Computational protocol: YAP is essential for tissue tension to ensure vertebrate 3D body shape

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Protocol publication

[…] Lists of homologs of ARHGAP18 family (TF314044) and its closely related families ARHGAP6 (TF316710) and ARHGAP11 (TF332212) in 11 metazoan model species were downloaded from Treefam database. We also obtained the members of the ARHGAP23 (TF329345) family. ARHGAP23 silencing mimics the round phenotype observed in an RNAi screen knocking down ARHGAP18 in HeLa cell line. Amino-acid sequences for these genes were downloaded from Ensembl. Multiple sequence alignment was performed using the PRANK package. This alignment was used to infer the phylogenetic relationship of these genes using Maximum Likelihood using FastTree 2.1. […]

Pipeline specifications

Software tools PRANK, FastTree
Databases TreeFam
Application Phylogenetics
Organisms Oryzias latipes, Homo sapiens