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Nucleic Acids Res. 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.

Author information

1
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
2
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
3
Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.
4
Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan.
5
Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.
6
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan knakai@ims.u-tokyo.ac.jp.
7
Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan knakai@ims.u-tokyo.ac.jp.

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.

PMID:
25378318
PMCID:
PMC4383915
DOI:
10.1093/nar/gku1080
[Indexed for MEDLINE]
Free PMC Article

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