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PRJEB1986: zebrafish developmental stages transcriptome

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Results for runx3

Z-value: 0.69

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Transcription factors associated with runx3

Gene Symbol Gene ID Gene Info
runx3
ENSDARG00000052826 RUNX family transcription factor 3

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
runx3dr11_v1_chr13_-_45155792_451557920.483.7e-02Click!

Activity profile of runx3 motif

Sorted Z-values of runx3 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr6_+_44163727 1.31 ENSDART00000064878
gxylt2
glucoside xylosyltransferase 2
chr21_-_30082414 1.04 ENSDART00000157307
ENSDART00000155188
ccnjl
cyclin J-like
chr2_+_46589798 0.95 ENSDART00000128457
ENSDART00000145347
ephb1
EPH receptor B1
chr5_+_27429872 0.88 ENSDART00000087894
zgc:165555
zgc:165555
chr24_-_14711597 0.87 ENSDART00000131830
jph1a
junctophilin 1a
chr2_-_52841762 0.84 ENSDART00000114682
ralbp1
ralA binding protein 1
chr20_-_43346049 0.83 ENSDART00000152888
afdna
afadin, adherens junction formation factor a
chr12_+_18744610 0.77 ENSDART00000153456
mkl1b
megakaryoblastic leukemia (translocation) 1b
chr19_-_24443867 0.75 ENSDART00000163763
ENSDART00000043133
thbs3b
thrombospondin 3b
chr16_+_41060161 0.74 ENSDART00000141130
scap
SREBF chaperone
chr9_-_20372977 0.72 ENSDART00000113418
igsf3
immunoglobulin superfamily, member 3
chr8_-_53803429 0.71 ENSDART00000188403
CABZ01086611.1

chr7_+_41160225 0.70 ENSDART00000074212
ENSDART00000164200
ENSDART00000174204
ENSDART00000174212
scrib
scribbled planar cell polarity protein
chr9_+_38883388 0.65 ENSDART00000135902
map2
microtubule-associated protein 2
chr22_+_21317597 0.63 ENSDART00000132605
shc2
SHC (Src homology 2 domain containing) transforming protein 2
chr5_+_62009765 0.63 ENSDART00000134335
akap10
A kinase (PRKA) anchor protein 10
chr6_+_54154807 0.63 ENSDART00000061735
nudt3b
nudix (nucleoside diphosphate linked moiety X)-type motif 3b
chr10_+_45148005 0.60 ENSDART00000182501
ogdhb
oxoglutarate (alpha-ketoglutarate) dehydrogenase b (lipoamide)
chr5_+_62009930 0.54 ENSDART00000082872
akap10
A kinase (PRKA) anchor protein 10
chr6_+_25282671 0.54 ENSDART00000157575
si:ch211-180m24.3
si:ch211-180m24.3
chr1_-_18446161 0.53 ENSDART00000089442
klhl5
kelch-like family member 5
chr14_-_42231293 0.52 ENSDART00000185486
BX890543.1

