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Detection of significant protein coevolution
2015
Computer applications in the biosciences : CABIOS
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From a practical point of view, co-evolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. ...
In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given co-evolutionary score (tree similarity). ...
DO was recipient of a fellowship from the Basque Country. ...
doi:10.1093/bioinformatics/btv102
pmid:25717190
fatcat:ykhbzgqgdfhnje5ncqmwrzxpdm
Reducing the false positive rate in the non-parametric analysis of molecular coevolution
2008
BMC Evolutionary Biology
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detect coevolution. ...
Application of these filters to three different proteins with known functional domains supports the importance of using biological filters to detect coevolution. ...
We would like to thank David McNally for his assistance with Figure 6 of this manuscript. We are very grateful to reviewers who have contributed significantly to the improvement of this manuscript. ...
doi:10.1186/1471-2148-8-106
pmid:18402697
pmcid:PMC2362121
fatcat:oin5qs3ryvg33k6tvc57s4keqq
Characterizing human genomic coevolution in locus-gene regulatory interactions
2019
BioData Mining
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Coevolution has been used to identify and predict interactions and functional relationships between proteins of many different organisms including humans. ...
Measures of coevolution are genome-wide and could potentially be used to prioritize the detection of distant or inter-chromosomal interactions such as trans-eQTL interactions in the human genome. ...
This work was supported by the National Libraries of Medicine and the National Cancer Institute at the National Institutes of Health (grant numbers RO1-LM04127, U01-CA198941). ...
doi:10.1186/s13040-019-0195-y
pmid:30923571
pmcid:PMC6419833
fatcat:kzx22izcobdlra4snchbay4yfi
Page 9 of Genetics Vol. 173, Issue 1
[page]
2006
Genetics
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All sites detected under adaptive evolution in these proteins belong to
coevolution groups, further underlining the importance of testing for coevolution in selective constraints
analyses. ...
Coevolution analysis and functional data for heat-shock proteins, Hsp90 and GroEL, highlight that almost all detected coevolving sites are functionally or structurally important. ...
Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods
2020
BMC Genomics
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We examined the effects of number of protein interactions and gene expression levels on coevolution, finding both factors are overall poor predictors of the strength of coevolution between a protein pair ...
Furthermore, our simulations indicate the use of a randomly-generated null distribution as a means of determining statistical significance for detecting coevolving genes with phylogenetically-uncorrected ...
Acknowledgements We would like to thank the two anonymous reviewers whose comments and suggestions greatly improved the quality of this article. 1 ...
doi:10.1186/s12864-020-6761-3
pmid:32434474
fatcat:yvoz537b7fdmvjadfbbtpfrd24
CAPS: coevolution analysis using protein sequences
2006
Bioinformatics
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going to be implemented in a future version of CAPS to allow for the detection of protein-protein interfaces based on analysis of coevolution. ...
Introduction CAPS implements a method to analyse amino acid coevolution in a protein multiple sequence alignment and has been successfully applied to detect intra-molecular coevolution in the Gag protein ...
in the three-dimensional structure of Figure 10 . ...
doi:10.1093/bioinformatics/btl493
pmid:17005535
fatcat:zdrgfqrdxzdyfhgnvt3i4ivdq4
A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses
2006
Genetics
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All sites detected under adaptive evolution in these proteins belong to coevolution groups, further underlining the importance of testing for coevolution in selective constraints analyses. ∑ = − = T S ...
Here we present a novel approach that vastly improves the sensitivity of previous methods to detect coevolution through a weighted comparison of divergence between amino acid sites. ...
Figure 4 . 4 Coevolution between amino acids in Gag protein from HIV-I. A) groups of coevolution detected prior to clade removal. ...
doi:10.1534/genetics.105.053249
pmid:16547113
pmcid:PMC1461439
fatcat:iq3lthk2wnevxdh3yoqrn3apzm
Coevolution of gene expression among interacting proteins
2004
Proceedings of the National Academy of Sciences of the United States of America
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We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. ...
Our results also suggest that expression coevolution can be used for computational prediction of protein-protein interactions. Materials and Methods Sequence Data. ...
