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PRJNA195909:zebrafish embryo and larva development

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Results for nkx3-2+nkx3.3-2

Z-value: 0.40

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Transcription factors associated with nkx3-2+nkx3.3-2

Gene Symbol Gene ID Gene Info
nkx3-2
ENSDARG00000037639 NK3 homeobox 2
nkx3.3-2
ENSDARG00000069327 NK3 homeobox 3

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
nkx3.2dr11_v1_chr14_-_215051_215051-0.608.9e-02Click!
nkx3.3dr11_v1_chr13_-_40401870_40401870-0.442.3e-01Click!

Activity profile of nkx3-2+nkx3.3-2 motif

Sorted Z-values of nkx3-2+nkx3.3-2 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr15_-_37929135 0.67 ENSDART00000157550
si:dkey-238d18.15
si:dkey-238d18.15
chr11_+_14333441 0.32 ENSDART00000171969
ptbp1b
polypyrimidine tract binding protein 1b
chr12_+_17754859 0.30 ENSDART00000112119
bhlha15
basic helix-loop-helix family, member a15
chr22_+_9922301 0.29 ENSDART00000105924
blf
bloody fingers
chr12_-_13729263 0.28 ENSDART00000078021
foxh1
forkhead box H1
chr17_+_51746830 0.25 ENSDART00000184230
odc1
ornithine decarboxylase 1
chr20_+_25568694 0.23 ENSDART00000063107
ENSDART00000063128
cyp2p7
cytochrome P450, family 2, subfamily P, polypeptide 7
chr9_-_9225980 0.23 ENSDART00000180301
cbsb
cystathionine-beta-synthase b
chr15_+_888704 0.22 ENSDART00000182796
si:dkey-7i4.9
si:dkey-7i4.9
chr8_+_25254435 0.21 ENSDART00000143554
ampd2b
adenosine monophosphate deaminase 2b
chr21_+_18353703 0.19 ENSDART00000181396
ENSDART00000166359
si:ch73-287m6.1
si:ch73-287m6.1
chr7_+_44715224 0.19 ENSDART00000184630
si:dkey-56m19.5
si:dkey-56m19.5
chr4_+_45357558 0.19 ENSDART00000150769
si:ch211-162i8.5
si:ch211-162i8.5
chr1_-_51710225 0.19 ENSDART00000057601
ENSDART00000152745
snrpb2
small nuclear ribonucleoprotein polypeptide B2
chr24_+_17005647 0.18 ENSDART00000149149
zfx
zinc finger protein, X-linked
chr1_+_7988052 0.18 ENSDART00000167552
CR855320.2

