World Library  


Add to Book Shelf
Flag as Inappropriate
Email this Book

Plos Computational Biology : the Ortholog Conjecture is Untestable by the Current Gene Ontology but is Supported by Rna Sequencing Data, Volume 8

By Chen, Xiaoshu

Click here to view

Book Id: WPLBN0003941464
Format Type: PDF eBook :
File Size:
Reproduction Date: 2015

Title: Plos Computational Biology : the Ortholog Conjecture is Untestable by the Current Gene Ontology but is Supported by Rna Sequencing Data, Volume 8  
Author: Chen, Xiaoshu
Volume: Volume 8
Language: English
Subject: Journals, Science, Computational Biology
Collections: Periodicals: Journal and Magazine Collection (Contemporary), PLoS Computational Biology
Historic
Publication Date:
Publisher: Plos

Citation

APA MLA Chicago

Chen, X. (n.d.). Plos Computational Biology : the Ortholog Conjecture is Untestable by the Current Gene Ontology but is Supported by Rna Sequencing Data, Volume 8. Retrieved from http://www.worldlibrary.in/


Description
Description : The ortholog conjecture posits that orthologous genes are functionally more similar than paralogous genes. This conjecture is a cornerstone of phylogenomics and is used daily by both computational and experimental biologists in predicting, interpreting, and understanding gene functions. A recent study, however, challenged the ortholog conjecture on the basis of experimentally derived Gene Ontology (GO) annotations and microarray gene expression data in human and mouse. It instead proposed that the functional similarity of homologous genes is primarily determined by the cellular context in which the genes act, explaining why a greater functional similarity of (within-species) paralogs than (between-species) orthologs was observed. Here we show that GO-based functional similarity between human and mouse orthologs, relative to that between paralogs, has been increasing in the last five years. Further, compared with paralogs, orthologs are less likely to be included in the same study, causing an underestimation in their functional similarity. A close examination of functional studies of homologs with identical protein sequences reveals experimental biases, annotation errors, and homology-based functional inferences that are labeled in GO as experimental. These problems and the temporary nature of the GO-based finding make the current GO inappropriate for testing the ortholog conjecture. RNA sequencing (RNA-Seq) is known to be superior to microarray for comparing the expressions of different genes or in different species. Our analysis of a large RNA-Seq dataset of multiple tissues from eight mammals and the chicken shows that the expression similarity between orthologs is significantly higher than that between within-species paralogs, supporting the ortholog conjecture and refuting the cellular context hypothesis for gene expression. We conclude that the ortholog conjecture remains largely valid to the extent that it has been tested, but further scrutiny using more and better functional data is needed.

 

Click To View

Additional Books


  • Plos Computational Biology : the Fidelit... (by )
  • Plos Computational Biology : Optimality ... (by )
  • Plos Computational Biology : a Cervid Vo... (by )
  • Plos Computational Biology : Transcripti... (by )
  • Plos Computational Biology : Meta-analys... (by )
  • Plos Computational Biology : Computation... (by )
  • Plos Computational Biology : Integrated ... (by )
  • Plos Computational Biology : Ten Simple ... (by )
  • Plos Computational Biology : How Synchro... (by )
  • Plos Computational Biology : Gag-pol Pro... (by )
  • Plos Computational Biology : Tension and... (by )
  • Plos Computational Biology : the Dynamic... (by )
Scroll Left
Scroll Right

 



Copyright © World Library Foundation. All rights reserved. eBooks from World Library are sponsored by the World Library Foundation,
a 501c(4) Member's Support Non-Profit Organization, and is NOT affiliated with any governmental agency or department.