In the nonsynonymous regions of these genes we compared the SIFT [13], PMUT [14], and PolyPhen [15] methods of predicting whether the variants were deleterious protein coding mutations.
To define housekeeping genes, we compared CRISPR screens from publicly available datasets40,41,42,43 and this study.
To test for signatures of positive selection acting on giraffe lineage for each of the genes, we compared the likelihood scores of selection models implemented in CODEML in the PAML package, version 4.7 (ref. 60), using likelihood ratio tests (LRTs).
To determine whether recruitment of NELF to the 3′ region of the U1 gene is simply because of the small size of this gene or whether it reflects a functional difference between snRNA and protein-coding genes, we compared the NELF with Pol II signal ratios of the genes encoding U1 and beta-actin as a function of the distance from the TSS (Supplementary Fig. 3).
In an effort to identify and clone psoriasis-specific genes, we compared gene expression in normal, tape-stripped (wounded), and psoriatic skin using the cDNA differential display technique.
To further confirm the phylogenetic relationship of the OPT genes, we compared the rice OsOPT genes with OPT genes from other species.
To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families.
Next, taking all the annotated, AS genes, we compared the relative numbers of constitutively and differentially expressed transcripts.
To identify taste bud-associated genes, we compared gene expression between isolated taste buds and lingual epithelium lacking taste buds.
Like the analysis performed on CNV genes, we compared these target genes with the 425 T2D-related genes.
To identify potential IBC-specific candidate genes, we compared in the 173 IBCs and nIBCs only the genes with deregulated mRNA expression in relation to CNA (Figure S1).