chr2_+_4146606 0.51 ENSDART00000171170
mib1
mindbomb E3 ubiquitin protein ligase 1
chr11_-_17755444 0.51 ENSDART00000154627
eogt
EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase
chr15_+_6117502 0.48 ENSDART00000188293
PCP4 (1 of many)
Purkinje cell protein 4
chr14_-_24332786 0.47 ENSDART00000173164
fam13b
family with sequence similarity 13, member B
chr12_+_28910762 0.47 ENSDART00000076342
ENSDART00000160939
ENSDART00000076572
rnf40
ring finger protein 40
chr24_-_21507627 0.47 ENSDART00000170984
rnf6
ring finger protein (C3H2C3 type) 6
chr13_+_45524475 0.46 ENSDART00000074567
ENSDART00000019113
maco1b
macoilin 1b
chr9_+_38074082 0.46 ENSDART00000017833
cacnb4a
calcium channel, voltage-dependent, beta 4a subunit
chr16_-_54907588 0.45 ENSDART00000185709
kdf1a
keratinocyte differentiation factor 1a
chr16_+_4133519 0.45 ENSDART00000174521
ENSDART00000175718
mtf1
metal-regulatory transcription factor 1
chr7_+_17937922 0.43 ENSDART00000147189
mta2
metastasis associated 1 family, member 2
chr20_-_53321499 0.43 ENSDART00000179894
ENSDART00000127427
ENSDART00000084952
wasf1
WAS protein family, member 1
chr8_-_25707421 0.42 ENSDART00000184404
sema3ga
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Ga
chr8_-_18899427 0.40 ENSDART00000079840
rorca
RAR-related orphan receptor C a
chr22_+_17203752 0.40 ENSDART00000143376
rab3b
RAB3B, member RAS oncogene family
chr15_+_29292154 0.39 ENSDART00000137817
rap1gap2a
RAP1 GTPase activating protein 2a
chr19_+_4062101 0.38 ENSDART00000166773
btr25
bloodthirsty-related gene family, member 25
chr12_-_43819253 0.36 ENSDART00000160261
ENSDART00000170045
ENSDART00000159106
si:ch73-329n5.6
si:ch73-329n5.6
chr1_+_53321878 0.35 ENSDART00000143909
tbc1d9
TBC1 domain family, member 9 (with GRAM domain)
chr16_-_32672883 0.34 ENSDART00000124515
ENSDART00000190920
ENSDART00000188776
pnisr
PNN-interacting serine/arginine-rich protein
chr17_+_41337246 0.33 ENSDART00000111238
mocs1
molybdenum cofactor synthesis 1
chr1_-_8012476 0.33 ENSDART00000177051
CR855320.3

chr25_-_210730 0.33 ENSDART00000187580
FP236318.1

chr22_-_25469751 0.33 ENSDART00000171670
CR769772.4

chr6_-_10740365 0.32 ENSDART00000150942
sp3b
Sp3b transcription factor
chr25_+_34407740 0.31 ENSDART00000012677
OTUD7A
si:dkey-37f18.2
chr19_+_42219165 0.31 ENSDART00000163192
CU896644.1

chr3_-_3372259 0.31 ENSDART00000140482
si:dkey-46g23.1
si:dkey-46g23.1
chr15_+_24005289 0.31 ENSDART00000088648
myo18ab
myosin XVIIIAb
chr25_-_225964 0.31 ENSDART00000193424
CABZ01113818.1

chr22_-_25502977 0.30 ENSDART00000181749
CR769772.4

chr12_+_20699534 0.30 ENSDART00000131883
si:ch211-119c20.2
si:ch211-119c20.2
chr3_-_49382896 0.29 ENSDART00000169115
si:ch73-167f10.1
si:ch73-167f10.1
chr19_+_2590182 0.26 ENSDART00000162293
si:ch73-345f18.3
si:ch73-345f18.3
chr17_-_27382826 0.25 ENSDART00000186657
ENSDART00000155986
ENSDART00000191060
ENSDART00000077608
si:ch1073-358c10.1
si:ch1073-358c10.1
chr7_+_17938128 0.24 ENSDART00000141044
mta2
metastasis associated 1 family, member 2
chr10_+_45148167 0.24 ENSDART00000172621
ogdhb
oxoglutarate (alpha-ketoglutarate) dehydrogenase b (lipoamide)
chr17_+_37310663 0.23 ENSDART00000157122
elmsan1b
ELM2 and Myb/SANT-like domain containing 1b
chr6_+_39930825 0.23 ENSDART00000182352
ENSDART00000186643
ENSDART00000190513
ENSDART00000065092
ENSDART00000188645
itpr1a
inositol 1,4,5-trisphosphate receptor, type 1a
chr3_+_14339728 0.22 ENSDART00000184127
plppr2a
phospholipid phosphatase related 2a
chr5_-_71995108 0.22 ENSDART00000124587
fam78ab
family with sequence similarity 78, member Ab
chr25_-_21894317 0.22 ENSDART00000089642
fbxo31
F-box protein 31
chr6_-_141564 0.21 ENSDART00000151245
ENSDART00000063876
s1pr5b
sphingosine-1-phosphate receptor 5b
chr7_+_73308566 0.20 ENSDART00000187039
ENSDART00000174244
CABZ01081777.1

