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Discovering functional transcription-factor combinations in the human cell cycle
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| Zeitschriftentitel: | Genome Research |
|---|---|
| Personen und Körperschaften: | , , |
| In: | Genome Research, 15, 2005, 6, S. 848-855 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Cold Spring Harbor Laboratory
|
| Schlagwörter: |
| author_facet |
Zhu, Zhou Shendure, Jay Church, George M. Zhu, Zhou Shendure, Jay Church, George M. |
|---|---|
| author |
Zhu, Zhou Shendure, Jay Church, George M. |
| spellingShingle |
Zhu, Zhou Shendure, Jay Church, George M. Genome Research Discovering functional transcription-factor combinations in the human cell cycle Genetics (clinical) Genetics |
| author_sort |
zhu, zhou |
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Zhu, Zhou Shendure, Jay Church, George M. 1088-9051 Cold Spring Harbor Laboratory Genetics (clinical) Genetics http://dx.doi.org/10.1101/gr.3394405 <jats:p>With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G<jats:sub>2</jats:sub>-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes.</jats:p> Discovering functional transcription-factor combinations in the human cell cycle Genome Research |
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| title |
Discovering functional transcription-factor combinations in the human cell cycle |
| title_unstemmed |
Discovering functional transcription-factor combinations in the human cell cycle |
| title_full |
Discovering functional transcription-factor combinations in the human cell cycle |
| title_fullStr |
Discovering functional transcription-factor combinations in the human cell cycle |
| title_full_unstemmed |
Discovering functional transcription-factor combinations in the human cell cycle |
| title_short |
Discovering functional transcription-factor combinations in the human cell cycle |
| title_sort |
discovering functional transcription-factor combinations in the human cell cycle |
| topic |
Genetics (clinical) Genetics |
| url |
http://dx.doi.org/10.1101/gr.3394405 |
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2005 |
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848-855 |
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<jats:p>With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G<jats:sub>2</jats:sub>-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes.</jats:p> |
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| author | Zhu, Zhou, Shendure, Jay, Church, George M. |
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| description | <jats:p>With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G<jats:sub>2</jats:sub>-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes.</jats:p> |
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| spelling | Zhu, Zhou Shendure, Jay Church, George M. 1088-9051 Cold Spring Harbor Laboratory Genetics (clinical) Genetics http://dx.doi.org/10.1101/gr.3394405 <jats:p>With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G<jats:sub>2</jats:sub>-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes.</jats:p> Discovering functional transcription-factor combinations in the human cell cycle Genome Research |
| spellingShingle | Zhu, Zhou, Shendure, Jay, Church, George M., Genome Research, Discovering functional transcription-factor combinations in the human cell cycle, Genetics (clinical), Genetics |
| title | Discovering functional transcription-factor combinations in the human cell cycle |
| title_full | Discovering functional transcription-factor combinations in the human cell cycle |
| title_fullStr | Discovering functional transcription-factor combinations in the human cell cycle |
| title_full_unstemmed | Discovering functional transcription-factor combinations in the human cell cycle |
| title_short | Discovering functional transcription-factor combinations in the human cell cycle |
| title_sort | discovering functional transcription-factor combinations in the human cell cycle |
| title_unstemmed | Discovering functional transcription-factor combinations in the human cell cycle |
| topic | Genetics (clinical), Genetics |
| url | http://dx.doi.org/10.1101/gr.3394405 |