Supp Table 2: GO:BP enrichment of genes with Dichaete binding (DamID 1%FDR)
GO Term	p-Value	Matches
organ development [GO:0048513]	1.980161e-84	640
single-organism developmental process [GO:0044767]	1.393900e-75	955
system development [GO:0048731]	3.008669e-66	891
anatomical structure morphogenesis [GO:0009653]	2.455167e-63	711
anatomical structure development [GO:0048856]	5.812913e-60	1046
biological regulation [GO:0065007]	6.748886e-60	1138
regulation of biological process [GO:0050789]	2.923939e-57	1060
regulation of cellular process [GO:0050794]	9.955256e-57	1000
multicellular organismal development [GO:0007275]	4.989977e-56	1001
single-multicellular organism process [GO:0044707]	7.328846e-55	1164
developmental process [GO:0032502]	2.451595e-54	1124
organ morphogenesis [GO:0009887]	4.107377e-54	373
tissue development [GO:0009888]	2.991708e-50	346
multicellular organismal process [GO:0032501]	2.310640e-46	1248
locomotion [GO:0040011]	1.343311e-45	285
single-organism process [GO:0044699]	3.266445e-44	1795
generation of neurons [GO:0048699]	2.918110e-42	374
cell development [GO:0048468]	2.692880e-41	521
single-organism cellular process [GO:0044763]	3.875119e-40	1550
imaginal disc development [GO:0007444]	3.095219e-39	314
post-embryonic organ development [GO:0048569]	1.415821e-37	254
cellular developmental process [GO:0048869]	1.347259e-36	779
cell differentiation [GO:0030154]	1.060664e-35	752
tissue morphogenesis [GO:0048729]	3.343803e-35	193
neuron differentiation [GO:0030182]	5.925910e-35	336
instar larval or pupal morphogenesis [GO:0048707]	7.161368e-35	268
imaginal disc morphogenesis [GO:0007560]	9.073464e-35	239
post-embryonic organ morphogenesis [GO:0048563]	9.073464e-35	239
embryo development [GO:0009790]	9.901565e-34	281
post-embryonic morphogenesis [GO:0009886]	1.360598e-33	269
regulation of RNA metabolic process [GO:0051252]	1.611447e-33	390
regulation of transcription, DNA-dependent [GO:0006355]	2.071649e-33	366
regulation of RNA biosynthetic process [GO:2001141]	2.071649e-33	366
appendage development [GO:0048736]	4.681473e-33	216
metamorphosis [GO:0007552]	6.981209e-33	274
regulation of nucleobase-containing compound metabolic process [GO:0019219]	8.590479e-33	416
cell communication [GO:0007154]	2.389975e-32	635
imaginal disc-derived appendage development [GO:0048737]	2.498918e-32	214
appendage morphogenesis [GO:0035107]	3.314033e-32	213
post-embryonic development [GO:0009791]	7.378085e-32	303
signaling [GO:0023052]	1.444179e-31	620
single organism signaling [GO:0044700]	1.444179e-31	620
imaginal disc-derived appendage morphogenesis [GO:0035114]	1.754688e-31	211
regulation of nitrogen compound metabolic process [GO:0051171]	1.819621e-31	425
sensory organ development [GO:0007423]	3.374294e-31	241
nervous system development [GO:0007399]	9.221429e-31	581
regulation of gene expression [GO:0010468]	1.091623e-30	447
post-embryonic appendage morphogenesis [GO:0035120]	1.630420e-30	207
transcription, DNA-dependent [GO:0006351]	2.106655e-30	377
regulation of macromolecule biosynthetic process [GO:0010556]	2.598964e-30	388
regulation of cellular macromolecule biosynthetic process [GO:2000112]	2.598964e-30	388
RNA biosynthetic process [GO:0032774]	3.974170e-30	377
pattern specification process [GO:0007389]	1.234428e-29	260
regulation of developmental process [GO:0050793]	3.512222e-29	260
instar larval or pupal development [GO:0002165]	4.227143e-29	286
morphogenesis of an epithelium [GO:0002009]	5.845304e-29	174
regulation of cellular biosynthetic process [GO:0031326]	7.545773e-29	397
cell fate commitment [GO:0045165]	8.015041e-29	245
regulation of biosynthetic process [GO:0009889]	1.013446e-28	397
epithelium development [GO:0060429]	1.789066e-28	181
cell morphogenesis [GO:0000902]	2.101241e-28	319
cell morphogenesis involved in differentiation [GO:0000904]	2.712496e-28	233
