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. 2004 Jan 1;32(Database issue):D78-81.
doi: 10.1093/nar/gkh076.

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004

Yutaka Suzuki  1 , Riu Yamashita, Sumio Sugano, Kenta Nakai
Affiliations

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004

Yutaka Suzuki et al. Nucleic Acids Res. .

Abstract

DBTSS (http://dbtss.hgc.jp) was originally constructed based on a collection of experimentally determined TSSs of human genes. Since its first release in 2002, it has been updated several times. First, the amount of stored data has increased significantly: e.g. the number of clones that match both the RefSeq mRNA set and the genome sequence has increased from 111,382 to 190,964, now covering 1,234 genes. Second, the positions of SNPs in dbSNP were displayed on the upstream regions of contained human genes. Third, DBTSS now covers other species such as mouse and the human malaria parasite. It will become a central database containing data for many more species with oligo-capping and related methods. Lastly, the database now serves for comparative promoter analyses: in the current version, comparative views of potentially orthologous promoters from human and mouse are presented with an additional function of searching potential transcription-factor binding sites, which are either conserved or diverged between species.

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Figures

Figure 1
Figure 1
Example of the output of a human gene including the correspondence with a mouse gene, gene position in the chromosome, comparison with Ensembl and RefSeq data, SNP positions and graphical representations of one-path cDNA clones.
Figure 2
Figure 2
A comparative view of human and mouse promoters. (a) Global view with potential transcription factor binding sites. Locally similar sequence segments are shown in boxes and the corresponding boxes are represented by the same number (e.g. ‘0’). (b) More detailed view around the corresponding TSSs.
Figure 2
Figure 2
A comparative view of human and mouse promoters. (a) Global view with potential transcription factor binding sites. Locally similar sequence segments are shown in boxes and the corresponding boxes are represented by the same number (e.g. ‘0’). (b) More detailed view around the corresponding TSSs.
See this image and copyright information in PMC

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References

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