Supp Table 9, GO:BP enrichment analysis of Dichaete targets genes
GO Term	p-Value	Matches
organ development [GO:0048513]	1.699882e-68	363
single-organism developmental process [GO:0044767]	9.431967e-66	516
system development [GO:0048731]	7.327922e-63	491
multicellular organismal development [GO:0007275]	3.973679e-59	547
anatomical structure development [GO:0048856]	8.976764e-59	562
anatomical structure morphogenesis [GO:0009653]	4.752907e-56	396
developmental process [GO:0032502]	3.071715e-54	595
single-multicellular organism process [GO:0044707]	2.513679e-47	597
organ morphogenesis [GO:0009887]	3.587800e-45	220
regulation of biological process [GO:0050789]	4.115493e-42	535
regulation of cellular process [GO:0050794]	4.654879e-41	506
multicellular organismal process [GO:0032501]	1.789537e-39	627
biological regulation [GO:0065007]	2.372043e-39	560
generation of neurons [GO:0048699]	2.485121e-39	222
imaginal disc development [GO:0007444]	9.387647e-37	190
tissue development [GO:0009888]	3.984908e-36	195
embryo development [GO:0009790]	5.411032e-36	177
cellular developmental process [GO:0048869]	3.484780e-35	417
cell differentiation [GO:0030154]	6.327251e-35	405
regulation of transcription, DNA-dependent [GO:0006355]	1.346500e-34	219
regulation of RNA biosynthetic process [GO:2001141]	1.346500e-34	219
regulation of RNA metabolic process [GO:0051252]	1.474808e-34	231
regulation of nucleobase-containing compound metabolic process [GO:0019219]	1.515406e-34	245
regulation of macromolecule biosynthetic process [GO:0010556]	1.482839e-33	232
regulation of cellular macromolecule biosynthetic process [GO:2000112]	1.482839e-33	232
neuron differentiation [GO:0030182]	1.868562e-33	200
pattern specification process [GO:0007389]	8.210140e-33	165
nervous system development [GO:0007399]	1.439292e-32	325
regulation of nitrogen compound metabolic process [GO:0051171]	1.866853e-32	247
post-embryonic organ development [GO:0048569]	5.531708e-32	153
regulation of primary metabolic process [GO:0080090]	9.736569e-32	278
post-embryonic development [GO:0009791]	1.612189e-31	183
regulation of gene expression [GO:0010468]	1.647423e-31	257
transcription, DNA-dependent [GO:0006351]	2.302397e-31	222
regulation of cellular biosynthetic process [GO:0031326]	2.564980e-31	234
regulation of biosynthetic process [GO:0009889]	3.101026e-31	234
RNA biosynthetic process [GO:0032774]	3.426407e-31	222
cell development [GO:0048468]	4.378343e-31	279
post-embryonic morphogenesis [GO:0009886]	1.605714e-30	162
instar larval or pupal morphogenesis [GO:0048707]	9.239185e-30	159
regulation of macromolecule metabolic process [GO:0060255]	3.419706e-29	279
regulation of cellular metabolic process [GO:0031323]	4.111826e-29	279
imaginal disc morphogenesis [GO:0007560]	5.549160e-29	143
post-embryonic organ morphogenesis [GO:0048563]	5.549160e-29	143
regionalization [GO:0003002]	1.113903e-28	149
regulation of metabolic process [GO:0019222]	1.618013e-28	304
cell morphogenesis involved in differentiation [GO:0000904]	2.095345e-28	145
metamorphosis [GO:0007552]	5.032420e-28	161
instar larval or pupal development [GO:0002165]	5.139119e-28	171
regulation of transcription from RNA polymerase II promoter [GO:0006357]	1.853372e-27	137
neuron development [GO:0048666]	2.338257e-27	176
nucleobase-containing compound biosynthetic process [GO:0034654]	1.556884e-26	234
sensory organ development [GO:0007423]	2.087429e-26	143
cellular component morphogenesis [GO:0032989]	6.590053e-26	200
neurogenesis [GO:0022008]	1.272535e-25	280
embryonic morphogenesis [GO:0048598]	2.644330e-25	94
