U12 genes were identified by running the U12db (22 (link)) annotation pipeline on the GRCh38 version of the human genome, with the gencode38 version of the annotations, or the GRCz11 version of the zebrafish genome. GO term analysis was performed with the TopGO (v2.38.1) R tool (37 (link)), with the default “weight01” algorithm, the Fisher-test and the org.Hs.eg.db (v3.10.0) R database of the genome-wide annotation for humans. Genes without any GO annotation were discarded.
To constitute a list of cilium-related genes, we combined three existing databases and defined a gene as cilium-related if 1) it was part of the Gene_Ontology (GO = Cilium) of the Gold_Standard (SysCilia, a curated list of known ciliary components) (17 (link)) or of the Predicted candidates based on a bayesian integration in CiliaCarta (38 (link)) (last updated version of March, 18th 2018); 2) it was in the CilDB table v3.0 and had the maximum human ciliary evidence stringency level and at least 3 ciliary evidence (39 (link), 40 (link)) (last update June 2014); and 3) it was a ciliopathy-related gene (18 (link)–20 (link, link)).
To constitute a list of cilium-related genes, we combined three existing databases and defined a gene as cilium-related if 1) it was part of the Gene_Ontology (GO = Cilium) of the Gold_Standard (SysCilia, a curated list of known ciliary components) (17 (link)) or of the Predicted candidates based on a bayesian integration in CiliaCarta (38 (link)) (last updated version of March, 18th 2018); 2) it was in the CilDB table v3.0 and had the maximum human ciliary evidence stringency level and at least 3 ciliary evidence (39 (link), 40 (link)) (last update June 2014); and 3) it was a ciliopathy-related gene (18 (link)–
