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

Nature Methods volume 14, pages 645–646 (2017)Cite this article

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To the Editor: With the broad availability of mass spectrometry methods for identifying protein–protein interactions, there is a growing need for applications that can simplify the challenges associated with managing, analyzing and visualizing the results obtained by these methods. Here we present ProHits-viz (prohits-viz.lunenfeld.ca), a suite of web-based tools for visualizing and analyzing protein interaction data.

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Figure 1: ProHits-viz at a glance.

References

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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.

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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

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  1. James D R Knight
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  2. Hyungwon Choi
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  3. Gagan D Gupta
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  4. Laurence Pelletier
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  5. Brian Raught
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  6. Alexey I Nesvizhskii
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  7. Anne-Claude Gingras
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Correspondence to Anne-Claude Gingras.

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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.

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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

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