*4.6. Phylogenetic Profiling and Cluster Analyses of Human MeCP2, CDKL5, and FOXG1 and Their Interacting Proteins*

Sequences of human MeCP2, CDKL5, and FOXG1 and their interaction partners identified with BioGRID (https://thebiogrid.org/; release 2019\_03) were obtained from the UniProtKB/Swiss-Prot database (https://www.uniprot.org/help/uniprotkb; release 2019\_04) and used as the dataset [45,46]. We generated phylogenetic profiles of 326 eukaryotes in the KEGG database (https://www.genome. jp/kegg/) using the dataset as a query [81]. Phylogenetic profiling is a method for detecting the presence or absence of orthologous proteins in a target organism [82]. The presence or absence of

proteins homologous to the query in each species was determined using KEGG Ortholog Cluster (https://www.genome.jp/tools/oc/; release 2019\_04), this tool uses Smith–Waterman similarity scores of ≥150 and symmetric similarity measures to classify the ortholog genes [83]. We suggest that it is a reliable tool to get ortholog data. Profiles were determined based on the Manhattan distance and then clustered using Ward's method [84].