chr23_-_33558161 0.17 ENSDART00000018301
itga5
integrin, alpha 5 (fibronectin receptor, alpha polypeptide)
chr7_-_6441865 0.17 ENSDART00000172831
hist1h2a10
histone cluster 1 H2A family member 10
chr18_-_22094102 0.17 ENSDART00000100904
pard6a
par-6 family cell polarity regulator alpha
chr25_+_16356083 0.16 ENSDART00000125925
ENSDART00000125444
tead1a
TEA domain family member 1a
chr9_-_49829685 0.16 ENSDART00000162271
ttc21b
tetratricopeptide repeat domain 21B
chr21_+_34814444 0.16 ENSDART00000161816
wdr55
WD repeat domain 55
chr20_-_25643667 0.16 ENSDART00000137457
si:dkeyp-117h8.4
si:dkeyp-117h8.4
chr22_+_2830703 0.16 ENSDART00000145463
ENSDART00000144785
si:dkey-20i20.8
si:dkey-20i20.8
chr12_-_16636627 0.15 ENSDART00000128811
si:dkey-239j18.3
si:dkey-239j18.3
chr7_+_20917966 0.14 ENSDART00000129161
wrap53
WD repeat containing, antisense to TP53
chr18_+_16943911 0.14 ENSDART00000157609
si:dkey-8l13.5
si:dkey-8l13.5
chr8_+_20455134 0.13 ENSDART00000079618
rexo1
REX1, RNA exonuclease 1 homolog
chr15_-_35246742 0.12 ENSDART00000131479
mff
mitochondrial fission factor
chr13_+_12606821 0.12 ENSDART00000140096
ENSDART00000145136
metap1
methionyl aminopeptidase 1
chr18_-_26781616 0.11 ENSDART00000136776
ENSDART00000076484
kti12
KTI12 chromatin associated homolog
chr6_-_39198912 0.10 ENSDART00000077938
c1galt1b
core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1b
chr22_-_27113332 0.10 ENSDART00000146951
ENSDART00000178855
xpnpep1
X-prolyl aminopeptidase (aminopeptidase P) 1, soluble
chr17_-_21278582 0.10 ENSDART00000157518
hspa12a
heat shock protein 12A
chr17_+_31742923 0.10 ENSDART00000086696
arhgap5
Rho GTPase activating protein 5
chr19_+_43604643 0.10 ENSDART00000151168
si:ch211-199g17.9
si:ch211-199g17.9
chr10_-_29831944 0.09 ENSDART00000063923
ENSDART00000136264
zpr1
ZPR1 zinc finger
chr18_-_20458412 0.09 ENSDART00000012241
kif23
kinesin family member 23
chr4_+_17327704 0.09 ENSDART00000016075
ENSDART00000133160
nup37
nucleoporin 37
chr16_+_26612401 0.09 ENSDART00000145571
epb41l4b
erythrocyte membrane protein band 4.1 like 4B
chr15_+_5360407 0.09 ENSDART00000110420
or112-1
odorant receptor, family A, subfamily 112, member 1
chr23_+_12840080 0.09 ENSDART00000081016
ENSDART00000121697
smc1al
structural maintenance of chromosomes 1A, like
chr4_+_13931578 0.09 ENSDART00000142466
pphln1
periphilin 1
chr16_+_28994709 0.09 ENSDART00000088023
gon4l
gon-4-like (C. elegans)
chr17_-_21278846 0.09 ENSDART00000181356
hspa12a
heat shock protein 12A
chr21_-_38031038 0.09 ENSDART00000179483
ENSDART00000076238
rbm41
RNA binding motif protein 41
chr15_+_24676905 0.08 ENSDART00000078014
ENSDART00000143137
poldip2
polymerase (DNA-directed), delta interacting protein 2
chr3_-_53559408 0.08 ENSDART00000073930
notch3
notch 3
chr1_-_48933 0.08 ENSDART00000171162
ildr1a
immunoglobulin-like domain containing receptor 1a
chr21_-_2348838 0.08 ENSDART00000160337
si:ch73-299h12.8
si:ch73-299h12.8
chr4_-_13931508 0.08 ENSDART00000067174
zcrb1
zinc finger CCHC-type and RNA binding motif 1
chr24_+_21676921 0.08 ENSDART00000066677
si:ch211-140b10.6
si:ch211-140b10.6
chr2_+_42135719 0.07 ENSDART00000008268
cyp7b1
cytochrome P450, family 7, subfamily B, polypeptide 1
chr4_+_72668095 0.07 ENSDART00000182282
ENSDART00000162637
CABZ01054391.1

chr3_-_18384501 0.07 ENSDART00000027630
kdelr2a
KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2a
chr23_+_25292147 0.07 ENSDART00000131486
pa2g4b
proliferation-associated 2G4, b
chr18_+_22220656 0.07 ENSDART00000191862
ripor1
RHO family interacting cell polarization regulator 1
chr2_+_55916911 0.07 ENSDART00000189483
ENSDART00000183647
ENSDART00000083470
atcayb
ataxia, cerebellar, Cayman type b
chr4_+_71018579 0.07 ENSDART00000186727
si:dkeyp-80d11.10
si:dkeyp-80d11.10
chr3_-_53559581 0.07 ENSDART00000183499
notch3
notch 3
chr22_-_20386982 0.06 ENSDART00000089015
zbtb7a
zinc finger and BTB domain containing 7a
chr16_+_27444098 0.06 ENSDART00000157690
invs
inversin
chr11_-_1948784 0.06 ENSDART00000082475
nr1d4b
nuclear receptor subfamily 1, group D, member 4b
chr12_+_26706745 0.06 ENSDART00000141401
arhgap12b
Rho GTPase activating protein 12b
chr11_-_12634017 0.06 ENSDART00000158286
ENSDART00000193090
CR450764.1

chr4_-_5077158 0.06 ENSDART00000155915
ahcyl2
adenosylhomocysteinase-like 2
chrM_+_9735 0.06 ENSDART00000093613
mt-co3
cytochrome c oxidase III, mitochondrial
chr8_+_24281512 0.06 ENSDART00000062845
mmp9
matrix metallopeptidase 9
chr24_-_31223232 0.06 ENSDART00000164155
alg14
ALG14, UDP-N-acetylglucosaminyltransferase subunit
chr5_-_68779747 0.06 ENSDART00000192636
ENSDART00000188039
mepce
methylphosphate capping enzyme
chr3_-_16413606 0.05 ENSDART00000127309
ENSDART00000017172
ENSDART00000136465
eftud2
elongation factor Tu GTP binding domain containing 2
chr6_+_13201358 0.05 ENSDART00000190290
CT009620.1

