ZENBU statistics

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Protocols

ZENBU specifications

Information


Unique identifier OMICS_03444
Name ZENBU
Interface Web user interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Programming languages C++, Javascript
Parallelization MapReduce
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline nicolas.bertin
  • person_outline Alistair Forrest

Publication for ZENBU

ZENBU citations

 (30)
library_books

Maternal 5mCpG Imprints at the PARD6G AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent of Origin Expression Effects in Multiple Human Tissues

2018
Front Genet
PMCID: 5838017
PMID: 29545821
DOI: 10.3389/fgene.2018.00036

[…] ring integrative large-scale functional- and comparative-genomics datasets on gene expression (RNA-Seq, cDNA mapping, active transcriptional start site (TSS) mapping, 5′-cap mapping) using the FANTOM ZENBU Browser (Severin et al., ). In summary, we analyzed secondary data from chromatin immunoprecipitation and DNA sequencing (ChIP-Seq) of 31 histone modification marks in 22 healthy human somatic t […]

library_books

CELSR2 is a candidate susceptibility gene in idiopathic scoliosis

2017
PLoS One
PMCID: 5730153
PMID: 29240829
DOI: 10.1371/journal.pone.0189591

[…] The tissue expression of any genes carrying putative candidate scoliosis risk variants was assessed through the FANTOM5 promoterome browser available at http://fantom.gsc.riken.jp/zenbu/, []. The potential effects of the identified variant were assessed by looking at the SIFT [], PolyPhen [], MutTaster [] and CADD [] scores of each variant. The conservation of the variant was a […]

library_books

Monitoring transcription initiation activities in rat and dog

2017
Sci Data
PMCID: 5704677
PMID: 29182598
DOI: 10.1038/sdata.2017.173

[…] All our data is visualized via our original genome browser ZENBU. Pre-configured views for rat and dog sets can be accessed at these URLs:http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=3eolUxzyN1nm167YHayYLC (rat)http://fantom.gsc.riken.jp/zenbu/gLyphs/#conf […]

library_books

Significance of functional disease causal/susceptible variants identified by whole genome analyses for the understanding of human diseases

2017
PMCID: 5743846
PMID: 29129848
DOI: 10.2183/pjab.93.042

[…] d be checked.Several computer tools for prediction include information regarding the location of SNPs in gene expression regulatory regions (e.g., HaploReg v4.1, Regulome DB, UCSC genome browser, and ZENBU).–) For the prediction of differences in specific TF binding to the variant, TRANSFAC professional can be used.) In vitro functional evaluation of SNPs that are located in gene expression regula […]

library_books

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

2017
Sci Data
PMCID: 5663209
PMID: 29087374
DOI: 10.1038/sdata.2017.163

[…] the expression profile for a sample, or even the expression levels for a single gene across samples, can be visualized, together with dynamic statistics and data pooling operations, via our original ZENBU genome browser (http://fantom.gsc.riken.jp/zenbu/). A tabular version of the expression values for a subset of genes and/or for a subset of samples from the FANTOM5 collection can be obtained fr […]

library_books

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

2017
Sci Data
PMCID: 5625555
PMID: 28972578
DOI: 10.1038/sdata.2017.147

[…] ANTOM5, thus revealing novel and alternative promoters to known genes. We made these data available along with the FANTOM5 CAGE atlas data, as well as ready for manual inspection and analysis via the ZENBU genome browser http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=ZkJi4RdBAFhnsudxePrZxD (see ). […]

Citations

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ZENBU institution(s)
RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Suehiro-cho, Tsurumi-ku, Yokohama, Japan; RIKEN Omics Science Center (OSC), Yokohama, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan; Cancer Science Institute of Singapore, National University of Singapore, Singapore
ZENBU funding source(s)
Supported by a research grant for RIKEN Omics Science Center from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan, Research Grants from MEXT through RIKEN Preventive Medicine and Diagnosis Innovation Program and RIKEN Center for Life Science Technologies, Division of Genomic Technologies.

ZENBU reviews

 (3)
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Anonymous user #688's avatar image No country

Anonymous user #688

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Web
An useful browser which allow to visualise and analyse sequencing dataset "on the fly".
Anonymous user #687's avatar image No country

Anonymous user #687

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Web
Very useful browser. The dynamic data massaging via script offers great possibilities to browse ENCODE data in ways that UCSC does not offer