PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.

Many biological processes are mediated by protein-protein interactions (PPIs). Because protein domains are the building blocks of proteins, PPIs likely rely on domain-domain interactions (DDIs). Several attempts exist to infer DDIs from PPI networks but the produced datasets are heterogeneous and so...

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Autores principales: Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W Ritchie, Marie-Dominique Devignes
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Publicado: Public Library of Science (PLoS) 2021
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Acceso en línea:https://doaj.org/article/bea29375aa16484d9ca040e127727ef8
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spelling oai:doaj.org-article:bea29375aa16484d9ca040e127727ef82021-12-02T19:58:07ZPPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.1553-734X1553-735810.1371/journal.pcbi.1008844https://doaj.org/article/bea29375aa16484d9ca040e127727ef82021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1008844https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Many biological processes are mediated by protein-protein interactions (PPIs). Because protein domains are the building blocks of proteins, PPIs likely rely on domain-domain interactions (DDIs). Several attempts exist to infer DDIs from PPI networks but the produced datasets are heterogeneous and sometimes not accessible, while the PPI interactome data keeps growing. We describe a new computational approach called "PPIDM" (Protein-Protein Interactions Domain Miner) for inferring DDIs using multiple sources of PPIs. The approach is an extension of our previously described "CODAC" (Computational Discovery of Direct Associations using Common neighbors) method for inferring new edges in a tripartite graph. The PPIDM method has been applied to seven widely used PPI resources, using as "Gold-Standard" a set of DDIs extracted from 3D structural databases. Overall, PPIDM has produced a dataset of 84,552 non-redundant DDIs. Statistical significance (p-value) is calculated for each source of PPI and used to classify the PPIDM DDIs in Gold (9,175 DDIs), Silver (24,934 DDIs) and Bronze (50,443 DDIs) categories. Dataset comparison reveals that PPIDM has inferred from the 2017 releases of PPI sources about 46% of the DDIs present in the 2020 release of the 3did database, not counting the DDIs present in the Gold-Standard. The PPIDM dataset contains 10,229 DDIs that are consistent with more than 13,300 PPIs extracted from the IMEx database, and nearly 23,300 DDIs (27.5%) that are consistent with more than 214,000 human PPIs extracted from the STRING database. Examples of newly inferred DDIs covering more than 10 PPIs in the IMEx database are provided. Further exploitation of the PPIDM DDI reservoir includes the inventory of possible partners of a protein of interest and characterization of protein interactions at the domain level in combination with other methods. The result is publicly available at http://ppidm.loria.fr/.Seyed Ziaeddin AlborziAmina Ahmed NacerHiba NajjarDavid W RitchieMarie-Dominique DevignesPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 8, p e1008844 (2021)
institution DOAJ
collection DOAJ
language EN
topic Biology (General)
QH301-705.5
spellingShingle Biology (General)
QH301-705.5
Seyed Ziaeddin Alborzi
Amina Ahmed Nacer
Hiba Najjar
David W Ritchie
Marie-Dominique Devignes
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
description Many biological processes are mediated by protein-protein interactions (PPIs). Because protein domains are the building blocks of proteins, PPIs likely rely on domain-domain interactions (DDIs). Several attempts exist to infer DDIs from PPI networks but the produced datasets are heterogeneous and sometimes not accessible, while the PPI interactome data keeps growing. We describe a new computational approach called "PPIDM" (Protein-Protein Interactions Domain Miner) for inferring DDIs using multiple sources of PPIs. The approach is an extension of our previously described "CODAC" (Computational Discovery of Direct Associations using Common neighbors) method for inferring new edges in a tripartite graph. The PPIDM method has been applied to seven widely used PPI resources, using as "Gold-Standard" a set of DDIs extracted from 3D structural databases. Overall, PPIDM has produced a dataset of 84,552 non-redundant DDIs. Statistical significance (p-value) is calculated for each source of PPI and used to classify the PPIDM DDIs in Gold (9,175 DDIs), Silver (24,934 DDIs) and Bronze (50,443 DDIs) categories. Dataset comparison reveals that PPIDM has inferred from the 2017 releases of PPI sources about 46% of the DDIs present in the 2020 release of the 3did database, not counting the DDIs present in the Gold-Standard. The PPIDM dataset contains 10,229 DDIs that are consistent with more than 13,300 PPIs extracted from the IMEx database, and nearly 23,300 DDIs (27.5%) that are consistent with more than 214,000 human PPIs extracted from the STRING database. Examples of newly inferred DDIs covering more than 10 PPIs in the IMEx database are provided. Further exploitation of the PPIDM DDI reservoir includes the inventory of possible partners of a protein of interest and characterization of protein interactions at the domain level in combination with other methods. The result is publicly available at http://ppidm.loria.fr/.
format article
author Seyed Ziaeddin Alborzi
Amina Ahmed Nacer
Hiba Najjar
David W Ritchie
Marie-Dominique Devignes
author_facet Seyed Ziaeddin Alborzi
Amina Ahmed Nacer
Hiba Najjar
David W Ritchie
Marie-Dominique Devignes
author_sort Seyed Ziaeddin Alborzi
title PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
title_short PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
title_full PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
title_fullStr PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
title_full_unstemmed PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
title_sort ppidomainminer: inferring domain-domain interactions from multiple sources of protein-protein interactions.
publisher Public Library of Science (PLoS)
publishDate 2021
url https://doaj.org/article/bea29375aa16484d9ca040e127727ef8
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