DBKERO

Quick-start: For the bignners

Release 1.2 Updated (Oct. 11, 2019)
Based on UCSC hg38, mm10
Formerly DBTSS

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Overview movie 1 in Japanese (9 min.)

Overview movie 2 in Japanese (53 min.)
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About this database

Welcome to DBKERO: The DataBase of Kashiwa Encyclopedia of Researches of multi-Omics data,

This database consists of various tools that are useful for the analysis of gene expression and their regulation, along with various collected data of genome, epigenome and transcriptome that were generated in Japan.

The tools are:

1, TSS-Viewer (formerly DBTSS): This tool displays transcriptional start sites (TSS) of various cells and tissues along the genome coordinates so that one can compare the promotor usage among the cells and tissues.

2, Multi-Omics-Viewer: A Genome Browser like tool that can display gene structures, genome variations, epigenetic modifications and gene expressions along the genome coordinates. You can freely choose display items from the list of our data. Also, you can upload your bed file for display.

3, Mutation Enriched Genes: By your choice of a dataset, this tool displays top 1000 genes that show enrichment of somatic mutation within the gene in descending order with the link to Multi-Omics-Viewer.

4, TF Binding Site Search: This tool shows predicted transcriptional factor binding sits of a stretch of the genome region of human, mouse, rat, nematode, fruit fry or yeast. Powered by Chip-Atlas* and GGGenome**.

5, Pathway Map: Choose one map from 45 maps of Cell Signaling Company or from 242 maps of KEGG in the list table, then choose a dataset and the type of the data using the pulldown menu. You can see each gene in the map that is colored according to the level of expression or to the level of modification depending on your choice of the type of data.

6, Chromatin-status Data Summary: An overview of the expression level or the modification level of a short region of the human genome among the entire datasets within our database. The short region can be chosen by the coordinates of the genome, SNP position or by a mutation position of a gene in COSMIC.

7, SNV Summary in Cancers: Searching by key words, you will get a list of genes that have a link to mutation frequency table of all cancer datasets within this database as well as the gene expression level and the gene modification table of 26 lung cancer cell-lines.

8, RDF gate: The link to the list of DBCLS RDF schema, RDF Browser and Sparql Endpoint.

Contact us
We welcome your comments and feedback about our database. Please feel free to contact us (ysuzuki´╝áims.u-tokyo.ac.jp)......