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Frequency distribution of TATA Box and extension sequences on human promoters

BACKGROUND: TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear. RESULTS: In this study, we conduct a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixtee...

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Detalles Bibliográficos
Autores principales: Shi, Wei, Zhou, Wanlei
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1780112/
https://www.ncbi.nlm.nih.gov/pubmed/17217512
http://dx.doi.org/10.1186/1471-2105-7-S4-S2
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author Shi, Wei
Zhou, Wanlei
author_facet Shi, Wei
Zhou, Wanlei
author_sort Shi, Wei
collection PubMed
description BACKGROUND: TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear. RESULTS: In this study, we conduct a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixteen TATA elements derived from the TATA Box motif, TATAWAWN, are classified into three distribution patterns: peak, bottom-peak, and bottom. Fourteen TATA extension sequences are predicted to be the new TATA Box elements due to their high motif factors, which indicate their statistical significance. Statistical analysis on the promoters of mice, zebrafish and drosophila melanogaster verifies seven of these elements. It is also observed that the distribution of TATA elements on the promoters of housekeeping genes are very similar with their distribution on the promoters of tissue specific genes in human. CONCLUSION: The dedicated statistical analysis on TATA box and its extension sequences yields new TATA elements. The statistical significance of these elements has been verified on random data sets by calculating their p values.
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spelling pubmed-17801122007-01-24 Frequency distribution of TATA Box and extension sequences on human promoters Shi, Wei Zhou, Wanlei BMC Bioinformatics Research BACKGROUND: TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear. RESULTS: In this study, we conduct a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixteen TATA elements derived from the TATA Box motif, TATAWAWN, are classified into three distribution patterns: peak, bottom-peak, and bottom. Fourteen TATA extension sequences are predicted to be the new TATA Box elements due to their high motif factors, which indicate their statistical significance. Statistical analysis on the promoters of mice, zebrafish and drosophila melanogaster verifies seven of these elements. It is also observed that the distribution of TATA elements on the promoters of housekeeping genes are very similar with their distribution on the promoters of tissue specific genes in human. CONCLUSION: The dedicated statistical analysis on TATA box and its extension sequences yields new TATA elements. The statistical significance of these elements has been verified on random data sets by calculating their p values. BioMed Central 2006-12-12 /pmc/articles/PMC1780112/ /pubmed/17217512 http://dx.doi.org/10.1186/1471-2105-7-S4-S2 Text en Copyright © 2006 Shi and Zhou; licensee BioMed Central Ltd http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Shi, Wei
Zhou, Wanlei
Frequency distribution of TATA Box and extension sequences on human promoters
title Frequency distribution of TATA Box and extension sequences on human promoters
title_full Frequency distribution of TATA Box and extension sequences on human promoters
title_fullStr Frequency distribution of TATA Box and extension sequences on human promoters
title_full_unstemmed Frequency distribution of TATA Box and extension sequences on human promoters
title_short Frequency distribution of TATA Box and extension sequences on human promoters
title_sort frequency distribution of tata box and extension sequences on human promoters
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1780112/
https://www.ncbi.nlm.nih.gov/pubmed/17217512
http://dx.doi.org/10.1186/1471-2105-7-S4-S2
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