chr16_-_16522013 0.05 ENSDART00000160602
nbeal2
neurobeachin-like 2
chr14_-_1200854 0.05 ENSDART00000106672
arl9
ADP-ribosylation factor-like 9
chr20_-_30377221 0.05 ENSDART00000126229
rps7
ribosomal protein S7
chr11_-_5953636 0.05 ENSDART00000140960
ENSDART00000123601
dda1
DET1 and DDB1 associated 1
chr20_-_438646 0.04 ENSDART00000009196
ufl1
UFM1-specific ligase 1
chr19_+_19989380 0.04 ENSDART00000142841
osbpl3a
oxysterol binding protein-like 3a
chr19_-_3777217 0.04 ENSDART00000160510
si:dkey-206d17.15
si:dkey-206d17.15
chr4_-_75812937 0.04 ENSDART00000125096
si:ch211-203c5.3
si:ch211-203c5.3
chr14_-_26392475 0.04 ENSDART00000170614
b4galt7
xylosylprotein beta 1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I)
chr22_+_19188809 0.04 ENSDART00000134791
ENSDART00000133682
si:dkey-21e2.8
si:dkey-21e2.8
chr3_+_19446997 0.04 ENSDART00000079352
zgc:123297
zgc:123297
chr21_+_4388489 0.04 ENSDART00000144555
HTRA2 (1 of many)
si:dkey-84o3.3
chr18_-_29977431 0.03 ENSDART00000135357
si:ch211-220f16.2
si:ch211-220f16.2
chr22_-_23545307 0.03 ENSDART00000166915
crb1
crumbs family member 1, photoreceptor morphogenesis associated
chr7_-_4843401 0.03 ENSDART00000137489
si:dkey-83f18.8
si:dkey-83f18.8
chr17_+_6563307 0.03 ENSDART00000156454
adgrf3a
adhesion G protein-coupled receptor F3a
chr15_-_36347858 0.03 ENSDART00000155274
ENSDART00000157936
si:dkey-23k10.2
si:dkey-23k10.2
chr13_+_15581270 0.03 ENSDART00000189880
ENSDART00000190067
ENSDART00000041293
mark3a
MAP/microtubule affinity-regulating kinase 3a
chr8_-_4971205 0.03 ENSDART00000184250
tmem230b
transmembrane protein 230b
chr2_-_59157790 0.03 ENSDART00000192303
ENSDART00000159362
ftr32
finTRIM family, member 32
chr19_+_32855139 0.03 ENSDART00000052082
rpl30
ribosomal protein L30
chr15_+_15173611 0.03 ENSDART00000155267
si:ch211-149e23.4
si:ch211-149e23.4
chr21_+_4403155 0.03 ENSDART00000161623
HTRA2 (1 of many)
si:dkey-84o3.3
chr10_+_24048883 0.02 ENSDART00000149265
gbe1a
glucan (1,4-alpha-), branching enzyme 1a
chr10_+_24048663 0.02 ENSDART00000184504
ENSDART00000186955
gbe1a
glucan (1,4-alpha-), branching enzyme 1a
chr19_+_30990129 0.02 ENSDART00000052169
ENSDART00000193376
sync
syncoilin, intermediate filament protein
chr4_-_71436560 0.02 ENSDART00000166884
si:dkey-82i20.1
si:dkey-82i20.1
chr8_+_28547687 0.02 ENSDART00000110291
srxn1
sulfiredoxin 1 homolog (S. cerevisiae)
chr5_-_8907819 0.02 ENSDART00000188523
adamts12
ADAM metallopeptidase with thrombospondin type 1 motif, 12
chr1_-_30039331 0.01 ENSDART00000086935
ENSDART00000143800
MARCH4 (1 of many)
zgc:153256
chr22_-_26514386 0.01 ENSDART00000125628
CR759791.1

chr18_+_22174630 0.01 ENSDART00000089549
ripor1
RHO family interacting cell polarization regulator 1
chr4_+_71382288 0.01 ENSDART00000181926
si:ch211-76m11.8
si:ch211-76m11.8
chr16_-_31933740 0.00 ENSDART00000125411
si:ch1073-90m23.1
si:ch1073-90m23.1
chr12_+_13404784 0.00 ENSDART00000167977
kcnh4b
potassium voltage-gated channel, subfamily H (eag-related), member 4b
chr18_-_27858123 0.00 ENSDART00000142068
iqcg
IQ motif containing G
chr5_+_61843752 0.00 ENSDART00000130940
CR759879.1
Danio rerio interferon-induced protein with tetratricopeptide repeats 5 (LOC572297), mRNA.

