Skip to main content
SpringerLink
Log in

ProHits-viz: a suite of web tools for visualizing interaction proteomics data

  • Correspondence
  • Published:

From Nature Methods

View current issue Submit your manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1: ProHits-viz at a glance.

References

  1. Choi, H. et al. Nat. Methods 8, 70–73 (2011).

    Article  CAS  Google Scholar 

  2. Sowa, M.E., Bennett, E.J., Gygi, S.P. & Harper, J.W. Cell 138, 389–403 (2009).

    Article  CAS  Google Scholar 

  3. Shannon, P. et al. Genome Res. 13, 2498–2504 (2003).

    Article  CAS  Google Scholar 

  4. Mellacheruvu, D. et al. Nat. Methods 10, 730–736 (2013).

    Article  CAS  Google Scholar 

  5. Knight, J.D. et al. Proteomics 15, 1432–1436 (2015).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to all members of the Gingras lab for feedback on ProHits-viz, particularly J.-Y. Youn and A.L. Couzens for comments during manuscript preparation. We would also like to thank D. Mellacheruvu for providing ProHits-viz-compatible downloadable files on the CRAPome website. We acknowledge funding from the Government of Canada through Genome Canada and the Ontario Genomics Institute (grant nos. OGI-088 and OGI-097 to A.-C.G. and L.P.), the Canadian Institutes of Health Research (to A.-C.G.; Foundation grant no. FDN143301); the US National Institutes of Health (to A.I.N. and A.-C.G.; grant no. 5R01GM94231); and the Singapore Ministry of Education (to H.C.; grant no. MOE T2-2-084). A.-C.G. is the Canada Research Chair in Functional Proteomics and the Lea Reichmann Chair in Cancer Proteomics.

Author information

Authors and Affiliations

  1. Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada

    James D R Knight, Gagan D Gupta, Laurence Pelletier & Anne-Claude Gingras

  2. Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore

    Hyungwon Choi

  3. Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore

    Hyungwon Choi

  4. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    Laurence Pelletier & Anne-Claude Gingras

  5. Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada

    Brian Raught

  6. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada

    Brian Raught

  7. Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA

    Alexey I Nesvizhskii

  8. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA

    Alexey I Nesvizhskii

Authors
  1. James D R Knight
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hyungwon Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gagan D Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Laurence Pelletier
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Brian Raught
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Alexey I Nesvizhskii
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Anne-Claude Gingras
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Anne-Claude Gingras.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Snapshot of the available parameters for the dot plot analytical tool.

Default options are shown; alternative options can be selected through dropdown menus or values can be typed in. SAINT and CRAPome analytical pipeline outputs are explicitly supported (columns are pre-recognized). When inputting another format, the user will be prompted to specify the score directionality. Parameters and clustering options are defined in the text and in the user manuals (available in the Supplementary Protocol).

Supplementary information

Supplementary Text and Figures

Supplementary Figure 1 and Supplementary Methods

Supplementary Protocol

ProHits-viz

Supplementary Table 1

Sample data set for use with ProHits-viz.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Knight, J., Choi, H., Gupta, G. et al. ProHits-viz: a suite of web tools for visualizing interaction proteomics data. Nat Methods 14, 645–646 (2017). https://doi.org/10.1038/nmeth.4330

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.4330

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation