* miRNA annotation of rhesus macaque is based on human annotation by mapping of macaque miRNA precursors to the human genome by the reciprocal LiftOver.
P cell-cell signaling was the only exceP cell-celle, signalingowasrothen conlyrvation basexceptional annotation and high protein caseervation on moushowingtation.
* miRNA annotation of rhesus macaque used for labelling of the identified novel miRNA-star sequences is based on human annotation by mapping of macaque miRNA precursors to the human genome by the reciprocal LiftOver.
Based on human genome annotations and a number of well-characterized RNA databases (see Materials and Methods), these small RNA sequences were annotated as known miRNA, degradation fragments of non-coding RNA (tRNA, rRNA, snRNA/snoRNA et al)., genomic repeat, mRNA or unclassified.
The set of cancer-hallmark GO terms listed in Table 1 of [ 37] were added to the above obtained GO term set, which was then remapped to a set of corresponding genes based on human GO annotations.
We used the single ranked list option based on human functional annotation, and imported SWISSPROT IDs, which is one of the designated preferred input identifiers for GOrilla analysis.
Human-chimpanzee orthologs and human-macaque orthologs were generated separately, based on human Ensembl annotation (v64) [ 4], human genome (hg19) [ 17], chimpanzee genome (panTro2) [ 18] and macaque genome (rheMac2) [ 20].
As an example of comparisons between closely-related species, our pipeline was first applied to generate human-chimpanzee orthologous genes based on human gene annotation (Ensembl v64) [ 4], human reference genome (hg19) [ 17], and chimpanzee reference genome (panTro2) [ 18].
Since there are no de novo annotations of chimpanzee genes and transcripts, the present study is based solely on human annotations [ 42].
Based on human RefSeq gene annotation from UCSC and 46 vertebrate species conservation (including primate and mammal subsets) (Table 1), we first show that blocks of highly conserved sequences are significantly enriched in first introns relative to other introns.
