PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages
Direct and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here we present a highly scalable and ti...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-08-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/3712.pdf |
| _version_ | 1797420306727436288 |
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| author | Yulong Niu Chengcheng Liu Shayan Moghimyfiroozabad Yi Yang Kambiz N. Alavian |
| author_facet | Yulong Niu Chengcheng Liu Shayan Moghimyfiroozabad Yi Yang Kambiz N. Alavian |
| author_sort | Yulong Niu |
| collection | DOAJ |
| description | Direct and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here we present a highly scalable and time-efficient computational framework for predicting linkages within the whole human proteome. We have validated this method through analysis of 3,697 human pathways and molecular complexes and a comparison of our results with the prediction outcomes of previously published co-occurrency model-based and normalization methods. Here we also introduce PrePhyloPro, a web-based software that uses our method for accurately predicting proteome-wide linkages. We present data on interactions of human mitochondrial proteins, verifying the performance of this software. PrePhyloPro is freely available at http://prephylopro.org/phyloprofile/. |
| first_indexed | 2024-03-09T07:00:39Z |
| format | Article |
| id | doaj.art-f86bb355bf4c41dea618d049ea41a692 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:00:39Z |
| publishDate | 2017-08-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-f86bb355bf4c41dea618d049ea41a6922023-12-03T09:54:53ZengPeerJ Inc.PeerJ2167-83592017-08-015e371210.7717/peerj.3712PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkagesYulong Niu0Chengcheng Liu1Shayan Moghimyfiroozabad2Yi Yang3Kambiz N. Alavian4Department of Medicine, Division of Brain Sciences, Imperial College London, London, United KingdomDepartment of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, ChinaDepartment of Biology, The Bahá’í Institute for Higher Education (BIHE), Tehran, IranKey Lab of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, ChinaDepartment of Medicine, Division of Brain Sciences, Imperial College London, London, United KingdomDirect and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here we present a highly scalable and time-efficient computational framework for predicting linkages within the whole human proteome. We have validated this method through analysis of 3,697 human pathways and molecular complexes and a comparison of our results with the prediction outcomes of previously published co-occurrency model-based and normalization methods. Here we also introduce PrePhyloPro, a web-based software that uses our method for accurately predicting proteome-wide linkages. We present data on interactions of human mitochondrial proteins, verifying the performance of this software. PrePhyloPro is freely available at http://prephylopro.org/phyloprofile/.https://peerj.com/articles/3712.pdfLinkage predictionWhole proteomePhylogenetic profile |
| spellingShingle | Yulong Niu Chengcheng Liu Shayan Moghimyfiroozabad Yi Yang Kambiz N. Alavian PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages PeerJ Linkage prediction Whole proteome Phylogenetic profile |
| title | PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages |
| title_full | PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages |
| title_fullStr | PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages |
| title_full_unstemmed | PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages |
| title_short | PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages |
| title_sort | prephylopro phylogenetic profile based prediction of whole proteome linkages |
| topic | Linkage prediction Whole proteome Phylogenetic profile |
| url | https://peerj.com/articles/3712.pdf |
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