A universal genomic coordinate translator for comparative genomics

BMC Bioinformatics

Table 5 Pairwise interspecies transcript relationships based on analyzing RNA-Sequence data generated and published by Brawand et al. 2011

Species in comparison		Total Source transcripts	Mapped transcripts w/hit	Ensembl transcripts	Protein coding transcripts	Singleton transcripts	Singleton loci	Families transcripts	Families loci
Source	Target	Total Source transcripts	Mapped transcripts w/hit	Ensembl transcripts	Protein coding transcripts	Singleton transcripts	Singleton loci	Families transcripts	Families loci
Chicken	Human	100823	51492	50278	49944	13149	3968	36795	8857
	Opossum		49500	48535	48271	12452	3702	35819	8497
	Chimp		47357	46466	46212	11786	3514	34426	8233
	Gorilla		48585	47604	47326	12146	3632	35180	8420
Opossum	Human	162989	80994	78492	77581	16936	4246	60645	12611
	Chimp		75338	73622	72979	15960	3979	57019	11581
	Gorilla		76486	74620	73935	16227	4049	57708	11837
Human	Chimp	253887	211785	205096	180964	41267	5486	139697	16234
	Gorilla		216536	210180	183659	41743	5588	141916	16498

For each source-target genome pair, we list the number of transcripts mapped from the source that overlap with annotations in the target, indicating the number of annotated transcripts, and the number annotated as protein coding genes in the target genome. We further list overlaps of single-copy genes and gene family members, determined by the genome of the source, with annotated protein coding genes in the target both at the transcript and locus level.

ISSN: 1471-2105