Computational protocol: Epidermal cornification is preceded by the expression of a keratinocyte-specific set of pyroptosis-related genes

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Protocol publication

[…] The genome sequences of bottlenose dolphin (Tursiops truncatus), orca (Orcinus orca), Yangtze river dolphin (Lipotes vexillifer), sperm whale (Physeter catodon), minke whale (Balaenoptera acutorostrata scammoni), cattle (Bos taurus), and humans (Homo sapiens) were investigated for the presence and sequence integrity of genes related to pyroptosis and IL-1 signaling. In addition, the genome sequences of other species were used for sequence comparisons. Because of good sequence assembly quality in pyroptosis-related genes, armadillo (Dasypus novemcinctus) and elephant shrew (Elephantulus edwardii), were chosen as representatives of Atlantogenata, which served as the outgroup to Boreoeutheria (including human, cattle, and cetaceans). The sequences were retrieved from the GenBank database of the National Center for Biotechnology Information (NCBI), USA (http://www.ncbi.nlm.nih.gov/). Gene predictions in the GenBank were used when exon-intron organisation and sequence similarities were compatible with orthology to human genes, otherwise the coding sequences were newly predicted based on these criteria. The Basic Local Alignment Search Tool (BLAST) was used to search for regions of local similarity between sequences. The conservation of blocks of order of genetic elements (synteny) was tested by manual alignment of gene maps including conserved genes on each side the gene(s) of interest. Nucleotide and amino acid sequences were aligned using Multalin with the default parameters for sequence alignments (http://multalin.toulouse.inra.fr/multalin/). […]

Pipeline specifications

Software tools BLASTN, MultAlin
Application Phylogenetics
Organisms Homo sapiens