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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for nkx3-2+nkx3.3-2

Z-value: 0.29

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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
nkx3.3dr11_v1_chr13_-_40401870_404018700.361.4e-01Click!
nkx3.2dr11_v1_chr14_-_215051_2150510.184.6e-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
chr19_+_43604643 0.52 ENSDART00000151168
si:ch211-199g17.9
si:ch211-199g17.9
chr1_-_30039331 0.50 ENSDART00000086935
ENSDART00000143800
MARCH4 (1 of many)
zgc:153256
chr20_-_438646 0.48 ENSDART00000009196
ufl1
UFM1-specific ligase 1
chr24_-_31223232 0.48 ENSDART00000164155
alg14
ALG14, UDP-N-acetylglucosaminyltransferase subunit
chr25_+_16356083 0.45 ENSDART00000125925
ENSDART00000125444
tead1a
TEA domain family member 1a
chr6_+_374875 0.40 ENSDART00000171698
si:zfos-169g10.3
si:zfos-169g10.3
chr16_-_24815091 0.34 ENSDART00000154269
ENSDART00000131025
kcnn4
potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4
chr24_-_11057305 0.29 ENSDART00000186494
asap1b
ArfGAP with SH3 domain, ankyrin repeat and PH domain 1b
chr15_-_41245962 0.28 ENSDART00000155359
smco4
single-pass membrane protein with coiled-coil domains 4
chr11_+_13207898 0.27 ENSDART00000060310
atp5f1b
ATP synthase F1 subunit beta
chr13_+_12606821 0.27 ENSDART00000140096
ENSDART00000145136
metap1
methionyl aminopeptidase 1
chr3_-_16413606 0.26 ENSDART00000127309
ENSDART00000017172
ENSDART00000136465
eftud2
elongation factor Tu GTP binding domain containing 2
chr19_-_31802296 0.26 ENSDART00000103640
hey1
hes-related family bHLH transcription factor with YRPW motif 1
chr2_-_51644044 0.25 ENSDART00000157899
dad1
defender against cell death 1
chr7_+_39688208 0.25 ENSDART00000189682
tbc1d14
TBC1 domain family, member 14
chr8_+_17987778 0.22 ENSDART00000133429
lrriq3
leucine-rich repeats and IQ motif containing 3
chr6_+_515181 0.22 ENSDART00000171374
CACNA1I (1 of many)
si:ch73-379f7.5
chr8_+_17987215 0.21 ENSDART00000113605
lrriq3
leucine-rich repeats and IQ motif containing 3
chr3_+_13190012 0.21 ENSDART00000179747
ENSDART00000109876
ENSDART00000124824
ENSDART00000130261
sun1
Sad1 and UNC84 domain containing 1
chr18_-_27858123 0.20 ENSDART00000142068
iqcg
IQ motif containing G
chr8_+_28547687 0.20 ENSDART00000110291
srxn1
sulfiredoxin 1 homolog (S. cerevisiae)
chr11_-_12634017 0.19 ENSDART00000158286
ENSDART00000193090
CR450764.1

chr15_-_35246742 0.19 ENSDART00000131479
mff
mitochondrial fission factor
chr21_-_38031038 0.18 ENSDART00000179483
ENSDART00000076238
rbm41
RNA binding motif protein 41
chr1_-_18803919 0.18 ENSDART00000020970
pgm2
phosphoglucomutase 2
chr17_+_6563307 0.17 ENSDART00000156454
adgrf3a
adhesion G protein-coupled receptor F3a
chr5_-_31716713 0.17 ENSDART00000131443
dpm2
dolichyl-phosphate mannosyltransferase polypeptide 2, regulatory subunit
chr22_-_27113332 0.17 ENSDART00000146951
ENSDART00000178855
xpnpep1
X-prolyl aminopeptidase (aminopeptidase P) 1, soluble
chr19_+_19989380 0.16 ENSDART00000142841
osbpl3a
oxysterol binding protein-like 3a
chr12_+_26706745 0.16 ENSDART00000141401
arhgap12b
Rho GTPase activating protein 12b
chr18_-_29977431 0.15 ENSDART00000135357
si:ch211-220f16.2
si:ch211-220f16.2
chr24_-_6501211 0.15 ENSDART00000186241
ENSDART00000109040
ENSDART00000136154
gpr158a
G protein-coupled receptor 158a
chr6_-_39198912 0.15 ENSDART00000077938
c1galt1b
core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1b
chr3_-_41791178 0.14 ENSDART00000049687
grifin
galectin-related inter-fiber protein
chr11_-_5953636 0.14 ENSDART00000140960
ENSDART00000123601
dda1
DET1 and DDB1 associated 1
chr19_-_6873107 0.14 ENSDART00000124440
CABZ01029822.1

