Table 1. Known Neural Tube Transcription Factors

Table 1. Known neural tube transcription factors

Gene Green White Probe Max. Fold ∆b Avg ∆c Review ref.d Functional Expression sets sig.a ref.e ref. f Mantle Zone Lhx2 None dI1 1 815 +3.4 na (1) nk (2) Lhx9 None dI1 3 269 +12.8 6.3 (1) nk (2) BarHl1 None dI1 2 100 +3.7 2.9† (1) nk (3) Brn3a dI5, dI4LB dI1,dI2,dI3 2 5556 -2.1 -2.3 (1) (4) (5) Foxd3 None dI2, V1 1 115 +7.5 na (1, 6) (7) (8, 9) Lhx1 dI4.dI6 dI2, M 2 5763 -7.3 -7.6 (1) nk (10, 11) Lhx5 dI4.dI6 dI2. 1 1589 -3.2 na (1) nk (10, 11) Isl1 None dI3, M 2 1215 +5.2 +5.0 (1, 6, 12) (13, 14) (15) Tlx3 dI5 dI3 1 729 -3.2 na (1, 6) (16) (17) Lbx1 dI4-dI6, dI4LA,dI4LB None 2 3374 -13.2 -11.8 (1, 6) (9, 18) (19) Pax2 dI4,dI6, dI4LA V0, V1 0 na na na (1, 6) nk (20) Drg11 dI4LB None 1 1467 -8.2 na (6) (21) (22) Ebf1 dI4L nk 4 1804 -1.9 -1.9* nk (23, 24) Ebf3 dI4L nk 2 2394 -1.9 -1.8* nk (23, 24) Phox2a dI5 None 1 23 -1.4*† na nk (25, 26) Lmx1b dI5, dI4LB None 2 601 -7.7* -4.5*† (1, 6) (26, 27) (10) Tlx1 dI5 None 1 214 -4.3* na (1, 6) (16, 28) (17, 29) Evx1 None V0 1 202 +5.1 na (6, 30) (31) (32) Evx2 None nk 1 3 no ∆† na (6) nk (33) En1 None V1 1 31 +3.5† na (6) (10, 34) (20) Gata2 None V2 2 160 +3.9 2.7* (35) (36) Gata3 None V2 1 189 +6.7 na (6) nk (36, 37) Sox14 None V1 1 17 +1.9*† na nk (38) Chx10 None V2 1 130 +5.9 na (6, 12) nk (39) Lhx3 None V2, MN 2 173 +6.6 +4.1* (12) (40, 41) (40) Lhx4 None MN 1 135 +3.7 +2.5† (12) (40, 41) (40) Isl2 None MN 1 27 1.2*† na (12) (42) (40) Hlxb9 None MN 1 7 no∆† na (12) (43, 44) (13) Etv1 None MN 3 197 +6.7 +4.4*† (6, 12) (45) (46) Etv4 None MN 2 7 no∆† no∆† (6, 12) (47) (46) Sim1 MZ V3 2 31 +1.8*† +1.3* (6) nk (39, 48) Ventricular Zone Atoh1 None p(dI1) 1 172 +9.4 na (1, 6, 12) (3, 49) (50) Lmx1a None rp 1 6 +1.2† na (1) (51, 52) (53) Olig3 None p(dI1-dI3) 1 988 +17.7 na (54-56) (54) Msx1 None rp, p(dI1) 2 232 +3.0 +2.2 (1) (57) (58-60) Msx2 None rp 2 60 +4.3 +2.7* nk (60) Msx3 None rp, p(dI1-dI4) 1 1570 +3.8 na (1) (57) (60, 61) Irx3 None p(dI2-V2) 1 1755 +2.7 na (1, 12, 30) (62) (63, 64) Pax3 None p(dI1-6) 2 311 +6.7 +7.1 (1, 6, 30) (65, 66) (67) Ngn1 None p(dI2, V0-V2) 2 1083 +7.1 +4.3* (1, 6, 12) (68) (69) Pax7 None p(dI2-dI6) 1 57 +5.1 na (1, 6, 12, 30) (66) (70) Ngn2 None p(dI2-V2) 1 1874 +2.0 na (1, 6, 12, 30) (68, 71) (69) Pax6 None p(dI4-pMN) 3 700 +9.8 +7.4 (1, 6, 12, 30) (20, 39) (72) Gli2 None p(dI1-M) 2 1135 +7.6 +6.2 (73-75) (76) Gli3 None P(dI1-V1) 3 698 +6.1 +4.3 (1) (77, 78) (76) Gsh2 None p(dI3-dI5) 1 347 +7.0 na (79) (80) Gsh1 None P(dI4-dI5) 1 117 +3.6 na (79) (81) Ascl1 None p(dI4-dI6) 2 3364 +6.8 +8.4 (1, 6, 12) (82) (49, 83) Dbx2 None p(dI6-V1) 1 11 +1.2*† na (1, 6, 12, 30) nk (84) Dbx1 None p(dI6-V0) 1 606 +8.9 na (6, 12, 30) (85) (84) Nkx6.2 None p(V0,V1) 1 12 no∆† na (6, 12) (86) (86) Nkx6.1 None p(V2,MN,V3), fp 1 133 +1.6* na (6, 12, 30) (87) (87) Olig1 None p(MN,ODC) 1 145 +6.3* na (6, 12, 30) (88) (89, 90) Olig2 None p(MN,ODC) 1 31 +2.7† na (6, 12, 30) (91-93) (89, 90) Ngn3 None p(ODC,AC) 2 111 +4.5 (94) (69) Nkx2.2 None p(V3) 1 141 +3.9 na (6, 12, 30) (48) (95) Nkx2.9 None p(V3) 1 31 +1.1*† na (12, 30) (96) (97) Zics Zic1 dI4L p(dI1-dI4) 1 14774 -1.3 na (1) (98) (99) Zic2 nk p(dI1-dI2) 1 344 +1.1* na (1) (100) (99) Zic5 nk dorsal 3 782 +1.6* +1.7 (101) (102) Zic4 nk p(dI2-dI3) 2 414 -1.4* -1.2* nk (103) Hoxes Hoxb6 dI4L nk 1 5169 -2.4 na nk (26) Hoxb8 dI4L nk 1 4850 -3.7 na nk (26) Hoxc8 nk nk 1 2607 -1.4 na (12) (104, 105) (106) Hoxd9 nk nk 1 723 +1.5* na (12) (107) (107) Hoxd10 nk nk 1 713 +2.6 na (12) (107, 108) (109) aAverage signal of the probe set with the highest average signal, in either green or white. bFold decline in the probe set with the highest signal. cAverage fold decline for all probe sets of that gene. dReferred to in the cited review article. Several other genes were included on the basis of follow up reading and direct functional evidence. eCited reference(s) shows differential expression data in the developing neural tube. fCited reference(s) describe some functional difference in the knockout mouse for that gene. In a few instances, frog and chicken studies were cited. *Fails t test at the 95% confidence interval. Most of these pass at the 90% confidence interval. In the fold ∆ column, it indicates that the highest probe set failed. In the Avg ∆ column, it indicates that at least one of the other probe sets failed. †Average signal of a probe set (the larger of G or W) was below the intensity threshold of 33. nk, not known; na, not applicable; no∆, no change.

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