KERO
Release 1.0 Updated (Jul. 9, 2015)
Based on UCSC hg38, mm10
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  About this database

Welcome to KERO.

To support transcriptional regulation studies, we have constructed the KERO, which represents exact positions of transcriptional start sites (TSSs) in the genome based on our unique experimentally validated TSS sequencing method, TSS-seq.

This database includes TSS data of a major part of human adult and embryonic tissues are covered. KERO now contains 491 million TSS tag sequences for collected from a total of 20 tissues and 7 cell cultures. We also integrated our newly generated RNA-seq data of subcellular- fractionated RNAs and ChIP-seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. We also included recently accumulating external epigenomic data, such as chromatin map of the ENCODE project.

In this update, we further associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions.

It is believed that single nucleotide variations (SNVs) in the transcriptional regulatory regions are responsible for many human diseases, including cancers. However, it remains difficult to identify functionally relevant SNVs from those having no explicit biological consequences. In this version of KERO, we attempt to associate SNVs with the omics information of the surrounding regions. We used SNVs which we identified from genomic analyses of various types of cancers, including somatic mutations of 100 lung adenocarcinoma and lung small cell carcinoma. For germline variations, we used SNVs in dbSNP as well as our unique dataset of variations in 1000 Japanese individuals. We integrated those SNV information with our original datasets of TSS-seq, RNA-seq, ChIP-seq of representative histone modifications and Bisulfite Sequencing of cytosine methylations of DNA. Particular, we present multi-omics data of 26 lung adenocarcinoma cells line for which TSS-seq, RNA-seq, ChIP-seq and BS-seq together with whole genome sequencing are collected from the same materials. We further connected the multi-omics data of model organisms by genome-genome alignment. We provide a unique data resource to investigate what genomic features are observed in a particular genomic coordinates in a wide variety of samples.

These data can be browsed in our new viewer which also supports versatile search conditions of users. We believe new KERO is helpful to understand biological consequences of the massively identified TSSs and identify human genetic valuations which are associated with disordered transcriptional regulations.



  References  

Suzuki A, Wakaguri H, Yamashita R, Kawano S, Tsuchihara K, Sugano S, Suzuki Y, Nakai K. DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. Nucleic Acids Res. 2015 (Database issue) 43 (D1): D1-D5.

Suzuki A, Mimaki S, Yamane Y, Kawase A, Matsushima K, Suzuki M, Goto K, Sugano S, Esumi H, Suzuki Y, Tsuchihara K. Identification and characterization of cancer mutations in Japanese lung adenocarcinoma without sequencing of normal tissue counterparts. PLoS One. 2013 Sep 12;8(9).

Yamashita R, Sathira NP, Kanai A, Tanimoto K, Arauchi T, Tanaka Y, Hashimoto S, Sugano S, Nakai K, Suzuki Y. (2011) Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res. 2011 Mar 3.

Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto S, Matsushima K, Mizushima-Sugano J, Yamashita R, Nakai K, Bentley D, Esumi H and Sugano S. (2009) Massive transcriptoional start site analysis of human genes in hypoxia cells. Nucleic Acids Res. 2009 Feb 22.

[Japanese]
"Database Manual" (Yodosha)



  Contact us
We welcome your comments and feedback about our database.
Please feel free to contact us......


News
  • 20 Apr. 2016: New HBZ over-expressed mouse data are now available. Raw data accession: DRA003229 and DRA003744(Genome Shien).


  • 27 Jan. 2016: New CD4Tcell/Bcell/EScell data of mouse are now available. Raw data accession: GSE73825 (Genome Shien).


  • 30 Nov. 2015: New Germ Cell Methylation data of mouse are now available. Raw data accession: DRA000484 and DRA000607 (Genome Shien).


  • 10 Nov. 2015: New granulocyte macrophage progenitors (GMPs) data of mouse are now available. Raw data accession: DRA000485, DRA000486, DRA000487, DRA000488 and DRA000858 (Genome Shien).


  • 10 Sep. 2015: New Reg1[-/-],Roquin[San/San] data of mouse embryonic fibroblasts are now available. Raw data accession: DRA003234(Genome Shien).


  • 20 Aug. 2015: New T helper cell data of mouse are now available. Raw data accession: GSE51079 and GSE28292 (Genome Shien).


  • 20 Aug. 2015: New CLOCK related data of mouse liver are now available. Raw data accession: DRA001050 and DRA001278(Genome Shien).


  • 09 Jul. 2015: New T helper cell data of mouse are now available. Raw data accession: DRA000928, DRA001102 and SRP007894 (Genome Shien).


  • 30 Jun. 2015: New BRIC-Seq data (UPF1 RNAi) are now available. Raw data accession: DRA000591 (Genome Shien).


  • 15 Sep. 2014: New DBTSS opened.


NBDC This database has been supported by the framework of National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST).

Kakenhi KERO is financially supported with a Grant-in-Aid for Publication of Scientific Research Results (Databases) by Japan Society for the Promotion of Science, a Grant-in-aid for Scientific Research on Innovative Areas 'Genome Science' [221S0002] from the Ministry of Education, Culture, Sports, Science and Technology of Japan

Copyright © 2001-2016 Yutaka Suzuki, the University of Tokyo, Japan. All rights reserved.
No reproduction or republication without permission.