Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation
Novel computational methods for finding transcription factor binding motifs have long been sought due to tedious work of experimentally identifying them. However, the current prevailing methods yield a large number of false positive predictions due to the short, variable nature of transcriptional fa...
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| Format: | Journal Article |
| Language: | English |
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2013
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| Online Access: | https://hdl.handle.net/10356/99457 http://hdl.handle.net/10220/17264 |
| _version_ | 1824453642772545536 |
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| author | Jia, Hui. Li, Jinming. |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Jia, Hui. Li, Jinming. |
| author_sort | Jia, Hui. |
| collection | NTU |
| description | Novel computational methods for finding transcription factor binding motifs have long been sought due to tedious work of experimentally identifying them. However, the current prevailing methods yield a large number of false positive predictions due to the short, variable nature of transcriptional factor binding sites (TFBSs). We proposed here a method that combines sequence overrepresentation and cross-species sequence conservation to detect TFBSs in upstream regions of a given set of coregulated genes. We applied the method to 35 S. cerevisiae transcriptional factors with known DNA binding motifs (with the support of orthologous sequences from genomes of S. mikatae, S. bayanus, and S. paradoxus), and the proposed method outperformed the single-genome-based motif finding methods MEME and AlignACE as well as the multiple-genome-based methods PHYME and Footprinter for the majority of these transcriptional factors. Compared with the prevailing motif finding software, our method has some advantages in finding transcriptional factor binding motifs for potential coregulated genes if the gene upstream sequences of multiple closely related species are available. Although we used yeast genomes to assess our method in this study, it might also be applied to other organisms if suitable related species are available and the upstream sequences of coregulated genes can be obtained for the multiple closely related species. |
| first_indexed | 2025-02-19T03:09:40Z |
| format | Journal Article |
| id | ntu-10356/99457 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T03:09:40Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | ntu-10356/994572023-02-28T17:04:32Z Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation Jia, Hui. Li, Jinming. School of Biological Sciences DRNTU::Science::Biological sciences Novel computational methods for finding transcription factor binding motifs have long been sought due to tedious work of experimentally identifying them. However, the current prevailing methods yield a large number of false positive predictions due to the short, variable nature of transcriptional factor binding sites (TFBSs). We proposed here a method that combines sequence overrepresentation and cross-species sequence conservation to detect TFBSs in upstream regions of a given set of coregulated genes. We applied the method to 35 S. cerevisiae transcriptional factors with known DNA binding motifs (with the support of orthologous sequences from genomes of S. mikatae, S. bayanus, and S. paradoxus), and the proposed method outperformed the single-genome-based motif finding methods MEME and AlignACE as well as the multiple-genome-based methods PHYME and Footprinter for the majority of these transcriptional factors. Compared with the prevailing motif finding software, our method has some advantages in finding transcriptional factor binding motifs for potential coregulated genes if the gene upstream sequences of multiple closely related species are available. Although we used yeast genomes to assess our method in this study, it might also be applied to other organisms if suitable related species are available and the upstream sequences of coregulated genes can be obtained for the multiple closely related species. Published version 2013-11-05T05:36:03Z 2019-12-06T20:07:42Z 2013-11-05T05:36:03Z 2019-12-06T20:07:42Z 2012 2012 Journal Article Jia, H., & Li, J. (2012). Finding Transcription Factor Binding Motifs for Coregulated Genes by Combining Sequence Overrepresentation with Cross-Species Conservation. Journal of Probability and Statistics, 2012,1-18. https://hdl.handle.net/10356/99457 http://hdl.handle.net/10220/17264 10.1155/2012/830575 en Journal of probability and statistics © 2012 The Authors. This paper was published in Journal of Probability and Statistics and is made available as an electronic reprint (preprint) with permission of the authors. The paper can be found at the following official DOI: [http://dx.doi.org/10.1155/2012/830575]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. application/pdf |
| spellingShingle | DRNTU::Science::Biological sciences Jia, Hui. Li, Jinming. Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation |
| title | Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation |
| title_full | Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation |
| title_fullStr | Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation |
| title_full_unstemmed | Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation |
| title_short | Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation |
| title_sort | finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross species conservation |
| topic | DRNTU::Science::Biological sciences |
| url | https://hdl.handle.net/10356/99457 http://hdl.handle.net/10220/17264 |
| work_keys_str_mv | AT jiahui findingtranscriptionfactorbindingmotifsforcoregulatedgenesbycombiningsequenceoverrepresentationwithcrossspeciesconservation AT lijinming findingtranscriptionfactorbindingmotifsforcoregulatedgenesbycombiningsequenceoverrepresentationwithcrossspeciesconservation |