Computational protocol: Effects of different kinds of essentiality on sequence evolution of human testis proteins

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Protocol publication

[…] In order to determine the extent and direction of selection acting on each protein, we extracted dN/dS estimates from ENSEMBL version 82, which had been calculated using CodeML as implemented in the PAML package. We exclusively collected dN/dS values derived from 1-to-1 orthologues of human (Homo sapiens; genome assembly GRCh38.p3) and mouse (Mus musculus; genome assembly GRCm38.p4). Since we considered only dN/dS estimates reported on the orthologues view pages of the genes included, we avoided values potentially biased by saturation of dS, which are masked out on these pages (http://sep2015.archive.ensembl.org/info/genome/compara/homology_method.html). For all proteins for which dN/dS values could be extracted from their Ensembl pages, we additionally derived dN and dS values via Ensembl Biomart (version 82).We investigated expression specificity of each protein using the tissue specificity index τ. Values of τ vary between 0 for genes expressed at similar levels in all examined tissues and 1 for genes expressed in only one tissue. Following Kaiser et al. τ was based on FPKM (fragments per kilobase of transcript per million fragments mapped) values which we downloaded from Human Protein Atlas version 12. Excluding data referring to three female-specific tissues (ovary, placenta, and uterus), we used FPKM values from altogether 24 tissues to calculate τ. In (, ), we also report analyses including this variable in which τ is based on all 27 tissues from Human Protein Atlas version 12 and with τ extracted from by Kryuchkova-Mostacci and Robinson-Rechavi, which was calculated with the same data, but different methodology. In analyses including the latter values of τ, one gene RECQL4, a member of the lethality category, was missing from the dataset since its tissue specificity index had not been calculated by Kryuchkova-Mostacci and Robinson-Rechavi. […]

Pipeline specifications

Software tools PAML, BioMart
Databases Human Protein Atlas
Application Genome annotation
Organisms Homo sapiens, Mus musculus
Diseases Infertility