ArticleNucleic acids research2008
Human PAML browser: a database of positive selection on human genes using phylogenetic methods.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects.Interdisciplinary sciences, computational life sciences · 2018Article
- Robustness and evolvability of the human signaling network.PLoS computational biology · 2014Article
- Heritability and genomics of gene expression in peripheral blood.Nature genetics · 2014Article
- Sex differences in the human peripheral blood transcriptome.BMC genomics · 2014Article
- The co-regulation mechanism of transcription factors in the human gene regulatory network.Nucleic acids research · 2012Article
- Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis.BMC systems biology · 2012Article
- Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.PloS one · 2012Article
- Patterns of positive selection and neutral evolution in the protein-coding genes of Tetraodon and Takifugu.PloS one · 2011Article
- African signatures of recent positive selection in human FOXI1.BMC evolutionary biology · 2010Article
- Evolutionary genomics of human intellectual disability.Evolutionary applications · 2010Article
- Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics.Molecular biology and evolution · 2009Article
- Selectome: a database of positive selection.Nucleic acids research · 2009Article
- An empirical test for branch-specific positive selection.Genetics · 2008Article
- Detecting clusters of mutations.PloS one · 2008Article
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3 authors.
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Abstract
With the recent increase in the number of mammalian genomes being sequenced, large-scale genome scans for human-specific positive selection are now possible. Selection can be inferred through phylogenetic analysis by comparing the rates of silent and replacement substitution between related species. Maximum-likelihood (ML) analysis of codon substitution models can be used to identify genes with an accelerated pattern of amino acid substitution on a particular lineage. However, the ML methods are computationally intensive and awkward to configure. We have created a database that contains the results of tests for positive selection along the human lineage in 13,721 genes with orthologs in the UCSC multispecies genome alignments. The Human PAML Browser is a resource through which researchers can search for a gene of interest or groups of genes by Gene Ontology category, and obtain coding sequence alignments for the gene and as well as results from tests of positive selection from the software package Phylogenetic Analysis by Maximum Likelihood. The Human PAML Browser is available at http://mendel.gene.cwru.edu/adamslab/pbrowser.py.
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