cell morphogenesis [GO:0000902]	3.850798e-25	183
locomotion [GO:0040011]	5.653448e-25	150
appendage development [GO:0048736]	9.479895e-25	126
single-organism process [GO:0044699]	1.200278e-24	827
cell morphogenesis involved in neuron differentiation [GO:0048667]	1.839682e-24	132
imaginal disc-derived appendage development [GO:0048737]	2.234087e-24	125
cellular nitrogen compound biosynthetic process [GO:0044271]	3.535715e-24	244
appendage morphogenesis [GO:0035107]	5.239337e-24	124
cell fate commitment [GO:0045165]	6.132234e-24	143
aromatic compound biosynthetic process [GO:0019438]	6.756598e-24	238
heterocycle biosynthetic process [GO:0018130]	7.413272e-24	239
imaginal disc-derived appendage morphogenesis [GO:0035114]	1.229977e-23	123
transcription from RNA polymerase II promoter [GO:0006366]	3.371313e-23	137
post-embryonic appendage morphogenesis [GO:0035120]	1.569305e-22	120
organic cyclic compound biosynthetic process [GO:1901362]	2.033135e-22	241
tissue morphogenesis [GO:0048729]	2.250133e-22	109
regulation of developmental process [GO:0050793]	3.758165e-22	147
neuron projection development [GO:0031175]	1.541330e-21	144
cell projection organization [GO:0030030]	1.912319e-21	162
neuron projection morphogenesis [GO:0048812]	4.186177e-21	143
single-organism cellular process [GO:0044763]	4.291997e-21	716
eye development [GO:0001654]	1.999455e-20	112
central nervous system development [GO:0007417]	1.605567e-18	84
compound eye development [GO:0048749]	2.931905e-18	105
cell projection morphogenesis [GO:0048858]	2.978028e-18	145
cell part morphogenesis [GO:0032990]	3.614516e-18	145
negative regulation of biological process [GO:0048519]	4.335507e-18	203
regulation of multicellular organismal development [GO:2000026]	9.751989e-18	109
regulation of multicellular organismal process [GO:0051239]	1.004808e-17	144
cell fate specification [GO:0001708]	1.922155e-17	50
wing disc development [GO:0035220]	3.086796e-17	124
positive regulation of biological process [GO:0048518]	4.839580e-17	173
RNA metabolic process [GO:0016070]	7.300039e-17	264
epithelium development [GO:0060429]	3.756800e-16	98
eye morphogenesis [GO:0048592]	1.422016e-15	90
cell fate determination [GO:0001709]	2.017225e-15	61
morphogenesis of an epithelium [GO:0002009]	2.078283e-15	93
anatomical structure formation involved in morphogenesis [GO:0048646]	4.409208e-15	132
tube development [GO:0035295]	5.534329e-15	64
positive regulation of cellular process [GO:0048522]	7.509775e-15	159
cell motility [GO:0048870]	1.078741e-14	83
cell migration [GO:0016477]	1.293693e-14	80
negative regulation of cellular process [GO:0048523]	1.524707e-14	176
negative regulation of gene expression [GO:0010629]	1.688831e-14	104
compound eye morphogenesis [GO:0001745]	3.856407e-14	85
regulation of cell differentiation [GO:0045595]	4.790237e-14	92
negative regulation of RNA metabolic process [GO:0051253]	4.981904e-14	86
negative regulation of macromolecule metabolic process [GO:0010605]	5.324441e-14	122
chemotaxis [GO:0006935]	5.409294e-14	79
negative regulation of biosynthetic process [GO:0009890]	6.577857e-14	94
negative regulation of cellular biosynthetic process [GO:0031327]	6.577857e-14	94
open tracheal system development [GO:0007424]	7.342483e-14	73
negative regulation of macromolecule biosynthetic process [GO:0010558]	8.911862e-14	93
negative regulation of cellular macromolecule biosynthetic process [GO:2000113]	8.911862e-14	93
negative regulation of transcription from RNA polymerase II promoter [GO:0000122]	9.868291e-14	60
