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. 2015 Jan;43(Database issue):D87-91.
doi: 10.1093/nar/gku1080. Epub 2014 Nov 5.

DBTSS as an Integrative Platform for Transcriptome, Epigenome and Genome Sequence Variation Data

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Free PMC article

DBTSS as an Integrative Platform for Transcriptome, Epigenome and Genome Sequence Variation Data

Ayako Suzuki et al. Nucleic Acids Res. .
Free PMC article

Abstract

DBTSS (http://dbtss.hgc.jp/) was originally constructed as a collection of uniquely determined transcriptional start sites (TSSs) in humans and some other species in 2002. Since then, it has been regularly updated and in recent updates epigenetic information has also been incorporated because such information is useful for characterizing the biological relevance of these TSSs/downstream genes. In the newest release, Release 9, we further integrated public and original single nucleotide variation (SNV) data into our database. For our original data, we generated SNV data from genomic analyses of various cancer types, including 97 lung adenocarcinomas and 57 lung small cell carcinomas from Japanese patients as well as 26 cell lines of lung cancer origin. In addition, we obtained publically available SNV data from other cancer types and germline variations in total of 11,322 individuals. With these updates, users can examine the association between sequence variation pattern in clinical lung cancers with its corresponding TSS-seq, RNA-seq, ChIP-seq and BS-seq data. Consequently, DBTSS is no longer a mere storage site for TSS information but has evolved into an integrative platform of a variety of genome activity data.

Figures

Figure 1.
Figure 1.
Basic usage. (A) Top page of DBTSS. A simple search for ‘TSS Viewer’ and ‘Genome Viewer’ can be made by specifying a keyword, such as a gene name ‘BRAF’ in the Database Search at the left frame (red box). Search by ‘SNV Summary in Cancers’ and ‘Pathway Map’ can be made from the positions indicated by orange and purple boxes, respectively. (B) A part of the TSS Viewer display for the BRAF gene. The overview and the detailed positions of the TSSs are shown in the upper and lower panels, respectively. Many of the fields are expandable. (C) The default display of Genome Viewer for the BRAF gene. Displayed items are as indicated in the margin. The displayed items can be controlled from the panels located under the ‘Select track items’ headline. (D) A sample output of SNV information for the BRAF gene. Surrounding region of a previously reported cancer driver mutation (V600E of the BRAF gene; highlighted in red box), is displayed.
Figure 2.
Figure 2.
Other useful information. (A) Upper panel: A part of the Mutation frequency table for the BRAF gene. Enriched fields are as highlighted; lower panel: Summary of multi-omics data mainly collected from cell lines. (B) Pathway Map representation of characteristic genes. In this example, gene expression level (in RPKM) of node genes in a lung adenocarcinoma cell line, LC2/ad, in the ErbB/HER signaling pathway is shown. Further links will appear when the users click the circle corresponding to each gene.

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References

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