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Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

Nature Biotechnology volume 32, pages 217–219 (2014)Cite this article

To the Editor

The advance of sequencing technology has spurred an ever-growing body of sequence tag–based data from protocols such as RNA-seq, chromatin immunoprecipitation (ChIP)-seq, DNaseI-hypersensitive site sequencing (DHS)-seq and cap analysis of gene expression (CAGE). Large-scale consortia are applying standardized versions of these protocols across broad collections of samples1,2 to elucidate genomic function. Beyond this, the affordability of these systems and availability of sequencing services has made these technologies accessible to smaller laboratories focusing on individual biological systems. Data generation is only the beginning, however, and a substantial bottleneck for many labs is going from sequence data to biological insight, especially when the volume of data overwhelms standard paradigms for data visualization. Here, we present a web-based system, ZENBU, which addresses this problem by extending the functionality of the genome browser (Supplementary Fig. 1).

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Figure 1: Overview of ZENBU genome browser interface showcasing several on-demand processing tracks of selected ENCODE project experiments related to Gm12878, HeLa and Nhek cell lines.

References

  1. Chadwick, L.H. Epigenomics 4, 317–324 (2012).

    Article CAS Google Scholar

  2. The ENCODE Project Consortium. Nature 489, 57–74 (2012).

  3. Li, H. et al. Bioinformatics 25, 2078–2079 (2009).

    Article Google Scholar

  4. Nielsen, C.B., Cantor, M., Dubchak, I., Gordon, D. & Wang, T. Nat. Methods 7, S5–S15 (2010).

    Article CAS Google Scholar

  5. Saito, T.L. et al. Bioinformatics 25, 1856–1861 (2009).

    Article CAS Google Scholar

  6. Stein, L.D. et al. Genome Res. 12, 1599–1610 (2002).

    Article CAS Google Scholar

  7. Kuhn, R.M., Haussler, D. & Kent, W.J. Brief. Bioinform. 14, 144–161 (2013).

    Article CAS Google Scholar

  8. Hubbard, T. et al. Nucleic Acids Res. 30, 38–41 (2002).

    Article CAS Google Scholar

  9. Robinson, J.T. et al. Nat. Biotechnol. 29, 24–26 (2011).

    Article CAS Google Scholar

  10. Zhang, J. et al. Database (Oxford) 2011, bar038 (2011).

    Google Scholar

  11. Derrien, T. et al. Genome Res. 22, 1775–1789 (2012).

    Article CAS Google Scholar

  12. Frith, M.C. et al. Genome Res. 18, 1–12 (2008).

    Article CAS Google Scholar

  13. Wei, G. et al. Immunity 35, 299–311 (2011).

    Article CAS Google Scholar

  14. Severin, J. et al. BMC Bioinformatics 11, 240 (2010).

    Article Google Scholar

  15. Carninci, P. et al. Science 309, 1559–1563 (2005).

    Article CAS Google Scholar

  16. Suzuki, H. et al. Nat. Genet. 41, 553–562 (2009).

    Article CAS Google Scholar

  17. Contrino, S. et al. Nucleic Acids Res. 40, D1082–D1088 (2012).

    Article CAS Google Scholar

  18. Giardine, B. et al. Genome Res. 15, 1451–1455 (2005).

    Article CAS Google Scholar

  19. The Cancer Genome Atlas Research Network et al. Nat. Genet. 45, 1113–1120 (2013).

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Acknowledgements

We would like to acknowledge C. Plessy, P. Carninci and the FANTOM5 consortium members for critical feedback during development of the system. The work was funded by a research grant for RIKEN Omics Science Center from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) to Y.H. and a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Y.H. This study is also supported by Research Grants from MEXT through RIKEN Preventive Medicine and Diagnosis Innovation Program to Y.H. and RIKEN Center for Life Science Technologies, Division of Genomic Technologies to Piero Carninci.

Author information

Author notes

  1. Nicolas Bertin

    Present address: Present address: Cancer Science Institute of Singapore, National University of Singapore, Singapore.,

Authors and Affiliations

  1. RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Suehiro-cho, Tsurumi-ku, Yokohama, Japan

    Jessica Severin, Marina Lizio, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Nicolas Bertin & Alistair R R Forrest

  2. RIKEN Omics Science Center (OSC), Yokohama, Japan

    Jessica Severin, Marina Lizio, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, Nicolas Bertin & Alistair R R Forrest

  3. RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan

    Hideya Kawaji & Yoshihide Hayashizaki

Authors
  1. Jessica Severin
  2. Marina Lizio
  3. Jayson Harshbarger
  4. Hideya Kawaji
  5. Carsten O Daub
  6. Yoshihide Hayashizaki
  7. Nicolas Bertin
  8. Alistair R R Forrest

Consortia

The FANTOM Consortium

Corresponding authors

Correspondence to Nicolas Bertin or Alistair R R Forrest.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–13, Supplementary Table 1 and Supplementary Note 1 (PDF 20041 kb)

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Severin, J., Lizio, M., Harshbarger, J. 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

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