Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.

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 li...

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Autores principales:	Amin R Mazloom, Ruth Dannenfelser, Neil R Clark, Arsen V Grigoryan, Kathryn M Linder, Timothy J Cardozo, Julia C Bond, Aislyn D W Boran, Ravi Iyengar, Anna Malovannaya, Rainer B Lanz, Avi Ma'ayan
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0cee1b71d698463991acce0891a5005a
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spelling	oai:doaj.org-article:0cee1b71d698463991acce0891a5005a2021-11-18T05:51:41ZRecovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.1553-734X1553-735810.1371/journal.pcbi.1002319https://doaj.org/article/0cee1b71d698463991acce0891a5005a2011-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22219718/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Coregulator 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. The networks that resulted from the predictions are provided as a web-based interactive application at http://maayanlab.net/HT-IP-MS-2-PPI-DDI/.Amin R MazloomRuth DannenfelserNeil R ClarkArsen V GrigoryanKathryn M LinderTimothy J CardozoJulia C BondAislyn D W BoranRavi IyengarAnna MalovannayaRainer B LanzAvi Ma'ayanPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 7, Iss 12, p e1002319 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Amin R Mazloom Ruth Dannenfelser Neil R Clark Arsen V Grigoryan Kathryn M Linder Timothy J Cardozo Julia C Bond Aislyn D W Boran Ravi Iyengar Anna Malovannaya Rainer B Lanz Avi Ma'ayan Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.
description	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. The networks that resulted from the predictions are provided as a web-based interactive application at http://maayanlab.net/HT-IP-MS-2-PPI-DDI/.
format	article
author	Amin R Mazloom Ruth Dannenfelser Neil R Clark Arsen V Grigoryan Kathryn M Linder Timothy J Cardozo Julia C Bond Aislyn D W Boran Ravi Iyengar Anna Malovannaya Rainer B Lanz Avi Ma'ayan
author_facet	Amin R Mazloom Ruth Dannenfelser Neil R Clark Arsen V Grigoryan Kathryn M Linder Timothy J Cardozo Julia C Bond Aislyn D W Boran Ravi Iyengar Anna Malovannaya Rainer B Lanz Avi Ma'ayan
author_sort	Amin R Mazloom
title	Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.
title_short	Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.
title_full	Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.
title_fullStr	Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.
title_full_unstemmed	Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.
title_sort	recovering protein-protein and domain-domain interactions from aggregation of ip-ms proteomics of coregulator complexes.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/0cee1b71d698463991acce0891a5005a
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Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes.

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