Rank . | Gene . | Peak . | Chr. . | Start . | End . | qPCR . | Orientation . | Gli concensus . | Gli matrix . |
---|---|---|---|---|---|---|---|---|---|
1 | Ptch1 | 2 | 13 | 60949397 | 60950371 | 34 | TSS −1.1k | −137, 219 | −154, −137 |
2 | Nkx2-2 | 1 | 2 | 146644626 | 146645570 | 29.2 | TSS −1.9k | −51 | −98, −51 |
3 | Ptch1 | 3 | 13 | 60951377 | 60952953 | 45.3 | TSS −3.7k | 78, 437 | −760, 78 |
4 | Nkx2-9 | 2 | 12 | 53347310 | 53348354 | 16.2 | TSS −8.7k | −25 | −222, −25, 45, 289 |
5 | Ptch1 | 5 | 13 | 60956284 | 60956777 | 65 | TSS −7.9k | −78 | −78 |
6 | Nkx2-9 | 1 | 12 | 53340519 | 53341015 | 37.7 | TSS −1.9k | −119 | −119 |
7 | Rab34 | 1 | 11 | 77915220 | 77915560 | 28.1 | Intron 1,2 | −71, 264 | −106, −71 |
8 | Ptch2 | 1 | 4 | 116057320 | 116057946 | 5.6 | Intron 2 | −106 | −106 |
9 | Ptch1 | 1 | 13 | 60945578 | 60945972 | 30 | Intron 2 | 101 | |
10 | Nkx 2-1 | 1 | 12 | 53245748 | 53246351 | 9.1 | TES + 11.5k | 152 | −355, 152 |
11 | Gli1 | 1 | 10 | 127076571 | 127078504 | 7.2/4.7/12.5 | Promoter, Intron 1,2 | −115, 543, 1422, 1580 | −115, 1580 |
12 | Hhip | 1 | 8 | 79270092 | 79270492 | 5.6 | Intron 1 | −51 | −184, −51 |
13 | FoxA2 | 1 | 2 | 147493701 | 147494245 | 6.4 | TES +5.8k | −148, 331 | −148, 331 |
14 | Ptch2 | 2 | 4 | 116054385 | 116054954 | 48.3 | TSS −0.3k | −136, 61 | −136, 65 |
15 | Cart1 | 1 | 10 | 102925949 | 102926177 | - | Intron 3 | NA | NA |
16 | Ptch1 | 4 | 13 | 60953950 | 60955072 | 9 | TSS −6.3k | −36 | 380 |
17 | Prdx2 | 1 | 8 | 84215218 | 84215559 | 1.4 | TSS −22.5k | NA | −78 |
18 | Cart1 | 2 | 10 | 102938108 | 102938308 | - | Intron 2 | −75 | −75 |
19 | Ptch1 | 6 | 13 | 61010241 | 61010714 | 2.8 | TSS −61.9k | NA | NA |
20 | Hhip | 2 | 8 | 79268419 | 79268867 | 8.9 | Intron 1 | NA | NA |
21 | Flrt3 | 1 | 2 | 140191468 | 140191692 | - | TSS −6.3k | NA | NA |
22 | Pax9 | 1 | 12 | 53443055 | 53443311 | - | TES +5.3k6 | −35 | NA |
23 | Ncor2 | 1 | 5 | 124340743 | 124341009 | - | TSS −0.4k | 60, 335 | 54, 60, 199 |
24 | Zic3 | 1 | X | 52789693 | 52789967 | - | TES −0.8k (3′ UTR) | NA | NA |
25 | Hand2 | 1 | 8 | 56373391 | 56373692 | 2.7 | TES +10.3k | −154 | −181, −154 |
Rank . | Gene . | Peak . | Chr. . | Start . | End . | qPCR . | Orientation . | Gli concensus . | Gli matrix . |
---|---|---|---|---|---|---|---|---|---|
1 | Ptch1 | 2 | 13 | 60949397 | 60950371 | 34 | TSS −1.1k | −137, 219 | −154, −137 |
2 | Nkx2-2 | 1 | 2 | 146644626 | 146645570 | 29.2 | TSS −1.9k | −51 | −98, −51 |
3 | Ptch1 | 3 | 13 | 60951377 | 60952953 | 45.3 | TSS −3.7k | 78, 437 | −760, 78 |