cellular component morphogenesis [GO:0032989]	8.764710e-27	346
neuron development [GO:0048666]	8.853900e-27	293
eye development [GO:0001654]	2.544780e-26	191
response to stimulus [GO:0050896]	2.549176e-26	872
chemotaxis [GO:0006935]	5.563788e-26	145
regulation of multicellular organismal process [GO:0051239]	4.508552e-25	263
compound eye development [GO:0048749]	5.547742e-25	182
cell morphogenesis involved in neuron differentiation [GO:0048667]	7.387779e-25	214
taxis [GO:0042330]	1.215377e-24	160
muscle structure development [GO:0061061]	1.602702e-24	173
wing disc development [GO:0035220]	1.631292e-24	223
nucleobase-containing compound biosynthetic process [GO:0034654]	2.407668e-24	405
regulation of macromolecule metabolic process [GO:0060255]	3.227696e-24	483
regulation of transcription from RNA polymerase II promoter [GO:0006357]	3.811065e-24	213
cell motility [GO:0048870]	6.632958e-24	148
regionalization [GO:0003002]	7.069315e-24	231
axonogenesis [GO:0007409]	7.094503e-24	166
cell migration [GO:0016477]	8.613873e-24	142
localization of cell [GO:0051674]	1.014337e-23	151
regulation of primary metabolic process [GO:0080090]	1.015751e-23	468
regulation of cellular metabolic process [GO:0031323]	3.719204e-23	480
axon guidance [GO:0007411]	4.785097e-23	136
wing disc morphogenesis [GO:0007472]	5.479706e-23	179
embryonic morphogenesis [GO:0048598]	7.667026e-23	138
imaginal disc-derived wing morphogenesis [GO:0007476]	1.306298e-22	176
response to external stimulus [GO:0009605]	2.381757e-22	216
positive regulation of biological process [GO:0048518]	3.950503e-22	319
cell projection organization [GO:0030030]	1.199400e-21	276
regulation of multicellular organismal development [GO:2000026]	2.383034e-21	185
neuron projection morphogenesis [GO:0048812]	3.462320e-21	239
central nervous system development [GO:0007417]	4.905204e-21	134
neuron projection development [GO:0031175]	4.946909e-21	239
regulation of metabolic process [GO:0019222]	5.709673e-21	526
eye morphogenesis [GO:0048592]	7.617907e-21	154
muscle organ development [GO:0007517]	1.100443e-20	147
signal transduction [GO:0007165]	1.511234e-20	468
negative regulation of biological process [GO:0048519]	1.624504e-20	371
cellular nitrogen compound biosynthetic process [GO:0044271]	2.154390e-20	424
negative regulation of cellular process [GO:0048523]	2.591811e-20	333
positive regulation of cellular process [GO:0048522]	2.765269e-20	296
transcription from RNA polymerase II promoter [GO:0006366]	4.143961e-20	218
compound eye morphogenesis [GO:0001745]	9.080211e-20	147
cellular component movement [GO:0006928]	1.313417e-19	194
regulation of cell differentiation [GO:0045595]	4.933454e-19	160
heterocycle biosynthetic process [GO:0018130]	5.374655e-19	411
neurogenesis [GO:0022008]	1.643159e-18	483
aromatic compound biosynthetic process [GO:0019438]	1.923769e-18	407
cell projection morphogenesis [GO:0048858]	2.879740e-18	247
cell part morphogenesis [GO:0032990]	3.944778e-18	247
cell fate specification [GO:0001708]	1.544626e-17	70
tube development [GO:0035295]	3.694666e-17	100
organic cyclic compound biosynthetic process [GO:1901362]	6.240510e-17	415
positive regulation of gene expression [GO:0010628]	5.813863e-16	134
regulation of anatomical structure morphogenesis [GO:0022603]	2.134540e-15	127
respiratory system development [GO:0060541]	2.669907e-15	119
open tracheal system development [GO:0007424]	2.742153e-15	117
positive regulation of transcription from RNA polymerase II promoter [GO:0045944]	3.797457e-15	106
positive regulation of transcription, DNA-dependent [GO:0045893]	4.820336e-15	130
cellular component organization [GO:0016043]	2.544177e-14	760
regulation of signaling [GO:0023051]	3.177580e-14	239
positive regulation of RNA metabolic process [GO:0051254]	3.388813e-14	133
cell adhesion [GO:0007155]	3.803746e-14	116
