Table 6. Motif enrichment in the lists of candidate cyclic genes from mouse, chicken, and zebrafish datasets.
We have compiled the lists of candidate cyclic genes with one and two peak of expression during mouse, chicken, and zebrafish somitogenesis and tested them against the reference of regulatory motifs. For each species, we reported the number of genes containing the corresponding motif in their promoter as well as the genes with the highest E-values. These genes represent leading cyclic candidate genes. As expected, none of the motifs discovered in mouse was found to be overrepresented in the promoter of zebrafish candidate cyclic genes.
| Motifs | Mouse unimodal [15] (164 genes) | Mouse bimodal [15] (173 genes) | Chicken unimodal (S1 Table, 211 genes) | Chicken bimodal (S2 Table, 131 genes) | Zebrafish unimodal (S3 Table, 111 genes) | Zebrafish bimodal (S4 Table, 61 genes) |
|---|---|---|---|---|---|---|
| A1 | (87 genes): Cmtm6, Ptpn11, Fgfrl1, Pole, Ccnd1, Skil, Llf3 | (52 genes): Fgf13, Wsb2, Reep5 Pik3ca, Arfip2, Ndfip1 | (90 genes): PSMB7, PCSK5, PTRH2, MAP2K6 | (50 genes): WBSCR22, SAMD15 | 0 | 0 |
| A2 | (52 genes): Start3, Psmd7, Timm44, Lrig3, Mark1, Ephb4 | (41 genes): Ddah2, Cdkn1a, Rnpep, Scand1, Bola2, Vps37a | (5 genes): FBLN2, MNAT1, CDC42BPA | (1 gene): ESD | 0 | 0 |
| A3 | (60 genes): Cmtm6, Safb2, Fgfrl1, Ankhd1, Msi2, Ccnd1 | (31 genes): Reep5, Rcor1, Creb3, Ube3b, Tcap, Isca2 | (38 genes): MAP2K6, EPC2, URM1, OLA1 | (1 gene): RNF126 | 0 | 0 |
| A4 | (85 genes): Ankhd1, Fam13c, Akap1, Mtm1, Nova1, Ogt, Thra | (72 genes): Oxa1l, Pik3ca, Rnpep, Csnk2a1, Antxr1, Surf4 | (10 genes): SHPK, MAD2L1, OLA1, WBP4 | (7 genes): RARB, FADD | 0 | 0 |
| A5 | (43 genes): Safb2, Cmtm6, Ccnd1, Fgfrl1, Qser1, Akirin1 | (35 genes): Fgf13, Vps37a, Zfp219, Tcap, Kap, Gnb1 | (54 genes): PSMB7, MAP2K6, CEP76, XPO7 | 0 | 0 | 0 |
| A6 | (62 genes): Tnpo3, Ube2l3, Urm1, Efemp2, Slc16a11, Trub2 | (45 genes): Ndfip1, Grn, Reep5, Rad17, Tor1b, Cdkn1a | 0 | 0 | 0 | 0 |
| A7 | (61 genes): Rps9, Rbm14, Paf1, Tnpo3, Ddx46, Slc16a11, Zfp7 | (46 genes): Phf20, Shmt1, Rab22a, Rad17, Tor1b, Vcp | 0 | 0 | 0 | 0 |
| A8 | (55 genes): Coro2b, Hsd17b7, Dnajc3, Cmtm6, Ugp2, Ephb4 | (41 genes): Spred2, 9030624J02Rik, Tcap, Copg2, Dgat2 | (35 genes): FAR1, MRPL32, PTRH2, CTNND1 | (2 genes): MEF2BNB, CCNK | 0 | 0 |
| A9 | (46 genes): Wdr33, Akap1, Timm44, Tnpo3, Ddx46, Trub2 | (39 genes): Tor1b, Zc3h11a, Med1, Gnpda2, Ddah2, Suz12 | (3 genes): SEC14L1, PEX16, PIGW | 0 | 0 | 0 |
| A10 | (41 genes): Wdr33, Fgfrl1, Ercc8, Safb2, Hdlbp, Thra, Exosc4, Coro2b | (28 genes): Add3, Tcap, Reep5, Creb3, Kap | 0 | 0 | 0 | 0 |