chr4_+_359970 0.19 ENSDART00000139832
tmem181
transmembrane protein 181
chr8_+_1065458 0.18 ENSDART00000081432
sprb
sepiapterin reductase b
chr8_+_17184602 0.17 ENSDART00000050228
ENSDART00000140531
dimt1l
DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)
chr18_+_35173859 0.17 ENSDART00000127379
ENSDART00000098292
cfap45
cilia and flagella associated protein 45
chr22_+_11144153 0.16 ENSDART00000047442
bcor
BCL6 corepressor
chr6_-_2154137 0.16 ENSDART00000162656
tgm5l
transglutaminase 5, like
chr21_+_11923701 0.16 ENSDART00000109292
ubap2a
ubiquitin associated protein 2a
chr7_-_12596727 0.16 ENSDART00000186413
adamtsl3
ADAMTS-like 3
chr9_+_37141836 0.15 ENSDART00000024555
gli2a
GLI family zinc finger 2a
chr24_-_27423697 0.14 ENSDART00000132590
si:dkey-25o1.7
si:dkey-25o1.7
chr19_-_72398 0.14 ENSDART00000165587
dnajc8
DnaJ (Hsp40) homolog, subfamily C, member 8
chr10_+_15608326 0.14 ENSDART00000188770
zfand5b
zinc finger, AN1-type domain 5b
chr3_-_25369557 0.13 ENSDART00000055491
smurf2
SMAD specific E3 ubiquitin protein ligase 2
chr21_-_43992027 0.12 ENSDART00000188612
cdx1b
caudal type homeobox 1 b
chr9_+_34148714 0.11 ENSDART00000078051
gpr161
G protein-coupled receptor 161
chr8_-_17184482 0.11 ENSDART00000025803
pola2
polymerase (DNA directed), alpha 2
chr16_+_35870456 0.10 ENSDART00000184321
thrap3a
thyroid hormone receptor associated protein 3a
chr15_-_20468302 0.09 ENSDART00000018514
dlc
deltaC
chr15_-_2657508 0.09 ENSDART00000102086
cldna
claudin a
chr18_-_50523399 0.08 ENSDART00000033591
cd276
CD276 molecule
chr2_-_56348727 0.08 ENSDART00000060745
uba52
ubiquitin A-52 residue ribosomal protein fusion product 1
chr15_-_22139566 0.07 ENSDART00000149017
scn3b
sodium channel, voltage-gated, type III, beta
chr10_-_24937070 0.06 ENSDART00000064459
si:ch211-214k5.3
si:ch211-214k5.3
chr5_+_7989210 0.06 ENSDART00000168071
gdnfb
glial cell derived neurotrophic factor b
chr21_-_21465111 0.05 ENSDART00000141487
nectin3b
nectin cell adhesion molecule 3b
chr5_-_10239079 0.05 ENSDART00000132739
si:ch73-42k18.1
si:ch73-42k18.1
chr22_+_29994093 0.05 ENSDART00000104778
si:dkey-286j15.3
si:dkey-286j15.3
chr1_+_23408622 0.04 ENSDART00000140706
chrna9
cholinergic receptor, nicotinic, alpha 9
chr6_-_11768198 0.04 ENSDART00000183463
march7
membrane-associated ring finger (C3HC4) 7
chr1_-_39859626 0.04 ENSDART00000053763
dctd
dCMP deaminase
chr23_+_36308717 0.03 ENSDART00000131711
hnrnpa1b
heterogeneous nuclear ribonucleoprotein A1b
chr18_-_7810214 0.03 ENSDART00000139505
ENSDART00000139188
shank3a
SH3 and multiple ankyrin repeat domains 3a
chr8_+_24861264 0.02 ENSDART00000099607
slc6a17
solute carrier family 6 (neutral amino acid transporter), member 17
chr20_-_34670236 0.01 ENSDART00000033325
slc25a24
solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24
chr7_+_3229828 0.01 ENSDART00000135367
CR855393.2

chr11_+_2642013 0.01 ENSDART00000111324
zgc:193807
zgc:193807
chr16_+_50089417 0.00 ENSDART00000153675
nr1d2a
nuclear receptor subfamily 1, group D, member 2a

Network of associatons between targets according to the STRING database.