regulation of biological quality [GO:0065008]	4.649691e-14	326
response to chemical stimulus [GO:0042221]	6.127173e-14	315
muscle cell differentiation [GO:0042692]	6.365925e-14	110
regulation of cell communication [GO:0010646]	7.254259e-14	239
cardiovascular system development [GO:0072358]	9.104819e-14	65
circulatory system development [GO:0072359]	9.104819e-14	65
digestive tract development [GO:0048565]	1.172334e-13	69
digestive system development [GO:0055123]	1.172334e-13	69
embryo development ending in birth or egg hatching [GO:0009792]	1.986503e-13	105
photoreceptor cell differentiation [GO:0046530]	2.186635e-13	101
heart development [GO:0007507]	2.778588e-13	63
cellular response to stimulus [GO:0051716]	3.018034e-13	545
positive regulation of macromolecule biosynthetic process [GO:0010557]	4.510054e-13	136
positive regulation of nucleobase-containing compound metabolic process [GO:0045935]	4.626439e-13	133
mesoderm development [GO:0007498]	7.162720e-13	68
embryonic development via the syncytial blastoderm [GO:0001700]	7.968257e-13	100
cell fate determination [GO:0001709]	1.116658e-12	87
cell-cell signaling [GO:0007267]	1.277983e-12	225
regulation of cell development [GO:0060284]	1.682877e-12	119
positive regulation of nitrogen compound metabolic process [GO:0051173]	2.636335e-12	141
anatomical structure formation involved in morphogenesis [GO:0048646]	2.708510e-12	219
cellular component organization or biogenesis [GO:0071840]	3.457812e-12	770
biological adhesion [GO:0022610]	3.633707e-12	117
regulation of nervous system development [GO:0051960]	4.337466e-12	102
localization [GO:0051179]	4.529777e-12	637
skeletal muscle organ development [GO:0060538]	4.827800e-12	102
gastrulation [GO:0007369]	5.718248e-12	58
positive regulation of biosynthetic process [GO:0009891]	7.389512e-12	144
positive regulation of cellular biosynthetic process [GO:0031328]	7.389512e-12	144
behavior [GO:0007610]	8.388049e-12	210
gland development [GO:0048732]	9.083580e-12	106
positive regulation of macromolecule metabolic process [GO:0010604]	9.869938e-12	153
regulation of cellular component organization [GO:0051128]	3.238230e-11	201
regulation of response to stimulus [GO:0048583]	4.220012e-11	253
striated muscle cell differentiation [GO:0051146]	8.297918e-11	99
RNA metabolic process [GO:0016070]	1.115503e-10	467
segmentation [GO:0035282]	1.440560e-10	122
embryonic pattern specification [GO:0009880]	1.554197e-10	113
urogenital system development [GO:0001655]	2.531972e-10	53
renal system development [GO:0072001]	2.531972e-10	53
cellular process [GO:0009987]	2.567789e-10	1942
negative regulation of developmental process [GO:0051093]	2.762869e-10	90
regulation of signal transduction [GO:0009966]	2.955063e-10	207
tube morphogenesis [GO:0035239]	3.759617e-10	74
reproductive process [GO:0022414]	4.597265e-10	355
regulation of neurogenesis [GO:0050767]	7.592408e-10	74
negative regulation of RNA metabolic process [GO:0051253]	8.061947e-10	130
growth [GO:0040007]	1.105754e-9	151
muscle tissue development [GO:0060537]	1.437156e-9	89
positive regulation of metabolic process [GO:0009893]	1.718737e-9	161
neuron recognition [GO:0008038]	1.859845e-9	63
negative regulation of transcription from RNA polymerase II promoter [GO:0000122]	1.870025e-9	84
blastoderm segmentation [GO:0007350]	2.094216e-9	104
compound eye photoreceptor cell differentiation [GO:0001751]	2.942173e-9	84
striated muscle tissue development [GO:0014706]	3.142074e-9	88
cell recognition [GO:0008037]	3.818481e-9	63
regulation of cell morphogenesis [GO:0022604]	4.373407e-9	86
negative regulation of biosynthetic process [GO:0009890]	5.128364e-9	143
negative regulation of cellular biosynthetic process [GO:0031327]	5.128364e-9	143
morphogenesis of embryonic epithelium [GO:0016331]	5.971245e-9	70
