ZENBU protocols

View ZENBU computational protocol

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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 No

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Publication for ZENBU

ZENBU in pipelines

 (4)
2017
PMCID: 5592927
PMID: 28720711
DOI: 10.1534/g3.117.044651

[…] assessment of gene function was obtained from the genecards database (www.genecards.org) () and a tissue expression profile was analyzed using the fantom5 database (http://fantom.gsc.riken.jp/zenbu/) (; ). the top 100 transcripts (mapping to 78 unique genes) that correlated with the pulmonary myocardium pca trait were submitted for enrichment analyses and gene ontology (go) using […]

2017
PMCID: 5600399
PMID: 28873399
DOI: 10.1371/journal.pbio.2002887

[…] a strong bias towards developmental functions []. to facilitate future analysis of ashces in developmental regulation, we mapped all ashces to galgal5 and integrated this information into chicken-zenbu (as hce and ashce tracks; label 11 in ). examples of hces and ashces in the msx1 and msx2 loci are shown in . other vertebrate comparative genomics resources, such as the 0.6 million conserved […]

2016
PMCID: 4832459
PMID: 27079381
DOI: 10.1186/s40478-016-0306-7

[…] (version 1.12) [] and mapped to the human genome (build grch37/hg19) using the burrows-wheeler aligner (bwa version 0.5.9) [] allowing up to two mismatches. the resulting bam files were uploaded in zenbu and the tpm normalized expression values of the c9orf72 tsss were downloaded (available in additional file : table s2)., library preparation and creation of the bam files containing mapped […]

2014
PMCID: 4161876
PMID: 25164183
DOI: 10.1186/1471-2164-15-729

[…] []. out of 499 regions, 100 had more tags than the 3rd quartile and 15 had more than 100 tags, an arbitrary cutoff that we chose after visual inspection of the data in fantom5’s instance of the zenbu genomic browser [], which showed that lower scores were enriched for apparently spurious accumulation of tags near pseudogenes., brain tissue was obtained from the institute of neuropathology […]


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ZENBU in publications

 (46)
PMCID: 5838017
PMID: 29545821
DOI: 10.3389/fgene.2018.00036

[…] 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 […]

PMCID: 5849332
PMID: 29494619
DOI: 10.1371/journal.pcbi.1005934

[…] only on the patterns in which parts of the genome are activated in different cell types., the full datasets used for this work are available from the fantom5 data interface at fantom.gsc.riken.jp/zenbu/., genome-wide association studies (gwas) have considerable untapped potential to reveal new mechanisms of disease[]. variants associated with disease are over-represented in regulatory, rather […]

PMCID: 5773682
PMID: 29348432
DOI: 10.1038/s41598-017-18241-w

[…] with <1% frequency in either cases or controls were placed in the “binned” category., we downloaded fantom5 cage rle expression data for hla-dqa1, hla-dqb1, hla-dqa2, hla-dqb2 genes from the zenbu browser: (http://fantom.gsc.riken.jp/zenbu/glyphs/#config = onhzqgf2e5xtmnpsh2gurb), for the “fantom5 cage phase1 ctss human tracks pooled filtered with 3 or more tags per library” track. […]

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

[…] artifacts., 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 […]

PMCID: 5704677
PMID: 29182598
DOI: 10.1038/sdata.2017.173

[…] function ‘calcnormfactors()’ and the plot was visualized with the function ‘plotmds()’. figures were all generated using r, version 3.1.3., 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), […]


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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

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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