Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data
Genre
Journal ArticleDate
2005-05-27Author
Rossness, REidhammer, I
Liberles, DA
Subject
Alternative SplicingAnimals
Biological Evolution
Brain
Cell Lineage
Computational Biology
Evolution, Molecular
Gene Expression
Gene Expression Regulation
Genome
Genomics
Humans
Liver
Models, Genetic
Molecular Sequence Data
Pan troglodytes
Phylogeny
Pongo pygmaeus
RNA, Messenger
Sequence Analysis, Protein
Software
Permanent link to this record
http://hdl.handle.net/20.500.12613/5648
Metadata
Show full item recordDOI
10.1186/1471-2105-6-127Abstract
Background: As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution. Results: A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at http://www.rossnes.org/phyrex. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression. Conclusion: Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes. © 2005 Rossnes et al., licensee BioMed Central Ltd.Citation to related work
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http://dx.doi.org/10.34944/dspace/5630