chr21_-_11791909 0.14 ENSDART00000180893
RHOBTB3
si:dkey-6b12.5
chr25_+_11456696 0.13 ENSDART00000171408
AGBL1
si:ch73-141f14.1
chr19_+_32855139 0.13 ENSDART00000052082
rpl30
ribosomal protein L30
chr7_+_44715224 0.13 ENSDART00000184630
si:dkey-56m19.5
si:dkey-56m19.5
chr20_-_30377221 0.11 ENSDART00000126229
rps7
ribosomal protein S7
chr8_+_20455134 0.11 ENSDART00000079618
rexo1
REX1, RNA exonuclease 1 homolog
chr3_-_53559581 0.11 ENSDART00000183499
notch3
notch 3
chr21_+_18353703 0.10 ENSDART00000181396
ENSDART00000166359
si:ch73-287m6.1
si:ch73-287m6.1
chr9_-_49829685 0.10 ENSDART00000162271
ttc21b
tetratricopeptide repeat domain 21B
chr7_-_23777445 0.10 ENSDART00000173527
si:ch211-200p22.4
si:ch211-200p22.4
chr16_+_49005321 0.10 ENSDART00000160919
CABZ01068499.1

chr20_+_25568694 0.10 ENSDART00000063107
ENSDART00000063128
cyp2p7
cytochrome P450, family 2, subfamily P, polypeptide 7
chr7_-_6441865 0.09 ENSDART00000172831
hist1h2a10
histone cluster 1 H2A family member 10
chr21_-_11996769 0.09 ENSDART00000143537
zgc:64106
zgc:64106
chr4_+_3287819 0.09 ENSDART00000168633
CABZ01085700.1

chr12_-_23009312 0.09 ENSDART00000111801
mkxa
mohawk homeobox a
chr1_-_14258409 0.09 ENSDART00000079359
pde5aa
phosphodiesterase 5A, cGMP-specific, a
chr14_-_21219659 0.09 ENSDART00000089867
ppp2r2cb
protein phosphatase 2, regulatory subunit B, gamma b
chr11_-_36474306 0.08 ENSDART00000170678
ENSDART00000123591
usp48
ubiquitin specific peptidase 48
chr6_+_13201358 0.07 ENSDART00000190290
CT009620.1

chr5_-_54300725 0.07 ENSDART00000163048
slc25a35
solute carrier family 25, member 35
chr8_-_17987547 0.07 ENSDART00000112699
ENSDART00000061747
fpgt
fucose-1-phosphate guanylyltransferase
chr17_+_24747209 0.07 ENSDART00000154623
stac
SH3 and cysteine rich domain
chr11_-_1948784 0.06 ENSDART00000082475
nr1d4b
nuclear receptor subfamily 1, group D, member 4b
chr2_+_42135719 0.06 ENSDART00000008268
cyp7b1
cytochrome P450, family 7, subfamily B, polypeptide 1
chr6_+_42918933 0.06 ENSDART00000064896
gnat1
guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1
chr3_-_53559408 0.05 ENSDART00000073930
notch3
notch 3
chr23_-_21471022 0.05 ENSDART00000104206
her4.2
hairy-related 4, tandem duplicate 2
chr24_+_17005647 0.05 ENSDART00000149149
zfx
zinc finger protein, X-linked
chr12_+_17754859 0.05 ENSDART00000112119
bhlha15
basic helix-loop-helix family, member a15
chr1_+_7988052 0.05 ENSDART00000167552
CR855320.2