eye photoreceptor cell differentiation [GO:0001754]	6.281899e-9	85
negative regulation of transcription, DNA-dependent [GO:0045892]	6.933567e-9	125
negative regulation of macromolecule biosynthetic process [GO:0010558]	8.999066e-9	141
negative regulation of cellular macromolecule biosynthetic process [GO:2000113]	8.999066e-9	141
positive regulation of cellular metabolic process [GO:0031325]	9.376022e-9	157
epithelial tube morphogenesis [GO:0060562]	1.633218e-8	61
negative regulation of nucleobase-containing compound metabolic process [GO:0045934]	1.868475e-8	131
system process [GO:0003008]	1.904697e-8	299
negative regulation of nitrogen compound metabolic process [GO:0051172]	1.956625e-8	132
transmission of nerve impulse [GO:0019226]	2.399547e-8	136
multicellular organismal signaling [GO:0035637]	2.399547e-8	136
salivary gland development [GO:0007431]	3.033351e-8	89
exocrine system development [GO:0035272]	3.033351e-8	89
negative regulation of gene expression [GO:0010629]	3.714476e-8	157
single-organism behavior [GO:0044708]	4.309855e-8	162
cell surface receptor signaling pathway [GO:0007166]	4.515099e-8	267
neuron fate commitment [GO:0048663]	7.193679e-8	49
developmental process involved in reproduction [GO:0003006]	7.904342e-8	239
establishment or maintenance of cell polarity [GO:0007163]	8.297386e-8	95
negative regulation of macromolecule metabolic process [GO:0010605]	8.510103e-8	191
synaptic transmission [GO:0007268]	9.996463e-8	132
intracellular signal transduction [GO:0035556]	1.113462e-7	181
establishment of planar polarity [GO:0001736]	1.302542e-7	61
establishment of tissue polarity [GO:0007164]	1.302542e-7	61
brain development [GO:0007420]	1.614666e-7	69
leg disc development [GO:0035218]	2.173756e-7	59
morphogenesis of a polarized epithelium [GO:0001738]	2.951304e-7	65
single organism reproductive process [GO:0044702]	3.108256e-7	285
negative regulation of metabolic process [GO:0009892]	3.123390e-7	194
sexual reproduction [GO:0019953]	3.989357e-7	276
multicellular organismal reproductive process [GO:0048609]	4.037443e-7	301
gamete generation [GO:0007276]	4.852727e-7	272
regulation of neuron differentiation [GO:0045664]	5.322590e-7	58
negative regulation of cellular metabolic process [GO:0031324]	6.972972e-7	162
muscle cell development [GO:0055001]	7.084108e-7	82
renal tubule development [GO:0061326]	7.727310e-7	45
Malpighian tubule development [GO:0072002]	7.727310e-7	45
skeletal muscle tissue development [GO:0007519]	8.843292e-7	80
gliogenesis [GO:0042063]	1.107984e-6	47
establishment of ommatidial planar polarity [GO:0042067]	1.315695e-6	43
cell-cell adhesion [GO:0016337]	1.357929e-6	58
dorsal closure [GO:0007391]	1.456907e-6	58
developmental growth [GO:0048589]	1.463834e-6	101
striated muscle cell development [GO:0055002]	1.476713e-6	81
cell proliferation [GO:0008283]	1.943385e-6	130
sex differentiation [GO:0007548]	3.971015e-6	61
organ formation [GO:0048645]	3.990263e-6	40
formation of anatomical boundary [GO:0048859]	3.991811e-6	40
eye-antennal disc development [GO:0035214]	5.527078e-6	42
neurological system process [GO:0050877]	6.265218e-6	274
digestive tract morphogenesis [GO:0048546]	7.444356e-6	45
head segmentation [GO:0035287]	8.908324e-6	24
formation of primary germ layer [GO:0001704]	9.102314e-6	28
regulation of cell fate specification [GO:0042659]	1.082809e-5	27
transmembrane receptor protein tyrosine kinase signaling pathway [GO:0007169]	1.290212e-5	77
regulation of cell fate commitment [GO:0010453]	1.484099e-5	28
imaginal disc pattern formation [GO:0007447]	1.615447e-5	60
head development [GO:0060322]	1.616305e-5	25
Ras protein signal transduction [GO:0007265]	1.809806e-5	53
cellular process involved in reproduction in multicellular organism [GO:0022412]	2.070049e-5	214
mesoderm morphogenesis [GO:0048332]	2.417387e-5	26
negative regulation of cell differentiation [GO:0045596]	2.737215e-5	65
