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...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) CA), 2017-08, Vol.5, p.e3712-e3712, Article e3712
Main Authors: Niu, Yulong, Liu, Chengcheng, Moghimyfiroozabad, Shayan, Yang, Yi, Alavian, Kambiz N
Format: Article
Language:English
Subjects:
Algorithms
Analysis
Bioinformatics
Biology
Computer applications
Computer programs
Datasets
Genomes
Genomics
Linkage prediction
Methods
Mitochondria
Organisms
Phylogenetic profile
Phylogenetics
Phylogeny
Protein research
Proteins
Proteomes
Signaling peptides and proteins
Whole proteome
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Description
Summary: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/.
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.3712