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

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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 

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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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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).

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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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