Network of associatons between targets according to the STRING database.

First level regulatory network of nkx3-2+nkx3.3-2

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
0.1 0.3 GO:0060063 Spemann organizer formation at the embryonic shield(GO:0060063)
0.1 0.2 GO:0050666 regulation of sulfur amino acid metabolic process(GO:0031335) regulation of homocysteine metabolic process(GO:0050666)
0.1 0.2 GO:0035019 somatic stem cell population maintenance(GO:0035019) symmetric cell division(GO:0098725)
0.0 0.1 GO:0070084 protein initiator methionine removal(GO:0070084)
0.0 0.2 GO:0090245 axis elongation involved in somitogenesis(GO:0090245)
0.0 0.1 GO:0030575 nuclear body organization(GO:0030575) Cajal body organization(GO:0030576)
0.0 0.2 GO:0033387 putrescine biosynthetic process from ornithine(GO:0033387)
0.0 0.2 GO:0060465 pharynx development(GO:0060465)
0.0 0.1 GO:0070987 error-free translesion synthesis(GO:0070987)
0.0 0.1 GO:0002676 granuloma formation(GO:0002432) chronic inflammatory response(GO:0002544) regulation of granuloma formation(GO:0002631) regulation of chronic inflammatory response(GO:0002676)
0.0 0.1 GO:1990173 positive regulation of protein localization to nucleus(GO:1900182) protein localization to nuclear body(GO:1903405) protein localization to Cajal body(GO:1904867) regulation of protein localization to Cajal body(GO:1904869) positive regulation of protein localization to Cajal body(GO:1904871) protein localization to nucleoplasm(GO:1990173)
0.0 0.1 GO:0097355 protein localization to heterochromatin(GO:0097355)
0.0 0.1 GO:0072116 kidney rudiment formation(GO:0072003) pronephros formation(GO:0072116)
0.0 0.2 GO:0032264 IMP salvage(GO:0032264)
0.0 0.2 GO:0035721 intraciliary retrograde transport(GO:0035721)
0.0 0.1 GO:0040016 embryonic cleavage(GO:0040016)
0.0 0.0 GO:0036344 platelet formation(GO:0030220) platelet morphogenesis(GO:0036344)
0.0 0.1 GO:0006699 bile acid biosynthetic process(GO:0006699) bile acid metabolic process(GO:0008206)
0.0 0.1 GO:0006621 protein retention in ER lumen(GO:0006621)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.2 GO:0030991 intraciliary transport particle A(GO:0030991)
0.0 0.1 GO:0033588 Elongator holoenzyme complex(GO:0033588)
0.0 0.1 GO:0042645 nucleoid(GO:0009295) mitochondrial nucleoid(GO:0042645)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.2 GO:0004122 cystathionine beta-synthase activity(GO:0004122)
0.0 0.2 GO:0004586 ornithine decarboxylase activity(GO:0004586)
0.0 0.1 GO:0030623 U5 snRNA binding(GO:0030623)
0.0 0.1 GO:0046923 ER retention sequence binding(GO:0046923)
0.0 0.2 GO:0030619 U1 snRNA binding(GO:0030619)
0.0 0.1 GO:0030626 U12 snRNA binding(GO:0030626)
0.0 0.2 GO:0047623 AMP deaminase activity(GO:0003876) adenosine-phosphate deaminase activity(GO:0047623)
0.0 0.0 GO:0071568 UFM1 transferase activity(GO:0071568)
0.0 0.0 GO:0003844 1,4-alpha-glucan branching enzyme activity(GO:0003844)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.2 PID SYNDECAN 4 PATHWAY Syndecan-4-mediated signaling events

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.2 REACTOME TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION Genes involved in TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)
0.0 0.3 REACTOME SIGNALING BY NODAL Genes involved in Signaling by NODAL
0.0 0.2 REACTOME RECEPTOR LIGAND BINDING INITIATES THE SECOND PROTEOLYTIC CLEAVAGE OF NOTCH RECEPTOR Genes involved in Receptor-ligand binding initiates the second proteolytic cleavage of Notch receptor
0.0 0.2 REACTOME METABOLISM OF POLYAMINES Genes involved in Metabolism of polyamines