Interaction repository tutorial. Page 1 Quick guide to the Gingras lab interaction proteomics repository at prohitsweb.lunenfeld.ca Website designed and maintained by JP Zhang and G Liu; tutorial prepared by AC Gingras, June 29 th , 2013 1) Access the website at prohitsweb.lunenfeld.ca. From the top menu bar, select “Data sets” and login to the desired project; here the “Hippo interactome” project. 2) Navigate through Hippo project home page using the left menu bar. The Supplementary Data section of the project provides all supplementary data as detailed in this manuscript: note that the tables are provided as Excel files. Additional Results files available only on the web are also provided. These consist of downloadable files, especially complete SAINT results output files. A link to the raw data repository MassIVE at UCSD (http://proteomics.ucsd.edu/ProteoSAFe/) is provided for each of the datasets included in the publication. For example, for this Hippo interactome publication, we have made three depositions in MassIVE, each accompanied by clear descriptions of the samples included and the experimental procedure used for sample generation and analysis.
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Interaction repository tutorial. Page 1
Quick guide to the Gingras lab interaction proteomics repository at prohits-‐web.lunenfeld.ca Website designed and maintained by JP Zhang and G Liu; tutorial prepared by AC Gingras, June 29th, 2013 1) Access the website at prohits-‐web.lunenfeld.ca. From the top menu bar, select “Data sets” and login to the desired project; here the “Hippo interactome” project.
2) Navigate through Hippo project home page using the left menu bar. The Supplementary Data section of the project provides all supplementary data as detailed in this manuscript: note that the tables are provided as Excel files. Additional Results files available only on the web are also provided. These consist of downloadable files, especially complete SAINT results output files. A link to the raw data repository MassIVE at UCSD (http://proteomics.ucsd.edu/ProteoSAFe/) is provided for each of the datasets included in the publication. For example, for this Hippo interactome publication, we have made three depositions in MassIVE, each accompanied by clear descriptions of the samples included and the experimental procedure used for sample generation and analysis.
Interaction repository tutorial. Page 2
3) Navigate through the bait-‐prey interaction data by selecting “Explore Baits”. This will take you by default to a pictorial view of the baits analyzed here (alternative views are the baits in a sorted list, or organized by categories). Clicking on any of the bait names will take you (by default) to the list of high confidence interactors for the given bait in the Hippo interactome dataset.
For example, the top of the interaction list for STK4 (MST1) is shown here. The upper left corner contains a zoomable version of the images presented in Figure S3 of the manuscript while the upper right corner is a dynamically generated network of the bait-‐prey interactions. Each row represents a bait-‐prey interaction associated with the quantitative evidence.
Interaction repository tutorial. Page 3
Interactions detected in each of the four main datasets included in this study (FLAG AP-‐MS, DMSO; FLAG AP-‐MS, OA; BioID HeLa; BioID HEK293) is considered independent and color-‐coded to match the Cytoscape image. By default, all high confidence data is listed. Specific experimental datasets can be turned off. For example, below is the list of the high confidence interactions restricted to the BioID datasets.
Clicking on the gene name for the prey protein will retrieve all interactions – at any confidence value – reported in this dataset. The accession number (Genbank) for the protein as identified in the mass spectrometer is listed in the third column. The “spectra” column lists the spectral counts for the prey protein across the two biological replicates purifications of the bait (“I” is use as a delimiter). The AvgP score by SAINT as well as the calculated Fold Change are listed. The column “ctrlCounts” lists the number of spectra for the prey protein across all controls used to model the dataset. The “frequency” is the proportion of baits within this project in which a given prey protein was detected (note that we are expecting high frequencies here due to the interconnectivity of the proteins within this dataset). Lastly, the “Pub” column lists those proteins for which an interaction has been reported in the selected primary interaction database (BioGRID, IntAct, MINT and DIP) as extracted from iRefIndex. Clicking this link takes you to the original publication in PubMed.
