ZENBU - omics interactive visualization system

FANTOM is an international research consortium established by Dr. Hayashizaki and his colleagues in 2000 to assign functional annotations to the full-length cDNAs that were collected during the Mouse Encyclopedia Project at RIKEN. FANTOM1-3 focused on identifying the transcribed components of mammalian cells, improving gene identification and alternative transcript isoforms in both human and mouse, and revealed that a large fraction of the transcriptome is non-coding. FANTOM4 focused on the dynamics of transcription start site (TSS) usage via deepCAGE monitoring during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1 helping to identifying key factors that determine cell fates. FANTOM5 focused on systematically investigating transciptional expression in virtually all cell types across the human body and mice. We aim to use this information to build transcriptional regulatory models for every primary cell type that makes up a human. All FANTOM5 views in data explorer
FANTOM5 Human hg38 promoterome FANTOM5 Human hg19 promoterome with gene expression FANTOM5 Human time course FANTOM4 ThP1 Human hg18 view FANTOM3: Mouse mm9 CAGE view	FANTOM5 Mouse mm9 promoterome FANTOM5 Mouse mm9 time course FANTOM5 Rat rn6 CAGE view FANTOM5 Dog canFam3 CAGE view FANTOM5 Chicken galGal5
ZENBU - Severin et al fig1. ENCODE RNAseq/CAGE many tracks from same data ZENBU - Severin et al. supp Fig 2. CAGE mapability, signal filtering - PMS2L2 ZENBU - Severin et al. supp Fig 3. shortRNA-Seq dynamic processing - MIR183 ZENBU - Severin et al. supp Fig 4. ChipSeq dynamic peak calling - SH3BP4 ENCODE wold lab RNAseq Human hg19
Basic annotation views
Human hs1 / T2T-CHM13v2.0 annotation view Human hg38 annotation view Human hg19 annotation view Human hg18 annotation view Mouse GRCm39 annotation view Mouse mm10 annotation view Mouse mm9 annotation view Rat rn6 annotation view Rat rn4 annotation view	Dog canFam3 annotation view Chicken galGal6 annotation view Chicken galGal5 annotation view Chicken galGal4 annotation view Chicken galGal3 annotation view Drosophila melanogaster R5/dm3 annotation view Zebrafish Zv9 annotation view Zebrafish GRCz10 annotation view
If you do not see your genome of interest, please search for a view configuration in the data explorer

ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.
Please check our documentation wiki for details on how to use the system, or check out some of the views above.

If you use ZENBU for your publications, please site the following papers:

Severin, Jessica, et al."Interactive visualization and analysis of large-scale sequencing datasets using ZENBU." Nat Biotechnol 32, 217-219 (2014). https://doi.org/10.1038/nbt.2840
Severin, Jessica, et al. "ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data" NAR Genomics and Bioinformatics Volume 5, Issue 3, September 2023, lqad075, https://doi.org/10.1093/nargab/lqad075

The ZENBU system is compatible with the majority of web browsers : Google Chrome, Firefox, Safari, Opera, and Edge.
currently ZENBU does not support InternetExplorer for lack of sufficient HTML5/SVG/XML support.