NDLI: Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

Content Provider	PubMed Central
Author	Borenstein, Elhanan Shlomi, Tomer Ruppin, Eytan Sharan, Roded
Copyright Year	2006
Abstract	The rate of conservation of a gene in evolution is believed to be correlated with its biological importance. Recent studies have devised various conservation measures for genes and have shown that they are correlated with several biological characteristics of functional importance. Specifically, the state-of-the-art propensity for gene loss (PGL) measure was shown to be strongly correlated with gene essentiality and its number of protein–protein interactions (PPIs). The observed correlation between conservation and functional importance varies however between conservation measures, underscoring the need for accurate and general measures for the rate of gene conservation. Here we develop a novel maximum-likelihood approach to computing the rate in which a gene is lost in evolution, motivated by the same principles as those underlying PGL. However, in difference to PGL which considers only the most parsimonious ancestral states of the internal nodes of the phylogenetic tree relating the species, our approach weighs in a probabilistic manner all possible ancestral states, and includes the branch length information as part of the probabilistic model. In application to data of 16 eukaryotic genomes, our approach shows higher correlations with experimental data than PGL, including data on gene lethality, level of connectivity in a PPI network and coherence within functionally related genes.
Related Links	http://dx.doi.org/10.1093/nar/gkl792
Starting Page	7
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	1
Volume Number	35
Language	English
Publisher	Oxford University Press
Publisher Date	2006-12-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes

Patterns of intron gain and conservation in eukaryotic genes

Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication

yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes

A change in the rate of transcription of a eukaryotic gene in response to cyclic AMP.

A comparison of the promoter strengths of two eukaryotic genes in vitro reveals a region of DNA that can influence the rate of transcription in cis over long distances.

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

Similar Documents

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes

Patterns of intron gain and conservation in eukaryotic genes

Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication

yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes

A change in the rate of transcription of a eukaryotic gene in response to cyclic AMP.

A comparison of the promoter strengths of two eukaryotic genes in vitro reveals a region of DNA that can influence the rate of transcription in cis over long distances.

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes