Supplementary Materials (Right-Click and Choose 'Save As' to Download Files)

Table S1. Interactions of kinases, phosphatases and associated subunits [excel][pdf]
Table S2. Sequence coverage for epitope tagged bait proteins [excel][pdf]
Table S3. Biological and technical repeats for Swe1 kinase [excel][pdf]
Table S4. Biological and technical repeats for Mps1 kinase [excel][pdf]
Table S5. Effect of bait induction level on spectral count coverage of interaction partners [excel][pdf]
Table S6. List of interactions tested by affinity capture-immunoblot [excel][pdf]
Table S7. Mps1 phosphorylation sites identified after IMAC enrichment [excel][pdf]
Table S8. Kinase-kinase interactions in the combined KPI, LTP and HTP-HC datasets [excel][pdf]
Table S9. Phosphorylation sites identified in this study [excel][pdf]
Table S10. Yeast strains used in this study [doc][pdf]
Table S11. Plasmids used in this study [doc][pdf]
Table S12. Data used to generate Table S9 phosphorylation sites [excel][pdf]
Table S13. List of probable contaminants removed by SAINT [excel][pdf]
Table S14. Additional proteins removed from final dataset [excel][pdf]
Table S15. Compilation of GO Slim terms [excel][pdf]

Supporting Online Material (Right-Click and Choose 'Save As' to Download Files)

Website Supplementary Table 1 - SAINT Datasets [zip format]

Listing of SAINT interaction data broken into separate files. This archive contains two folders, RAW and FILTERED. RAW contains all the SAINT interactions grouped by TAG with attributes in individual columns delimited by |. FILTERED follows the same format, but only contains interactions with a probability score greater than or equal to 0.85.

Inside the RAW folder, there are four individual files:

• RAW-FLAG - All raw interaction data with the FLAG TAG
• RAW-HA - All raw interaction data with the HA TAG
• RAW-TAP - All raw interaction data with the TAP TAG
• RAW-UNIQUE - All raw interaction data grouped together according to unique BAIT - HIT interactions.

Inside the FILTERED folder, there are four individual files:

• FILTERED-FLAG - All filtered interaction data with the FLAG TAG
• FILTERED-HA - All filtered interaction data with the HA TAG
• FILTERED-TAP - All filtered interaction data with the TAP TAG
• FILTERED-UNIQUE - All filtered interaction data grouped together according to unique BAIT - HIT interactions.

Website Supplementary Table 2 - GO SLIM Process Interactor Overlap [excel format]

GO Slim Process Annotation mappings off all Kinase Associated, Kinase Catalytic, Phosphatase Associated, and Phosphatase Catalytic protein interactors in Our Study, LTP, and HTP-HC.

Description of Columns:

• Column A - pk Yorf - Yorf name off all Kinase Associated, Kinase Catalytic, Phosphatase Associated, Phosphatase Catalytic
• Column B - pk Gene - Common name off all Kinase Associated, Kinase Catalytic, Phosphatase Associated, Phosphatase Catalytic
• Column C - pk GO SLIM PROCESS - GO Slim Process of the Phosphatase Protein or Kinase Protein
• Column D - This Study ( >= 0.85 ) Interactors - Every protein that interacts with the Phosphatase Protein or Kinase Protein in column A
• Column E - This Study ( >= 0.85 ) Pooled GO SLIM PROCESS - Pooled all the GO SLIM PROCESS terms for each of the proteins in column D
• Column F and G - Same as C and D but for LTP (Supplementary Table X) interactions
• Column H and I - Same as C and D but for HTP-HC (Supplementary Tabl X) interactions
• Column J - This Study ( >= 0.85 ) - All GO SLIM PROCESS unique to the Saint set
• Column K - LTP - All GO SLIM PROCESS unique to the LC set
• Column L - HTP-HC - All GO SLIM PROCESS unique to the HTP HC set
• Column M - This Study ( >= 0.85 ) intersect LTP - All GO SLIM PROCESS in the intersection of SAINT and LC set
• Column N - This Study ( >= 0.85 ) intersect HTP-HC - All GO SLIM PROCESS in the intersection of SAINT and HTP set
• Column O - LTP n HTP-HC - All GO SLIM PROCESS in the intersection of LC and HTP set
• Column P - This Study ( >= 0.85 ) intersect LTP intersect HTP-HC - All GO SLIM PROCESS in the intersection of SAINT and LC and HTP
• Columns Q - Z - Counts of the GO SLIM PROCESS for each set

Website Supplementary Table 3 - LTP Dataset [txt format]

All protein interactions from publications curated in the BioGRID that contain less than 100 protein interactions. Excluded from this set are interactions with the Co-Localization, Affinity Capture-RNA, Protein RNA, and Co-Fractionation experimental systems.

Website Supplementary Table 4 - HTP-HC Dataset [txt format]

Start with all protein interactions in the BioGRID from publications containing 100 or more protein interactions, excluding Gavin AC (2002) 11805826, Grandi (2000) 12150911, and Collins (2007) 17200106. Also, interactions with experimental systems of Co-Localization, Affinity Capture-RNA, Protein RNA, and Co-Fractionation are excluded. Each interaction in the initial dataset is checked for multi-validation. Multi-validation occurs if any of the following criteria is met for a given interaction X with interactors A-B. All multi-validated interactions are combined to create HTP-HC.

1. X is found within the dataset, in reverse order. (ie. A-B is validated by B-A).
2. X is found within the dataset, with the same A-B, but with a different experimental system.
3. X is found within the dataset, with the same A-B, but with a different publication.