif detection may single out motifs from the coding regions. The mapping of TFBSs to promoters may result in a misleading picture of 'promoter' content. We illustrate these issues using the example of histones H2A and H2B and show how such analysis could be misleading if care is not exercised to eliminate coding regions from the presumed promoter sequences.

AB - The standard practice in the analysis of promoters is to select promoter regions of convenient length. This may lead to false results when searching for Transcription Factor Binding Sites (TFBSs), since the sequences may contain coding segments. In such cases, motif detection may single out motifs from the coding regions. The mapping of TFBSs to promoters may result in a misleading picture of 'promoter' content. We illustrate these issues using the example of histones H2A and H2B and show how such analysis could be misleading if care is not exercised to eliminate coding regions from the presumed promoter sequences.

KW - Motifs

KW - Promoter

KW - Transcription Factor Binding Sites (TFBSs)

KW - Transcription Start Sites (TSSs)

KW - Translation Initiation Sites (TIS)

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JO - International Journal of Bioinformatics Research and Applications

JF - International Journal of Bioinformatics Research and Applications

IS - 3

ER -

Finding functional promoter motifs by computational methods: A word of caution

Abstract

Keywords

ASJC Scopus subject areas

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