synapse organization [GO:0050808]	2.972303e-5	81
actin cytoskeleton organization [GO:0030036]	3.467784e-5	97
neuroblast differentiation [GO:0014016]	4.666905e-5	31
photoreceptor cell fate commitment [GO:0046552]	5.388748e-5	40
actin filament-based process [GO:0030029]	5.423348e-5	100
enzyme linked receptor protein signaling pathway [GO:0007167]	5.535552e-5	100
regulation of growth [GO:0040008]	5.536703e-5	96
reproductive structure development [GO:0048608]	5.856074e-5	51
reproductive system development [GO:0061458]	5.856074e-5	51
leg disc morphogenesis [GO:0007478]	8.352336e-5	48
mesoderm formation [GO:0001707]	8.534705e-5	25
cardiocyte differentiation [GO:0035051]	1.106541e-4	25
regulation of organ morphogenesis [GO:2000027]	1.196002e-4	50
genital disc development [GO:0035215]	1.225576e-4	33
formation of organ boundary [GO:0010160]	1.346559e-4	34
morphogenesis of a branching structure [GO:0001763]	1.391813e-4	39
tissue migration [GO:0090130]	1.407856e-4	33
motor neuron axon guidance [GO:0008045]	1.891518e-4	33
imaginal disc-derived leg morphogenesis [GO:0007480]	2.036658e-4	47
limb morphogenesis [GO:0035108]	2.036658e-4	47
post-embryonic limb morphogenesis [GO:0035127]	2.036658e-4	47
limb development [GO:0060173]	2.036658e-4	47
development of primary sexual characteristics [GO:0045137]	2.195022e-4	46
female gamete generation [GO:0007292]	2.638042e-4	200
hindgut morphogenesis [GO:0007442]	2.639339e-4	39
ovarian follicle cell development [GO:0030707]	3.480296e-4	107
oogenesis [GO:0048477]	3.572044e-4	197
ovarian follicle cell migration [GO:0007297]	3.646769e-4	56
regulation of small GTPase mediated signal transduction [GO:0051056]	3.953258e-4	61
anterior/posterior pattern specification [GO:0009952]	4.217993e-4	83
branching morphogenesis of an epithelial tube [GO:0048754]	4.506396e-4	37
branching involved in open tracheal system development [GO:0060446]	4.506396e-4	37
morphogenesis of a branching epithelium [GO:0061138]	4.506396e-4	37
regulation of Ras protein signal transduction [GO:0046578]	4.776506e-4	57
regulation of cell shape [GO:0008360]	6.665474e-4	60
negative regulation of signaling [GO:0023057]	7.122732e-4	89
muscle fiber development [GO:0048747]	8.659218e-4	65
eye photoreceptor cell fate commitment [GO:0042706]	0.001014	37
eye-antennal disc morphogenesis [GO:0007455]	0.001142	29
ventral cord development [GO:0007419]	0.001161	26
dendrite development [GO:0016358]	0.001190	81
synapse assembly [GO:0007416]	0.001224	58
negative regulation of cell communication [GO:0010648]	0.001329	89
programmed cell death [GO:0012501]	0.001399	113
photoreceptor cell development [GO:0042461]	0.001406	54
midgut development [GO:0007494]	0.001612	26
salivary gland morphogenesis [GO:0007435]	0.001872	68
gland morphogenesis [GO:0022612]	0.001872	68
dendrite morphogenesis [GO:0048813]	0.002201	80
cellular process involved in reproduction [GO:0048610]	0.002235	241
compound eye photoreceptor fate commitment [GO:0001752]	0.002645	36
ameboidal cell migration [GO:0001667]	0.002853	31
negative regulation of signal transduction [GO:0009968]	0.002921	84
reproduction [GO:0000003]	0.007904	393
cell death [GO:0008219]	0.008171	119
gastrulation with mouth forming first [GO:0001703]	0.008778	27
gastrulation involving germ band extension [GO:0010004]	0.008778	27
ectoderm development [GO:0007398]	0.009804	20
death [GO:0016265]	0.009968	120
border follicle cell migration [GO:0007298]	0.014121	50
peripheral nervous system development [GO:0007422]	0.015161	50
glial cell migration [GO:0008347]	0.017922	24
segment specification [GO:0007379]	0.022631	29
regulation of developmental growth [GO:0048638]	0.024084	51
dorsal/ventral pattern formation [GO:0009953]	0.029039	70
wing disc pattern formation [GO:0035222]	0.034570	42
regulation of cell proliferation [GO:0042127]	0.046536	68