negative regulation of metabolic process [GO:0009892]	9.901035e-14	124
localization of cell [GO:0051674]	1.003456e-13	83
gland development [GO:0048732]	1.284272e-13	70
axonogenesis [GO:0007409]	1.407377e-13	90
wing disc morphogenesis [GO:0007472]	1.467730e-13	97
negative regulation of transcription, DNA-dependent [GO:0045892]	3.365624e-13	83
respiratory system development [GO:0060541]	3.390024e-13	73
muscle structure development [GO:0061061]	3.906182e-13	92
imaginal disc-derived wing morphogenesis [GO:0007476]	4.343395e-13	95
digestive tract development [GO:0048565]	5.924104e-13	47
digestive system development [GO:0055123]	5.924104e-13	47
negative regulation of nucleobase-containing compound metabolic process [GO:0045934]	1.026459e-12	86
eye-antennal disc development [GO:0035214]	1.141510e-12	36
cell communication [GO:0007154]	1.680246e-12	292
negative regulation of nitrogen compound metabolic process [GO:0051172]	2.123672e-12	86
axon guidance [GO:0007411]	2.531316e-12	74
cardiovascular system development [GO:0072358]	2.650061e-12	44
circulatory system development [GO:0072359]	2.650061e-12	44
gastrulation [GO:0007369]	3.579065e-12	41
leg disc development [GO:0035218]	5.035994e-12	45
positive regulation of RNA metabolic process [GO:0051254]	6.984439e-12	79
segmentation [GO:0035282]	7.966307e-12	77
signaling [GO:0023052]	8.058723e-12	284
single organism signaling [GO:0044700]	8.058723e-12	284
negative regulation of cellular metabolic process [GO:0031324]	1.214434e-11	103
taxis [GO:0042330]	1.308662e-11	83
positive regulation of transcription, DNA-dependent [GO:0045893]	1.620127e-11	76
salivary gland development [GO:0007431]	1.625462e-11	61
exocrine system development [GO:0035272]	1.625462e-11	61
cellular component movement [GO:0006928]	1.968938e-11	103
positive regulation of gene expression [GO:0010628]	2.002223e-11	77
positive regulation of macromolecule metabolic process [GO:0010604]	2.281726e-11	91
heart development [GO:0007507]	2.966996e-11	42
positive regulation of nucleobase-containing compound metabolic process [GO:0045935]	3.070068e-11	79
organ formation [GO:0048645]	5.161038e-11	33
dendrite morphogenesis [GO:0048813]	5.627046e-11	61
positive regulation of macromolecule biosynthetic process [GO:0010557]	5.940852e-11	80
imaginal disc pattern formation [GO:0007447]	7.254611e-11	46
dendrite development [GO:0016358]	7.736954e-11	61
signal transduction [GO:0007165]	1.543505e-10	227
embryonic pattern specification [GO:0009880]	1.581161e-10	70
response to stimulus [GO:0050896]	1.655417e-10	399
mesoderm development [GO:0007498]	1.726362e-10	44
positive regulation of transcription from RNA polymerase II promoter [GO:0045944]	1.790335e-10	62
cell adhesion [GO:0007155]	2.134836e-10	68
urogenital system development [GO:0001655]	4.583934e-10	37
renal system development [GO:0072001]	4.583934e-10	37
positive regulation of cellular metabolic process [GO:0031325]	5.912878e-10	94
positive regulation of metabolic process [GO:0009893]	6.194761e-10	95
nucleic acid metabolic process [GO:0090304]	9.533082e-10	286
positive regulation of nitrogen compound metabolic process [GO:0051173]	1.017499e-9	81
blastoderm segmentation [GO:0007350]	1.095146e-9	65
muscle organ development [GO:0007517]	1.690603e-9	76
response to external stimulus [GO:0009605]	2.695371e-9	106
regulation of cell development [GO:0060284]	2.850440e-9	69
cellular process [GO:0009987]	3.182107e-9	894
positive regulation of biosynthetic process [GO:0009891]	3.213105e-9	82
positive regulation of cellular biosynthetic process [GO:0031328]	3.213105e-9	82
brain development [GO:0007420]	4.063874e-9	47
