Suppl. Table 5: Transcription factors in the ASE SAGE dataset. Broadly/ubiquitously-expressed transcriptional co-factors or chromatin-associated factors are not considered. Singletons are not shown. Note that we tested one singleton (nhr-253) and found it to be expressed in ASE (see main text). Grey shading indicates TFs with previously described expression and function in ASE. Other previously known TF expressed in ASE (e.g. cog-1 or die-1) are present in the ASE SAGE library, but not enriched relative to AFD (see Suppl. Table 2C)

Gene name

/

description

/ location
(LG) / ASE tags / AFD tags / other tags1 / ASE motif score / GFP reporter 2
Comparison Criterion #1: Tags only in ASE library
F37B4.10 / C2H2 Zn fingers / V:8.61 / 7 / 0 / ++ / 0.60‡ / NG
nhr-204 / C4-type Zn fingers / V:-20.00 / 6 / 0 / ++ / 0.58# / NG
nhr-124 / C4-type Zn fingers / V:-7.63 / 5 / 0 / + / 0.68‡ / NG
nhr-232 / C4-type Zn fingers / V:2.43 / 5 / 0 / ++ / 0.57‡ / NG
nhr-177 / C4-type Zn fingers / V:-18.20 / 4 / 0 / ++ / 0.62‡ / NG
nhr-197 / C4-type Zn fingers / V:8.64 / 4 / 0 / + / 0.65‡ / NG
cfi-1 / ARID domain / I:4.14 / 4 / 0 / ++ / 0.62# / N
aha-1 / bHLH-PAS / I:4.75 / 4 / 0 / ++ / 0.53‡ / Y
nhr-270 / C4-type Zn fingers / V:-19.99 / 3 / 0 / ++ / 0.63 / NG
Y62E10A.17 / AP-2-like / IV:9.00 / 3 / 0 / ++ / 0.60 / NG
tbx-8 / T box / III:2.44 / 3 / 0 / ++ / 0.64‡ / N
nhr-26 / C4-type Zn fingers / X:8.01 / 3 / 0 / - / 0.55‡ / NG
C26E1.3 / homeobox-like / V:5.13 / 3 / 0 / ++ / 0.62‡ / NG
nhr-116 / C4-type Zn fingers / V:11.32 / 2 / 0 / ++ / 0.62 / NG
nhr-176 / C4-type Zn fingers / V:9.47 / 2 / 0 / ++ / 0.53‡ / NG
fkh-8 / forkhead / II:-0.41 / 2 / 0 / ++ / 0.64‡ / Y
nhr-203 / C4-type Zn fingers / V:-20.00 / 2 / 0 / ++ / 0.56 / NG
ahr-1 / bHLH / I:3.79 / 2 / 0 / ++ / 0.60 / N
nhr-98 / C4-type Zn fingers / V:-20.00 / 2 / 0 / ++ / 0.53‡ / NG
zim-2 / C2H2 Zn fingers / IV:4.62 / 2 / 0 / ++ / 0.56‡ / NG
T08G5.7 / C2H2 Zn fingers / V:6.10 / 2 / 0 / ++ / 0.57‡ / NG
nhr-217 / C4-type Zn fingers / I:13.16 / 2 / 0 / + / 0.61‡ / NG
nhr-228 / C4-type Zn fingers / V:-15.01 / 2 / 0 / ++ / 0.60‡ / NG
mef-2 / MADS box / I:3.57 / 2 / 0 / ++ / 0.66# / P§
dsc-1 / homeobox / X:21.81 / 2 / 0 / ++ / 0.63 / Y
C04F5.9 / C2H2 Zn fingers / V:-2.48 / 2 / 0 / ++ / 0.63‡ / NG
Y66A7A.5 / homeobox-like / III:11.34 / 2 / 0 / ++ / 0.59‡ / P
C29E4.13 / C2H2 Zn fingers / III:-0.49 / 2 / 0 / ++ / 0.50‡ / NG
efl-2 / Winged helix / II: 17.01 / 2 / 0 / ++ / 0.55# / NG
nhr-277 / C4-type Zn fingers / IV:-6.67 / 2 / 0 / ++ / 0.53 / NG
sdz-38 / C2H2 Zn fingers / II:1.82 / 2 / 0 / ++ / 0.67 / NG
Comparison Criterion #2: 3x enriched in ASE vs. AFD SAGE library

