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Detection of significant protein coevolution

David Ochoa, David Juan, Alfonso Valencia, Florencio Pazos
2015 Computer applications in the biosciences : CABIOS  
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

Francisco M Codoñer, Shirley O'Dea, Mario A Fares
2008 BMC Evolutionary Biology  
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

Daniel Savel, Mehmet Koyutürk
2019 BioData Mining  
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  
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

Alexander L. Cope, Brian C. O'Meara, Michael A. Gilchrist
2020 BMC Genomics  
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

M. A. Fares, D. McNally
2006 Bioinformatics  
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

M. A. Fares
2006 Genetics  
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

Hunter B. Fraser, Aaron E. Hirsh, Dennis P. Wall, Michael B. Eisen
2004 Proceedings of the National Academy of Sciences of the United States of America  
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

Alberto Vicens, Eduardo R.S. Roldan
2014 Biology of Reproduction  
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

D. Juan, F. Pazos, A. Valencia
2008 Proceedings of the National Academy of Sciences of the United States of America  
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

Fei Shi, Song Qin, Yin-Chu Wang
2011 Comparative and Functional Genomics  
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]

Zhengyuan O. Wang, David D. Pollock
2005 Methods in Enzymology  
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

N Cobbe, M M S Heck
2004 Heredity  
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

J Gregory Caporaso, Sandra Smit, Brett C Easton, Lawrence Hunter, Gavin A Huttley, Rob Knight
2008 BMC Evolutionary Biology  
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

L. Hakes, S. C. Lovell, S. G. Oliver, D. L. Robertson
2007 Proceedings of the National Academy of Sciences of the United States of America  
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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