Detection of Sequence Coevolution. ...
doi:10.1073/pnas.0402591101
pmid:15175431
pmcid:PMC439012
fatcat:tyywrl5g5be4rhs7xydy4rrnhu
Coevolution of Positively Selected IZUMO1 and CD9 in Rodents: Evidence of Interaction Between Gamete Fusion Proteins?1
2014
Biology of Reproduction
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A process of coevolution between proteins in male and female gametes may promote rapid divergence of fertilization proteins. ...
signatures of coevolution. ...
ACKNOWLEDGMENTS We are grateful to François Bonhomme and Annie Orth (Institut des Sciences de l'Evolution, CNRS-Université Montpellier 2, France) for facilitating purchase of animals. ...
doi:10.1095/biolreprod.113.116871
pmid:24671880
fatcat:w2eub73q7fcmjdokgvjkl4ny3m
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks
2008
Proceedings of the National Academy of Sciences of the United States of America
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Results Improving Coevolution-Based Prediction of Protein Interactions. ...
This improvement was a direct consequence of using the evolutionary information of the whole proteome for confirming the coevolution of a given pair of proteins. ...
We thank the members of the Computational Systems Biology Group and the Structural Bioinformatics Group for interesting discussions and support. ...
doi:10.1073/pnas.0709671105
pmid:18199838
pmcid:PMC2242690
fatcat:7pc4ma35ijd4vjcoox7mefu4xq
The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution
2011
Comparative and Functional Genomics
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Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. ...
Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. ...
Acknowledgments This work was supported by National Natural Science Foundation of China (40876082) and Typical Environmental Process and Effects on Resources in Coastal Zone Area in International Innovation ...
doi:10.1155/2011/230236
pmid:21904470
pmcid:PMC3166575
fatcat:dlpy7cxstrdvbbeabobdhv7k3q
Context Dependence and Coevolution Among Amino Acid Residues in Proteins
[chapter]
2005
Methods in Enzymology
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Coevolution between amino acid residues and the context dependence of the evolutionary process are often ignored, however, because of their complexity, but they are critical for the accurate interpretation ...
genomics and a complete understanding of selection in proteins require a better understanding of how context dependence affects protein evolution. ...
Despite regular detection of coevolution, results have not been obviously consistent as to the conditions and manner in which coevolution apparently occurs. ...
doi:10.1016/s0076-6879(05)95040-4
pmid:15865995
pmcid:PMC2943952
fatcat:satrzotapzc5bd4njpsw6yjueq
Evolutionary proteomics: Computer dating for proteins
2004
Heredity
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Although coevolution between interacting proteins may be inferred when proteins are simultaneously lost in the same species, specific interactions may also be detected based on statistically significant ...
Consequently, most discerning biologists will not usually be convinced of the significance of a protein interaction either in vitro or in vivo unless strong evidence can be produced using two or more independent ...
doi:10.1038/sj.hdy.6800594
pmid:15508019
fatcat:cm5cqdba55actoxvedfozqthye
Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
2008
BMC Evolutionary Biology
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Identifying coevolving positions in protein sequences has myriad applications, ranging from understanding and predicting the structure of single molecules to generating proteome-wide predictions of interactions ...
Algorithms for detecting coevolving positions can be classified into two categories: tree-aware, which incorporate knowledge of phylogeny, and treeignorant, which do not. ...
Utility of alpha-helical protein alignments for comparing coevolution algorithms This article presents a comparison of nine coevolution detection methods on two different molecules which are entirely ( ...
doi:10.1186/1471-2148-8-327
pmid:19055758
pmcid:PMC2637866
fatcat:dygoninahzaurcwbl2lhlukdzm
Specificity in protein interactions and its relationship with sequence diversity and coevolution
2007
Proceedings of the National Academy of Sciences of the United States of America
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Here, we analyze the coevolution of interacting proteins in yeast and demonstrate correlated evolution of binding partners in eukaryotes. ...
Studies of interacting proteins have found correlated evolution of the sequences of binding partners, apparently as a result of compensating mutations to maintain specificity (i.e., molecular coevolution ...
of significant correlations is used to infer probable coevolution. ...
doi:10.1073/pnas.0609962104
pmid:17468399
pmcid:PMC1876561
fatcat:mj3tf3j6pzgyjkf4244foscov4
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