Table 2.
Comparison of our zCNE set to previous zebrafish CNE sets
| Pairwise comparisona | |||||||
|---|---|---|---|---|---|---|---|
| Total (bp) | In both CNE sets | Unique in our zCNE set | Unique in other CNE set | ||||
| zCNEs all | 6 643 241 | ||||||
| zCNEs teleost + lamprey | 6 072 642 | ||||||
| zCNEs human | 1 769 804 | ||||||
| ECRBrowser | bp | % of other set | bp | % of our set | bp | % of other set | |
| Fugu | 4 014 503 | 2 509 862 | 62.52% | 3 562 780 | 58.67% | 1 504 641 | 37.48% |
| Human | 1 262 653 | 874 451 | 69.26% | 895 353 | 50.59% | 388 202 | 30.74% |
| ANCORA | |||||||
| Fugu | 4 085 372 | 2 870 306 | 70.26% | 3 202 336 | 52.73% | 1 215 066 | 29.74% |
| Tetraodon | 3 582 692 | 2 634 273 | 73.53% | 3 438 369 | 56.62% | 948 419 | 26.47% |
| Stickleback | 5 020 698 | 3 220 581 | 64.15% | 2 852 061 | 46.97% | 1 800 117 | 35.85% |
| Medaka | 4 745 417 | 2 945 151 | 62.06% | 3 127 491 | 51.50% | 1 800 266 | 37.94% |
| Human | 1 403 083 | 996 067 | 70.99% | 773 737 | 43.72% | 407 016 | 29.01% |
| CNEViewer | |||||||
| All CNEs | 563 113 | 416 675 | 73.99% | 1 353 129 | 76.46% | 146 438 | 26.01% |
| Syntenic CNEs | 248 105 | 196 911 | 79.37% | 1 572 893 | 88.87% | 51 194 | 20.63% |
| Union of all previous setsb | |||||||
| In zCNEs and other sets | Unique in our zCNE set | Unique in other sets | |||||
| Union of all previous resources | 10 765 678 | 5 204 466 | 48.34% | 1 438 775 | 21.66% | 5 561 212 | 51.66% |
| Breakdown of 5 561 212 bp unique to other sets | bp | % | |||||
| Do not align to zebrafish by our approach | 191 704 | 3.4% | |||||
| Are not syntenic according to our criteria | 3 714 572 | 66.8% | |||||
| Do not overlap well-aligning windows | 981 312 | 17.6% | |||||
| Overlap well-aligning windows but the region is <50 bp | 496 580 | 8.3% | |||||
| Overlap well-aligning window ≥50 bp but not supported by ≥2 species | 155 813 | 2.8% | |||||
| GREAT enrichment (top annotation term)c | |||||||
| # GREAT version 2.0.1 | In zCNEs and other sets | Unique in our zCNE set | Unique in other sets | ||||
| Ontology and term name | Binom FDR Q-Val | Binom fold enrichment | Binom FDR Q-Val | Binom fold enrichment | Binom FDR Q-Val | Binom fold enrichment | |
| GO molecular function | |||||||
| Sequence-specific DNA binding | 0 | 3.1 | 7 E-279 | 2.2 | n.d. | n.d. | |
| GO biological process | |||||||
| Regulation of transcription, DNA-dependent | 0 | 2.7 | 3 E-314 | 2.0 | n.d. | n.d. | |
| Wiki pathways | |||||||
| Nuclear receptors | 3 E-128 | 5.0 | 5 E-41 | 3.0 | n.d. | n.d. | |
| InterPro | |||||||
| Homeodomain-like | 0 | 3.7 | 5 E-199 | 2.5 | n.d. | n.d. | |
aTo exclude any differences because of our stringent filtering procedure, we applied the same filters for repeats and genic regions to the ECR Browser (pairwise zebrafish–fugu/human), Ancora (pairwise zebrafish–fugu/tetraodon/stickleback/medaka/human) and CNEViewer (pairwise zebrafish–human) sets (Supplementary Table S5). We used our set of CNEs built from the teleosts and lamprey multiple alignment (6 072 642 bp in 51 997 CNEs) to compare with pairwise zebrafish–teleost sets. We used our set of CNEs that are conserved to human (1 769 804 bp in 11 573 CNEs) to compare with pairwise zebrafish–human sets. We found that, despite our stringent synteny filter and requiring at least two other aligning species, our CNE set is substantially larger than any of these pairwise sets, as 44–89% of the bases in zCNEs are not contained in the other sets.
bCompared with the union of all previous sets, zCNEs still add 1.4 Mb (22% of our set). Other sets contain 5.6 Mb that are not in our zCNE set for reasons listed in the table.
cCNEs that are in both our zCNE and other sets as well as CNEs that are unique to our set show the expected enrichments for transcription factors using the zebrafish GREAT webserver http://great.stanford.edu. In contrast, these enrichments were not detected (n.d.) for CNEs unique to other sets. Top enrichment is shown. Size-matched sets were compared to assure equal statistical power of GREAT.