02371nas a2200289   4500008004100000022001400041245012000055210006900175260001300244300001000257490000700267520143700274653001201711653002301723653002501746653002101771653002001792653001101812653001101823653000901834653002201843100002401865700002001889700002301909700002001932856012901952       2011                        eng d  a1477-405400aEvidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.0 aEvidence for shorttime divergence and longtime conservation of t  c2011 Sep  a442-80 v123 a<p>Gene duplication is one of the main mechanisms by which genomes can acquire novel functions. It has been proposed that the retention of gene duplicates can be associated to processes of tissue expression divergence. These models predict that acquisition of divergent expression patterns should be acquired shortly after the duplication, and that larger divergence in tissue expression would be expected for paralogs, as compared to orthologs of a similar age. Many studies have shown that gene duplicates tend to have divergent expression patterns and that gene family expansions are associated with high levels of tissue specificity. However, the timeframe in which these processes occur have rarely been investigated in detail, particularly in vertebrates, and most analyses do not include direct comparisons of orthologs as a baseline for the expected levels of tissue specificity in absence of duplications. To assess the specific contribution of duplications to expression divergence, we combine here phylogenetic analyses and expression data from human and mouse. In particular, we study differences in spatial expression among human-mouse paralogs, specifically duplicated after the radiation of mammals, and compare them to pairs of orthologs in the same species. Our results show that gene duplication leads to increased levels of tissue specificity and that this tends to occur promptly after the duplication event.</p>10aAnimals10aConserved Sequence10aEvolution, Molecular10aGene Duplication10agene expression10aGenome10aHumans10aMice10aOrgan Specificity1 aHuerta-Cepas, Jaime1 aDopazo, Joaquin1 aHuynen, Martijn, A1 aGabaldón, Toni  uhttp://clinbioinfosspa.es/content/evidence-short-time-divergence-and-long-time-conservation-tissue-specific-expression-after02125nas a2200301   4500008004100000022001400041245007500055210006900130260001300199300001100212490000700223520123800230653001801468653002101486653001001507653001301517653002101530653001101551653001401562653001301576653002901589653002301618100002401641700001801665700002001683700002001703856010001723       2008                        eng d  a1362-496200aPhylomeDB: a database for genome-wide collections of gene phylogenies.0 aPhylomeDB a database for genomewide collections of gene phylogen  c2008 Jan  aD491-60 v363 a<p>The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. To provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at http://phylomedb.bioinfo.cipf.es.</p>10aBase Sequence10aEscherichia coli10aGenes10aGenomics10aHistory, Ancient10aHumans10aPhylogeny10aProteins10aSaccharomyces cerevisiae10aSequence Alignment1 aHuerta-Cepas, Jaime1 aBueno, Anibal1 aDopazo, Joaquin1 aGabaldón, Toni  uhttp://clinbioinfosspa.es/content/phylomedb-database-genome-wide-collections-gene-phylogenies-0