ArticleNucleic acids research2009
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- Properties of human disease genes and the role of genes linked to Mendelian disorders in complex disease aetiology.Human molecular genetics · 2017Article
- ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling.Nucleic acids research · 2015Article
- ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.PLoS computational biology · 2012Article
- Widespread establishment and regulatory impact of Alu exons in human genes.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Similarly strong purifying selection acts on human disease genes of all evolutionary ages.Genome biology and evolution · 2009Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic patterns show the presence or absence of certain genes in a set of full genomes derived from different species. They can also be used to determine sets of genes that occur only in certain evolutionary branches. Previously, we presented a database named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns. Here, we describe an updated version of PhyloPat which can be queried by an improved web server. We used a single linkage clustering algorithm to create 241,697 phylogenetic lineages, using all the orthologies provided by Ensembl v49. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a phylogenetic tree of the 39 included species. Users can also input a list of Ensembl, EMBL, EntrezGene or HGNC IDs to check which phylogenetic lineage any gene belongs to. A link to the FatiGO web interface has been incorporated in the HTML output. For each gene, the surrounding genes on the chromosome, color coded according to their phylogenetic lineage can be viewed, as well as FASTA files of the peptide sequences of each lineage. Furthermore, lists of omnipresent, polypresent, oligopresent and anticorrelating genes have been included. PhyloPat is freely available at http://www.cmbi.ru.nl/phylopat.
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Registered trials
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