regulation of anatomical structure morphogenesis [GO:0022603]	4.108816e-9	70
biological adhesion [GO:0022610]	4.654050e-9	68
formation of anatomical boundary [GO:0048859]	5.628139e-9	31
cell surface receptor signaling pathway [GO:0007166]	5.893415e-8	145
response to chemical stimulus [GO:0042221]	6.716197e-8	158
nucleobase-containing compound metabolic process [GO:0006139]	7.378469e-8	315
developmental process involved in reproduction [GO:0003006]	1.024656e-7	131
renal tubule development [GO:0061326]	1.303645e-7	32
Malpighian tubule development [GO:0072002]	1.303645e-7	32
formation of organ boundary [GO:0010160]	1.319388e-7	27
cellular component organization [GO:0016043]	1.319736e-7	359
neuron recognition [GO:0008038]	1.729033e-7	40
imaginal disc-derived leg morphogenesis [GO:0007480]	1.780815e-7	35
limb morphogenesis [GO:0035108]	1.780815e-7	35
post-embryonic limb morphogenesis [GO:0035127]	1.780815e-7	35
limb development [GO:0060173]	1.780815e-7	35
cell recognition [GO:0008037]	2.548881e-7	40
genital disc development [GO:0035215]	2.804355e-7	26
leg disc morphogenesis [GO:0007478]	2.819001e-7	35
cellular aromatic compound metabolic process [GO:0006725]	3.688726e-7	328
eye-antennal disc morphogenesis [GO:0007455]	3.754086e-7	24
sex differentiation [GO:0007548]	3.990941e-7	41
formation of primary germ layer [GO:0001704]	4.615602e-7	22
negative regulation of developmental process [GO:0051093]	8.850618e-7	52
regulation of neurogenesis [GO:0050767]	1.430656e-6	44
heterocycle metabolic process [GO:0046483]	1.520016e-6	321
regulation of nervous system development [GO:0051960]	1.607636e-6	56
embryo development ending in birth or egg hatching [GO:0009792]	2.299852e-6	56
regulation of tube architecture, open tracheal system [GO:0035152]	2.376138e-6	32
cellular nitrogen compound metabolic process [GO:0034641]	2.838804e-6	328
organic cyclic compound metabolic process [GO:1901360]	2.992214e-6	332
tube morphogenesis [GO:0035239]	4.323567e-6	43
cellular component organization or biogenesis [GO:0071840]	4.347430e-6	361
reproductive structure development [GO:0048608]	4.562052e-6	35
reproductive system development [GO:0061458]	4.562052e-6	35
salivary gland morphogenesis [GO:0007435]	5.186646e-6	46
gland morphogenesis [GO:0022612]	5.186646e-6	46
reproductive process [GO:0022414]	7.094687e-6	176
mesoderm morphogenesis [GO:0048332]	7.160330e-6	20
enzyme linked receptor protein signaling pathway [GO:0007167]	7.866789e-6	61
establishment of ommatidial planar polarity [GO:0042067]	8.330032e-6	29
cellular response to stimulus [GO:0051716]	9.603142e-6	256
neuron fate commitment [GO:0048663]	1.551909e-5	31
growth [GO:0040007]	1.593522e-5	80
embryonic development via the syncytial blastoderm [GO:0001700]	3.258949e-5	52
mesoderm formation [GO:0001707]	4.409746e-5	19
compound eye photoreceptor cell differentiation [GO:0001751]	4.586387e-5	47
wing disc pattern formation [GO:0035222]	5.222971e-5	31
epithelial tube morphogenesis [GO:0060562]	5.617316e-5	36
gliogenesis [GO:0042063]	5.680163e-5	30
regulation of response to stimulus [GO:0048583]	6.566669e-5	124
midgut development [GO:0007494]	9.813794e-5	20
anterior/posterior pattern specification [GO:0009952]	1.008077e-4	51
photoreceptor cell differentiation [GO:0046530]	1.207661e-4	51
eye photoreceptor cell differentiation [GO:0001754]	1.235914e-4	47
photoreceptor cell fate commitment [GO:0046552]	1.266244e-4	27
transmembrane receptor protein tyrosine kinase signaling pathway [GO:0007169]	1.290732e-4	46
ameboidal cell migration [GO:0001667]	1.437616e-4	23
