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DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.

Ayako Suzuki1, Hiroyuki Wakaguri2, Riu Yamashita3

  • 1Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

Nucleic Acids Research
|November 8, 2014
PubMed
Summary

The DBTSS database now integrates single nucleotide variation (SNV) data with epigenetic information. This allows researchers to explore associations between genetic variations in lung cancer and transcriptional start site (TSS) activity.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • The Database of Transcriptional Start Sites (DBTSS) was established in 2002 to catalog human transcriptional start sites (TSSs).
  • Recent updates incorporated epigenetic data to enhance the characterization of TSSs and their associated genes.
  • DBTSS has evolved into a comprehensive resource for genomic and epigenomic information.

Purpose of the Study:

  • To update the DBTSS database with single nucleotide variation (SNV) data, including both public and original datasets.
  • To integrate diverse genomic and epigenomic data types for comprehensive analysis.
  • To provide a platform for examining the relationship between sequence variations and genome activity in cancer.

Main Methods:

  • Generation of original SNV data from genomic analyses of lung cancer types (adenocarcinoma, small cell carcinoma) and cell lines.
  • Acquisition of public SNV data from various cancer types and germline variations.
  • Integration of SNV data with existing TSS-seq, RNA-seq, ChIP-seq, and BS-seq data within the DBTSS platform.

Main Results:

  • Release 9 of DBTSS now includes extensive SNV data from clinical samples and public sources.
  • The database facilitates the examination of sequence variation patterns in relation to transcriptional start site activity and gene expression.
  • Users can now correlate SNV data with multiple types of genome activity data.

Conclusions:

  • DBTSS has transformed from a simple TSS repository into an integrated platform for diverse genomic data.
  • The updated database enables advanced research into the functional impact of genetic variations in cancer.
  • This resource supports a deeper understanding of genome regulation and its alterations in disease.