First level regulatory network of runx3

PNG image of the network

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 1.3 GO:0016266 O-glycan processing(GO:0016266)
0.2 0.5 GO:0021519 optic cup formation involved in camera-type eye development(GO:0003408) spinal cord association neuron specification(GO:0021519)
0.1 0.6 GO:1901906 diphosphoinositol polyphosphate metabolic process(GO:0071543) diadenosine pentaphosphate metabolic process(GO:1901906) diadenosine pentaphosphate catabolic process(GO:1901907) diadenosine hexaphosphate metabolic process(GO:1901908) diadenosine hexaphosphate catabolic process(GO:1901909) adenosine 5'-(hexahydrogen pentaphosphate) metabolic process(GO:1901910) adenosine 5'-(hexahydrogen pentaphosphate) catabolic process(GO:1901911)
0.1 0.7 GO:1902946 protein localization to early endosome(GO:1902946)
0.1 0.4 GO:0071276 cellular response to cadmium ion(GO:0071276)
0.1 0.5 GO:0023041 neuronal signal transduction(GO:0023041)
0.1 0.5 GO:0010481 epidermal cell division(GO:0010481) regulation of epidermal cell division(GO:0010482)
0.1 0.7 GO:0071501 response to sterol depletion(GO:0006991) SREBP signaling pathway(GO:0032933) cellular response to sterol depletion(GO:0071501)
0.0 0.2 GO:0031571 mitotic G1 DNA damage checkpoint(GO:0031571)
0.0 0.2 GO:0048618 post-embryonic foregut morphogenesis(GO:0048618)
0.0 0.3 GO:0006777 Mo-molybdopterin cofactor biosynthetic process(GO:0006777) Mo-molybdopterin cofactor metabolic process(GO:0019720) molybdopterin cofactor biosynthetic process(GO:0032324) molybdopterin cofactor metabolic process(GO:0043545) prosthetic group metabolic process(GO:0051189)
0.0 0.4 GO:2000601 positive regulation of actin nucleation(GO:0051127) positive regulation of Arp2/3 complex-mediated actin nucleation(GO:2000601)
0.0 0.8 GO:0006099 tricarboxylic acid cycle(GO:0006099)
0.0 0.1 GO:0030579 ubiquitin-dependent SMAD protein catabolic process(GO:0030579)
0.0 1.0 GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity(GO:0000079) regulation of cyclin-dependent protein kinase activity(GO:1904029)
0.0 0.5 GO:0010390 histone monoubiquitination(GO:0010390)
0.0 0.1 GO:0090184 regulation of morphogenesis of a branching structure(GO:0060688) positive regulation of mesonephros development(GO:0061213) regulation of mesonephros development(GO:0061217) regulation of kidney development(GO:0090183) positive regulation of kidney development(GO:0090184) regulation of branching involved in ureteric bud morphogenesis(GO:0090189) positive regulation of branching involved in ureteric bud morphogenesis(GO:0090190)
0.0 0.3 GO:0040033 miRNA mediated inhibition of translation(GO:0035278) negative regulation of translation, ncRNA-mediated(GO:0040033) regulation of translation, ncRNA-mediated(GO:0045974)
0.0 0.5 GO:0006493 protein O-linked glycosylation(GO:0006493)
0.0 0.2 GO:0006729 tetrahydrobiopterin biosynthetic process(GO:0006729) tetrahydrobiopterin metabolic process(GO:0046146)
0.0 0.1 GO:0086005 ventricular cardiac muscle cell action potential(GO:0086005)
0.0 0.1 GO:0060842 arterial endothelial cell differentiation(GO:0060842)
0.0 1.2 GO:0030098 lymphocyte differentiation(GO:0030098)
0.0 0.2 GO:1902254 negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator(GO:1902254)
0.0 0.0 GO:0009162 deoxyribonucleoside monophosphate metabolic process(GO:0009162)
