About
Coregulator proteins (CoRegs) are part of multi-protein complexes that transiently assemble with transcription factors and chromatin modifiers to regulate gene expression. In this study we analyzed data from 3,290 immuno-precipitations (IP) followed by mass spectrometry (MS) applied to human cell lines aimed at identifying CoRegs complexes. Using the semi-quantitative spectral counts, we scored binary protein-protein and domain-domain associations with several equations. Unlike previous applications, our methods scored prey-prey protein-protein interactions regardless of the baits used. We also predicted domain-domain interactions underlying predicted protein-protein interactions. The quality of predicted protein-protein and domain-domain interactions was evaluated using known binary interactions from the literature, whereas one protein-protein interaction, between STRN and CTTNBP2NL, was validated experimentally; and one domain-domain interaction, between the HEAT domain of PPP2R1A and the Pkinase domain of STK25, was validated using molecular docking simulations. The scoring schemes presented here recovered known, and predicted many new, complexes, protein-protein, and domain-domain interactions.
Citation
Mazloom AR, Dannenfelser R, Clark NR, Grigoryan AV, Linder KM, Cardozo TJ, Bond JC, Boran AD, Iyengar R, Malovannaya A, Lanz RB, and Ma'ayan A. Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. PLoS Comp. Bio. 7: 12 (2011). PMID: 22219718.
Data and Tables
| Entity | Counts |
|---|---|
| Experiments | 3,290 |
| Records in experiment-2-gene | 407,000 |
| Antibodies | 1,796 |
| Antigens (Baits) | 1,083 |
| Antibodies with redundant antigen targets | 419 |
| Antigens used in more than one experiments | 25 |
| Records in antibody-2-gene (ab2gene) | 315,245 |
| Total Gene products | 11,485 |
| Gene products recovered in 1 antibody IP (non-reciprocal) | 3,666 |
| Gene products recovered in 2-4 antibodies (low reciprocal occurences) | 3,271 |
| Gene products recovered in 5-10 antibodies | 1,708 |
| Gene products recovered in 10-20 antibodies | 931 |
| Gene products recovered in >20 antibodies | 1,909 |
| Non-specific proteins (Blacklist) | 290 |
Data for download (Click the icon to download the folllowing files)
| Ranking of All Predicted PPI |  |
| Antibody to Gene Mapping | |
| DDI Methods Scores | |
| Experiment Annotation | |
| Detailed PPI Scores | |
| Top 10% of Predicted PPIs | |
| DDI Scores for 114 Experiments | |
| PPI Scores for 114 Experiments | |
| Statistics for 114 Experiments | |
Figures
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