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DBTSS: database of transcription start sites, progress report 2008.

Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K - Nucleic Acids Res. (2007)

Bottom Line: In this update, we expanded the human transcriptional start site dataset by 19 million uniquely mapped, and RefSeq-associated, 5'-end sequences, which were generated by a newly introduced Solexa sequencer.Moreover, in order to provide means for interpreting those massive TSS data, we implemented two new analytical tools: one for connecting expression information with predicted transcription factor binding sites; the other for examining evolutionary conservation or species-specificity of promoters and transcripts, which can be browsed by our own comparative genome viewer.With the expanded dataset and the enhanced functionalities, DBTSS provides a unique platform that enables in-depth transcriptome analyses.

View Article: PubMed Central - PubMed

Affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

ABSTRACT
DBTSS is a database of transcriptional start sites, based on our unique collection of precise, experimentally determined 5'-end sequences of full-length cDNAs. Since its first release in 2002, several major updates have been made. In this update, we expanded the human transcriptional start site dataset by 19 million uniquely mapped, and RefSeq-associated, 5'-end sequences, which were generated by a newly introduced Solexa sequencer. Moreover, in order to provide means for interpreting those massive TSS data, we implemented two new analytical tools: one for connecting expression information with predicted transcription factor binding sites; the other for examining evolutionary conservation or species-specificity of promoters and transcripts, which can be browsed by our own comparative genome viewer. With the expanded dataset and the enhanced functionalities, DBTSS provides a unique platform that enables in-depth transcriptome analyses. DBTSS is accessible at http://dbtss.hgc.jp/.

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Screenshot from the search engine for enrichment of the putative transcription factor binding sites (A). The figure exemplifies the search for common TF binding sites appearing in the promoters of genes with which more than 10 Solexa sequences are associated and the relative expression levels are more than 2-fold elevated both by the 1 μm trichostatin A treatment and by the 1 μm wortmannin treatment (B). From the resultant list of the enriched sites, the link can be followed to the main viewer to retrieve further detailed information (C).
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Figure 2: Screenshot from the search engine for enrichment of the putative transcription factor binding sites (A). The figure exemplifies the search for common TF binding sites appearing in the promoters of genes with which more than 10 Solexa sequences are associated and the relative expression levels are more than 2-fold elevated both by the 1 μm trichostatin A treatment and by the 1 μm wortmannin treatment (B). From the resultant list of the enriched sites, the link can be followed to the main viewer to retrieve further detailed information (C).

Mentions: In addition to the incorporation of the MCF7 expression data, we implemented an analytical tool. This analytical tool looks for putative transcription factor binding sites commonly occurring in the promoters, which show similar behaviors on various drug perturbations. It is assumed that those promoters should be under the regulations of similar transcription factors, thus, containing particular transcription factor binding sites in common. As shown in Figure 2, as for the user-specified group of promoters or promoters which satisfy some specified search conditions on the expression profiles, transcription factor binding sites are predicted by the matrix search of the TRANFAC database (12) under any cut-off values. The degree of enrichment of the predicted transcription factor binding sites is evaluated assuming the hypergeometric distributions. Thereby, the enriched binding sites are listed and users can further retrieve the information regarding in which promoters and in which part of them these sites are located. Although the MCF7 dataset is currently the only resource of the expression data, we will further expand the dataset to cover expression profiles in various cell types and conditions. Moreover, further increases in the amount of the Solexa data for TSS determination themselves will enrich the source of expression information. Such data will directly couple the positional information within promoters with the changes of expression levels, as the latter should be represented by the number of allocated sequences.Figure 2.


DBTSS: database of transcription start sites, progress report 2008.

Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K - Nucleic Acids Res. (2007)

Screenshot from the search engine for enrichment of the putative transcription factor binding sites (A). The figure exemplifies the search for common TF binding sites appearing in the promoters of genes with which more than 10 Solexa sequences are associated and the relative expression levels are more than 2-fold elevated both by the 1 μm trichostatin A treatment and by the 1 μm wortmannin treatment (B). From the resultant list of the enriched sites, the link can be followed to the main viewer to retrieve further detailed information (C).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238895&req=5

Figure 2: Screenshot from the search engine for enrichment of the putative transcription factor binding sites (A). The figure exemplifies the search for common TF binding sites appearing in the promoters of genes with which more than 10 Solexa sequences are associated and the relative expression levels are more than 2-fold elevated both by the 1 μm trichostatin A treatment and by the 1 μm wortmannin treatment (B). From the resultant list of the enriched sites, the link can be followed to the main viewer to retrieve further detailed information (C).
Mentions: In addition to the incorporation of the MCF7 expression data, we implemented an analytical tool. This analytical tool looks for putative transcription factor binding sites commonly occurring in the promoters, which show similar behaviors on various drug perturbations. It is assumed that those promoters should be under the regulations of similar transcription factors, thus, containing particular transcription factor binding sites in common. As shown in Figure 2, as for the user-specified group of promoters or promoters which satisfy some specified search conditions on the expression profiles, transcription factor binding sites are predicted by the matrix search of the TRANFAC database (12) under any cut-off values. The degree of enrichment of the predicted transcription factor binding sites is evaluated assuming the hypergeometric distributions. Thereby, the enriched binding sites are listed and users can further retrieve the information regarding in which promoters and in which part of them these sites are located. Although the MCF7 dataset is currently the only resource of the expression data, we will further expand the dataset to cover expression profiles in various cell types and conditions. Moreover, further increases in the amount of the Solexa data for TSS determination themselves will enrich the source of expression information. Such data will directly couple the positional information within promoters with the changes of expression levels, as the latter should be represented by the number of allocated sequences.Figure 2.

Bottom Line: In this update, we expanded the human transcriptional start site dataset by 19 million uniquely mapped, and RefSeq-associated, 5'-end sequences, which were generated by a newly introduced Solexa sequencer.Moreover, in order to provide means for interpreting those massive TSS data, we implemented two new analytical tools: one for connecting expression information with predicted transcription factor binding sites; the other for examining evolutionary conservation or species-specificity of promoters and transcripts, which can be browsed by our own comparative genome viewer.With the expanded dataset and the enhanced functionalities, DBTSS provides a unique platform that enables in-depth transcriptome analyses.

View Article: PubMed Central - PubMed

Affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

ABSTRACT
DBTSS is a database of transcriptional start sites, based on our unique collection of precise, experimentally determined 5'-end sequences of full-length cDNAs. Since its first release in 2002, several major updates have been made. In this update, we expanded the human transcriptional start site dataset by 19 million uniquely mapped, and RefSeq-associated, 5'-end sequences, which were generated by a newly introduced Solexa sequencer. Moreover, in order to provide means for interpreting those massive TSS data, we implemented two new analytical tools: one for connecting expression information with predicted transcription factor binding sites; the other for examining evolutionary conservation or species-specificity of promoters and transcripts, which can be browsed by our own comparative genome viewer. With the expanded dataset and the enhanced functionalities, DBTSS provides a unique platform that enables in-depth transcriptome analyses. DBTSS is accessible at http://dbtss.hgc.jp/.

Show MeSH