T22C8.3

/ C2H2 Zn fingers / II 0.83 / 8 / 1 / ++ / 0.59‡ / NG
ztf-3 / C2H2 Zn fingers / I –19.15 / 6 / 1 / ++ / 0.69‡ / Y
nhr-51 / C4-type Zn fingers / V:8.61 / 6 / 1 / ++ / 0.57‡ / NG
hlh-10 / bHLH / V:1.98 / 6 / 1 / ++ / 0.64‡ / Y
C28G1.4 / C2H2 Zn fingers / X:0.44 / 5 / 1 / ++ / 0.62‡ / NG
che-1 / C2H2 Zn fingers / I:1.20 / 5 / 1 / + / 0.62‡ / Y
ceh-38 / homeobox / II:0.14 / 5 / 1 / ++ / 0.60‡ / Y
nhr-4 / C4-type Zn fingers / IV:4.44 / 5 / 1 / ++ / 0.61‡ / N
nhr-34 / C4-type Zn fingers / IV:4.35 / 5 / 1 / ++ / 0.67 / NG
nhr-134 / C4-type Zn fingers / V:-15.20 / 5 / 1 / ++ / 0.52‡ / NG
nhr-48 / C4-type Zn fingers / X:22.94 / 5 / 1 / ++ / 0.70 / P
ceh-36 / homeobox / X:16.66 / 8 / 2 / ++ / 0.72‡ / Y
elt-3 / GATA / X:15.53 / 4 / 1 / ++ / 0.68 / P
nhr-256 / C4-type Zn fingers / V:-17.72 / 4 / 1 / ++ / 0.54 / NG
ehn-3 / C2H2 Zn fingers / IV: 1.66 / 4 / 1 / ++ / 0.64 / P
F55A3.2 / C2H2 Zn fingers / I: 5.20 / 4 / 1 / ++ / 0.57‡ / NG
Y37F4.6 / C2H2 Zn fingers / I: 5.51 / 4 / 1 / ++ / 0.62‡ / NG
K09H9.7 / C2H2 Zn fingers / I: 5.51 / 4 / 1 / ++ / 0.56‡ / NG
K06A1.1 / AP-2-type / II:-0.27 / 4 / 1 / ++ / 0.58‡ / NG
hsf-1 / Heat shock factor / I:13.02 / 13 / 4 / ++ / 0.67 / NG
nhr-152 / C4-type Zn fingers / V:0.85 / 3 / 1 / ++ / 0.52‡ / NG
nhr-2 / C4-type Zn fingers / I:0.46 / 3 / 1 / ++ / 0.64‡ / P
nhr-21 / C4-type Zn fingers / II:0.50 / 9 / 3 / ++ / 0.62 / NG
F37D6.2 / C2H2 Zn fingers / I:5.03 / 9 / 3 / ++ / 0.55‡ / NG
nhr-143 / C4-type Zn fingers / V:1.90 / 3 / 1 / ++ / 0.58 / NG
nhr-144 / C4-type Zn fingers / V:1.90 / 3 / 1 / ++ / 0.60‡ / NG
nhr-58 / C4-type Zn fingers / V:-20.00 / 9 / 3 / ++ / 0.53‡ / NG
Y37E11B.1 / C2H2 Zn fingers / IV:-3.45 / 6 / 2 / ++ / 0.56‡ / NG
F48F7.5 / C2H2 Zn fingers / X:15.90 / 6 / 2 / ++ / 0.62 / NG
nhr-14 / C4-type Zn fingers / X:0.06 / 3 / 1 / ++ / 0.54‡ / NG
F27D4.6 / C2H2 Zn fingers / I:2.32 / 3 / 1 / ++ / 0.60 / NG
F26F4.8 / C2H2 Zn fingers / III:-2.39 / 3 / 1 / ++ / 0.63 / P
ceh-10 / homeobox / III:-1.45 / 3 / 1 / ++ / 0.59‡ / P
nhr-86 / C4-type Zn fingers / V:-16.03 / 3 / 1 / ++ / 0.61# / NG
dlx-1 / homeobox / V:18.27 / 3 / 1 / ++ / 0.63# / P
C33A11.4 / Ets domain / X: 22.48 / 3 / 1 / ++ / 0.64 / NG
Comparison Criterion #3: ASE>AFD (>1 to <3; p<0.05)
Y97E10AR.1 / BTB/PPZ domain / V: 1.0 / 28 / 13 / ++ / 0.59 / N
T24H10.7 / bZIP / II: 1.04 / 24 / 12 / ++ / 0.66 / N
not enriched, but >20 tags
hbl-1 / C2H2 Zn fingers / X:-4.28 / 61 / 57 / ++ / 0.61 / N
pha-4 / forkhead / V:25.11 / 41 / 42 / ++ / 0.66‡ / P
atf-5 / bZIP / X:21.36 / 42 / 37 / ++ / 0.65‡ / NG
tbx-32 / T-box / X:-17.85 / 59 / 190 / ++ / 0.52‡ / NG
atf-2 / bZIP / II:0.87 / 31 / 28 / ++ / 0.60‡ / P
ztf-10 / C2H2 Zn fingers / X:-1.79 / 25 / 42 / ++ / 0.62 / Y
ceh-34 / homeobox / V:-2.33 / 21 / 27 / ++ / 0.61# / P
others
nhr-50 / C4-type Zn fingers / V:9.32 / 4 / 2 / ++ / 0.59 / Y
nhr-253 / C2H2 Zn fingers / V: -20 / 1 / 0 / - / 0.68 / Y

1 indicates presence in other SAGE dataset ( “-“ no other set;

“+” 1 or 2 other sets; “++” >2 other sets.

2 GFP reporter:

Y = Exists and is expressed in ASE.

P = Exists, but gfp expression in ASE has not been specifically examined.

N = Exists, no gfp expression in ASE in larval/adult stages (at least 3 independent transgenic lines scored), but reporter may not contain all regulatory information, expression levels may be too low to be detectable and/or expression may be temporally restricted to embryonic stages which we have not examined.

NG = Has not been generated

‡Indicates ASE motif found within 1 kilobase upstream of ATG start codon.

# Indicates ASE motif found in an intron or 3’ UTR.