morphogenesis of a polarized epithelium [GO:0001738]	2.466033e-4	38
head development [GO:0060322]	2.602669e-4	18
tissue migration [GO:0090130]	2.617969e-4	23
morphogenesis of embryonic epithelium [GO:0016331]	2.753616e-4	39
development of primary sexual characteristics [GO:0045137]	4.595694e-4	30
cell fate commitment involved in pattern specification [GO:0060581]	5.006763e-4	19
cell proliferation [GO:0008283]	5.131652e-4	70
dorsal/ventral pattern formation [GO:0009953]	5.563452e-4	45
regulation of biological quality [GO:0065008]	6.296186e-4	149
head segmentation [GO:0035287]	6.561551e-4	17
hindgut morphogenesis [GO:0007442]	6.857368e-4	26
establishment of planar polarity [GO:0001736]	7.127420e-4	35
establishment of tissue polarity [GO:0007164]	7.127420e-4	35
nitrogen compound metabolic process [GO:0006807]	7.417493e-4	349
digestive tract morphogenesis [GO:0048546]	7.925489e-4	28
compound eye photoreceptor fate commitment [GO:0001752]	8.525736e-4	25
muscle cell differentiation [GO:0042692]	8.664419e-4	53
cell fate commitment involved in formation of primary germ layer [GO:0060795]	9.944509e-4	14
regulation of cell communication [GO:0010646]	0.001047	110
gastrulation with mouth forming first [GO:0001703]	0.001049	20
gastrulation involving germ band extension [GO:0010004]	0.001049	20
eye photoreceptor cell fate commitment [GO:0042706]	0.001347	25
regulation of signaling [GO:0023051]	0.001545	109
peripheral nervous system development [GO:0007422]	0.001773	33
gonad development [GO:0008406]	0.001839	25
localization [GO:0051179]	0.001861	288
mesodermal cell fate commitment [GO:0001710]	0.002036	13
mesodermal cell differentiation [GO:0048333]	0.002036	13
negative regulation of cell differentiation [GO:0045596]	0.002248	38
regulation of cellular component organization [GO:0051128]	0.002514	95
regulation of signal transduction [GO:0009966]	0.002569	99
gamete generation [GO:0007276]	0.003718	133
cellular process involved in reproduction in multicellular organism [GO:0022412]	0.003757	109
sexual reproduction [GO:0019953]	0.005518	134
regulation of cell morphogenesis [GO:0022604]	0.006700	44
ectoderm development [GO:0007398]	0.010766	15
regulation of tube size [GO:0035150]	0.011922	22
developmental growth [GO:0048589]	0.012009	53
regulation of neuron differentiation [GO:0045664]	0.012588	32
epithelial cell migration, open tracheal system [GO:0007427]	0.013145	19
epithelial cell migration [GO:0010631]	0.013145	19
epithelium migration [GO:0090132]	0.013145	19
programmed cell death [GO:0012501]	0.013719	62
regulation of cell fate commitment [GO:0010453]	0.014998	18
positive regulation of developmental process [GO:0051094]	0.019403	27
embryonic hindgut morphogenesis [GO:0048619]	0.020237	22
antennal development [GO:0007469]	0.020645	15
cell-cell adhesion [GO:0016337]	0.022466	32
segment specification [GO:0007379]	0.023800	20
macromolecule biosynthetic process [GO:0009059]	0.025690	272
establishment or maintenance of cell polarity [GO:0007163]	0.026782	48
single organism reproductive process [GO:0044702]	0.028406	135
cellular macromolecule biosynthetic process [GO:0034645]	0.029631	270
specification of segmental identity, head [GO:0007380]	0.030644	13
proximal/distal pattern formation, imaginal disc [GO:0007449]	0.033729	14
oogenesis [GO:0048477]	0.034797	100
epithelial cell differentiation [GO:0030855]	0.035271	20
Notch signaling pathway [GO:0007219]	0.035780	33
female gamete generation [GO:0007292]	0.038602	101
dorsal/ventral pattern formation, imaginal disc [GO:0007450]	0.048271	23
somatic muscle development [GO:0007525]	0.049782	21