0.0 0.6 GO:0000187 activation of MAPK activity(GO:0000187)
0.0 0.1 GO:0060575 intestinal epithelial cell differentiation(GO:0060575)
0.0 0.5 GO:1901385 regulation of voltage-gated calcium channel activity(GO:1901385)
0.0 0.7 GO:0016575 histone deacetylation(GO:0016575)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 0.9 GO:0030314 junctional membrane complex(GO:0030314)
0.1 0.8 GO:0045252 oxoglutarate dehydrogenase complex(GO:0045252)
0.1 0.3 GO:0019008 molybdopterin synthase complex(GO:0019008)
0.0 0.7 GO:0016581 NuRD complex(GO:0016581) CHD-type complex(GO:0090545)
0.0 0.4 GO:0031209 SCAR complex(GO:0031209)
0.0 0.1 GO:0005658 alpha DNA polymerase:primase complex(GO:0005658)
0.0 1.0 GO:0000307 cyclin-dependent protein kinase holoenzyme complex(GO:0000307)
0.0 0.7 GO:0012507 ER to Golgi transport vesicle membrane(GO:0012507)
0.0 0.5 GO:0030867 rough endoplasmic reticulum membrane(GO:0030867)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 1.3 GO:0035252 UDP-xylosyltransferase activity(GO:0035252)
0.1 0.6 GO:0008486 endopolyphosphatase activity(GO:0000298) diphosphoinositol-polyphosphate diphosphatase activity(GO:0008486) bis(5'-adenosyl)-hexaphosphatase activity(GO:0034431) bis(5'-adenosyl)-pentaphosphatase activity(GO:0034432)
0.1 0.8 GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity(GO:0004591)
0.1 0.5 GO:0016262 protein N-acetylglucosaminyltransferase activity(GO:0016262)
0.1 0.9 GO:0005005 transmembrane-ephrin receptor activity(GO:0005005)
0.0 1.6 GO:0051018 protein kinase A binding(GO:0051018)
0.0 0.2 GO:0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity(GO:0000179)
0.0 0.2 GO:0038036 sphingosine-1-phosphate receptor activity(GO:0038036)
0.0 0.7 GO:0001103 RNA polymerase II repressing transcription factor binding(GO:0001103)
0.0 0.2 GO:0030332 cyclin binding(GO:0030332)
0.0 0.7 GO:0030971 receptor tyrosine kinase binding(GO:0030971)
0.0 0.2 GO:0005220 inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity(GO:0005220)
0.0 0.3 GO:0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor(GO:0016671)
0.0 1.0 GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity(GO:0016538)
0.0 0.5 GO:0008331 high voltage-gated calcium channel activity(GO:0008331)
0.0 0.7 GO:0032934 sterol binding(GO:0032934)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.6 PID VEGFR1 PATHWAY VEGFR1 specific signals
0.0 0.7 SA CASPASE CASCADE Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade.
0.0 0.9 PID EPHRINB REV PATHWAY Ephrin B reverse signaling
0.0 0.8 ST TUMOR NECROSIS FACTOR PATHWAY Tumor Necrosis Factor Pathway.
0.0 0.4 SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES Genes related to regulation of the actin cytoskeleton
0.0 0.6 PID LKB1 PATHWAY LKB1 signaling events
0.0 0.2 PID HDAC CLASSII PATHWAY Signaling events mediated by HDAC Class II

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 1.3 REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS Genes involved in A tetrasaccharide linker sequence is required for GAG synthesis
0.0 0.6 REACTOME SIGNAL ATTENUATION Genes involved in Signal attenuation
0.0 0.6 REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus
0.0 1.2 REACTOME SIGNALING BY RHO GTPASES Genes involved in Signaling by Rho GTPases
0.0 0.1 REACTOME SIGNALING BY BMP Genes involved in Signaling by BMP