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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: 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.

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 the evolutionary conservation of the promoters and transcripts (A). The figure exemplifies the results of the search for promoters for which more than 10 Solexa sequences are associated, the alignable region in the promoters in human–mouse comparison is <300 bp and the overall base substitution of the downstream transcript region is <20% (B). The regions specified between red (one selection) and green (second selection) vertical lines (or one left click) can be magnified up to the sequence level.
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Figure 3: Screenshot from the search engine for the evolutionary conservation of the promoters and transcripts (A). The figure exemplifies the results of the search for promoters for which more than 10 Solexa sequences are associated, the alignable region in the promoters in human–mouse comparison is <300 bp and the overall base substitution of the downstream transcript region is <20% (B). The regions specified between red (one selection) and green (second selection) vertical lines (or one left click) can be magnified up to the sequence level.

Mentions: As shown in Figure 3, our new comparative browser enables users to examine evolutionary conservation of the surrounding regions of TSSs, based on the genomic sequences of various kinds of mammals, such as mice, rats and monkeys, as well as their mutual base-pair alignments from the UCSC Genome Browser (14). Furthermore, users can search for the promoters or transcripts according to the degree of evolutionary conservation, using variable parameters, including the coverage of alignable regions and the base substitution rate therein. Further detailed searches focusing on limited regions of the transcripts, such as UTRs, CDSs or the ‘coding exons’ are also supported. These results are browsed with our new comparative browser, which provides the dynamic magnification from the sequence level to the overview level. This viewer currently supports up to four-way comparisons between four genomes of user's choice.Figure 3.


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 the evolutionary conservation of the promoters and transcripts (A). The figure exemplifies the results of the search for promoters for which more than 10 Solexa sequences are associated, the alignable region in the promoters in human–mouse comparison is <300 bp and the overall base substitution of the downstream transcript region is <20% (B). The regions specified between red (one selection) and green (second selection) vertical lines (or one left click) can be magnified up to the sequence level.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Screenshot from the search engine for the evolutionary conservation of the promoters and transcripts (A). The figure exemplifies the results of the search for promoters for which more than 10 Solexa sequences are associated, the alignable region in the promoters in human–mouse comparison is <300 bp and the overall base substitution of the downstream transcript region is <20% (B). The regions specified between red (one selection) and green (second selection) vertical lines (or one left click) can be magnified up to the sequence level.
Mentions: As shown in Figure 3, our new comparative browser enables users to examine evolutionary conservation of the surrounding regions of TSSs, based on the genomic sequences of various kinds of mammals, such as mice, rats and monkeys, as well as their mutual base-pair alignments from the UCSC Genome Browser (14). Furthermore, users can search for the promoters or transcripts according to the degree of evolutionary conservation, using variable parameters, including the coverage of alignable regions and the base substitution rate therein. Further detailed searches focusing on limited regions of the transcripts, such as UTRs, CDSs or the ‘coding exons’ are also supported. These results are browsed with our new comparative browser, which provides the dynamic magnification from the sequence level to the overview level. This viewer currently supports up to four-way comparisons between four genomes of user's choice.Figure 3.

Bottom Line: 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.

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