4 | Nkx2-9 | 2 | 12 | 53347310 | 53348354 | 16.2 | TSS −8.7k | −25 | −222, −25, 45, 289 |
5 | Ptch1 | 5 | 13 | 60956284 | 60956777 | 65 | TSS −7.9k | −78 | −78 |
6 | Nkx2-9 | 1 | 12 | 53340519 | 53341015 | 37.7 | TSS −1.9k | −119 | −119 |
7 | Rab34 | 1 | 11 | 77915220 | 77915560 | 28.1 | Intron 1,2 | −71, 264 | −106, −71 |
8 | Ptch2 | 1 | 4 | 116057320 | 116057946 | 5.6 | Intron 2 | −106 | −106 |
9 | Ptch1 | 1 | 13 | 60945578 | 60945972 | 30 | Intron 2 | 101 | |
10 | Nkx 2-1 | 1 | 12 | 53245748 | 53246351 | 9.1 | TES + 11.5k | 152 | −355, 152 |
11 | Gli1 | 1 | 10 | 127076571 | 127078504 | 7.2/4.7/12.5 | Promoter, Intron 1,2 | −115, 543, 1422, 1580 | −115, 1580 |
12 | Hhip | 1 | 8 | 79270092 | 79270492 | 5.6 | Intron 1 | −51 | −184, −51 |
13 | FoxA2 | 1 | 2 | 147493701 | 147494245 | 6.4 | TES +5.8k | −148, 331 | −148, 331 |
14 | Ptch2 | 2 | 4 | 116054385 | 116054954 | 48.3 | TSS −0.3k | −136, 61 | −136, 65 |
15 | Cart1 | 1 | 10 | 102925949 | 102926177 | - | Intron 3 | NA | NA |
16 | Ptch1 | 4 | 13 | 60953950 | 60955072 | 9 | TSS −6.3k | −36 | 380 |
17 | Prdx2 | 1 | 8 | 84215218 | 84215559 | 1.4 | TSS −22.5k | NA | −78 |
18 | Cart1 | 2 | 10 | 102938108 | 102938308 | - | Intron 2 | −75 | −75 |
19 | Ptch1 | 6 | 13 | 61010241 | 61010714 | 2.8 | TSS −61.9k | NA | NA |
20 | Hhip | 2 | 8 | 79268419 | 79268867 | 8.9 | Intron 1 | NA | NA |
21 | Flrt3 | 1 | 2 | 140191468 | 140191692 | - | TSS −6.3k | NA | NA |
22 | Pax9 | 1 | 12 | 53443055 | 53443311 | - | TES +5.3k6 | −35 | NA |
23 | Ncor2 | 1 | 5 | 124340743 | 124341009 | - | TSS −0.4k | 60, 335 | 54, 60, 199 |
24 | Zic3 | 1 | X | 52789693 | 52789967 | - | TES −0.8k (3′ UTR) | NA | NA |
25 | Hand2 | 1 | 8 | 56373391 | 56373692 | 2.7 | TES +10.3k | −154 | −181, −154 |
First-tier peaks (ranked 1-13) include all known Gli enhancer sites (gene name is underlined in `Gene' column). Negative values indicate regions upstream (5′) of the specified reference site in the orientation column,and positive values are downstream (3′) of the site. Gli consensus and matrix sites were mapped to the defined peak regions and are displayed as values relative to the peak center (see Table S2 in the supplementary material). Our Gli-site mapping tolerates only a 1 bp mismatch from the TGGGTGGTC consensus. Sites that are identified by both consensus and matrix mapping are underlined. Chr., chromosome; NA, not applicable (no Gli sites present); TSS, transcriptional start site; TES, transcriptional end site; UTR,untranslated region.