chr7_-_52842007 0.05 ENSDART00000182710
map1aa
microtubule-associated protein 1Aa
chr12_+_19030391 0.05 ENSDART00000153927
si:ch73-139e5.2
si:ch73-139e5.2
chr9_-_34882516 0.04 ENSDART00000011163
asmtl
acetylserotonin O-methyltransferase-like
chr18_+_16943911 0.04 ENSDART00000157609
si:dkey-8l13.5
si:dkey-8l13.5
chr3_-_34054081 0.04 ENSDART00000151590
ighv1-2
immunoglobulin heavy variable 1-2
chr25_+_19670273 0.04 ENSDART00000073472
zgc:113426
zgc:113426
chr6_-_29105727 0.04 ENSDART00000184355
fam69ab
family with sequence similarity 69, member Ab
chr1_+_1789357 0.04 ENSDART00000006449
atp1a1a.2
ATPase Na+/K+ transporting subunit alpha 1a, tandem duplicate 2
chr21_+_4388489 0.03 ENSDART00000144555
HTRA2 (1 of many)
si:dkey-84o3.3
chr22_-_23545307 0.03 ENSDART00000166915
crb1
crumbs family member 1, photoreceptor morphogenesis associated
chr3_-_32169754 0.03 ENSDART00000179010
tnnt1
troponin T type 1 (skeletal, slow)
chr17_+_48164536 0.03 ENSDART00000161750
ENSDART00000156923
plekhd1
pleckstrin homology domain containing, family D (with coiled-coil domains) member 1
chr5_-_23117078 0.03 ENSDART00000051529
uprt
uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)
chr14_-_1949277 0.03 ENSDART00000159435
pcdh2g5
protocadherin 2 gamma 5
chr3_-_32603191 0.03 ENSDART00000150997
si:ch73-248e21.7
si:ch73-248e21.7
chr2_+_39618951 0.03 ENSDART00000077108
zgc:136870
zgc:136870
chr21_+_4403155 0.03 ENSDART00000161623
HTRA2 (1 of many)
si:dkey-84o3.3
chr12_+_22580579 0.03 ENSDART00000171725
ENSDART00000192290
capgb
capping protein (actin filament), gelsolin-like b
chr4_+_17327704 0.02 ENSDART00000016075
ENSDART00000133160
nup37
nucleoporin 37
chr5_-_42083363 0.02 ENSDART00000162596
cxcl11.5
chemokine (C-X-C motif) ligand 11, duplicate 5
chr3_-_41795917 0.02 ENSDART00000182662
grifin
galectin-related inter-fiber protein
chr19_+_30990129 0.02 ENSDART00000052169
ENSDART00000193376
sync
syncoilin, intermediate filament protein
chr15_-_36347858 0.02 ENSDART00000155274
ENSDART00000157936
si:dkey-23k10.2
si:dkey-23k10.2
chr2_+_55916911 0.02 ENSDART00000189483
ENSDART00000183647
ENSDART00000083470
atcayb
ataxia, cerebellar, Cayman type b
chr8_+_25254435 0.02 ENSDART00000143554
ampd2b
adenosine monophosphate deaminase 2b
chr10_-_39153959 0.02 ENSDART00000150193
ENSDART00000111362
slc37a4b
solute carrier family 37 (glucose-6-phosphate transporter), member 4b
chr15_-_12319065 0.02 ENSDART00000162973
ENSDART00000170543
fxyd6
FXYD domain containing ion transport regulator 6
chr6_-_40038543 0.01 ENSDART00000154792
si:dkey-197j19.6
si:dkey-197j19.6
chr4_+_71018579 0.01 ENSDART00000186727
si:dkeyp-80d11.10
si:dkeyp-80d11.10
chr21_-_2348838 0.01 ENSDART00000160337
si:ch73-299h12.8
si:ch73-299h12.8
chr7_+_39446247 0.01 ENSDART00000033610
ENSDART00000099015
tnnt3b
troponin T type 3b (skeletal, fast)
chr12_-_16636627 0.01 ENSDART00000128811
si:dkey-239j18.3
si:dkey-239j18.3
chr4_+_19534833 0.01 ENSDART00000140028
lrrc4.1
leucine rich repeat containing 4.1
chr5_+_61843752 0.01 ENSDART00000130940
CR759879.1
Danio rerio interferon-induced protein with tetratricopeptide repeats 5 (LOC572297), mRNA.
chr18_-_38216584 0.01 ENSDART00000144622
si:dkey-10o6.2
si:dkey-10o6.2
chr22_+_9431853 0.01 ENSDART00000181028
si:ch211-11p18.6
si:ch211-11p18.6
chr3_+_19446997 0.01 ENSDART00000079352
zgc:123297
zgc:123297
chr20_+_46172649 0.00 ENSDART00000111317
taar13e
trace amine associated receptor 13e
chr20_+_6773790 0.00 ENSDART00000169966
igfbp3
insulin-like growth factor binding protein 3
chr16_-_31933740 0.00 ENSDART00000125411
si:ch1073-90m23.1
si:ch1073-90m23.1
chr3_-_34060153 0.00 ENSDART00000151610
ighv1-1
immunoglobulin heavy variable 1-1
chr10_+_25726694 0.00 ENSDART00000140308
ugt5d1
UDP glucuronosyltransferase 5 family, polypeptide D1
chr2_+_49631850 0.00 ENSDART00000114274
ENSDART00000114516
si:dkey-53k12.18
si:dkey-53k12.18
chr2_+_42177113 0.00 ENSDART00000056441
tmeff1a
transmembrane protein with EGF-like and two follistatin-like domains 1a
chr15_+_5360407 0.00 ENSDART00000110420
or112-1
odorant receptor, family A, subfamily 112, member 1

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 0.5 GO:1990564 IRE1-mediated unfolded protein response(GO:0036498) protein polyufmylation(GO:1990564) protein K69-linked ufmylation(GO:1990592)
0.1 0.3 GO:0042776 mitochondrial ATP synthesis coupled proton transport(GO:0042776)
0.1 0.3 GO:0070084 protein initiator methionine removal(GO:0070084)
0.1 0.2 GO:0098725 somatic stem cell population maintenance(GO:0035019) symmetric cell division(GO:0098725)
0.0 0.5 GO:0006488 dolichol-linked oligosaccharide biosynthetic process(GO:0006488)
0.0 0.2 GO:0019348 dolichol metabolic process(GO:0019348)
0.0 0.2 GO:0007288 sperm axoneme assembly(GO:0007288)
0.0 0.5 GO:0070193 synaptonemal complex assembly(GO:0007130) synaptonemal complex organization(GO:0070193)
0.0 0.3 GO:2000785 regulation of autophagosome assembly(GO:2000785)
0.0 0.5 GO:0035329 hippo signaling(GO:0035329)
0.0 0.1 GO:1901387 positive regulation of voltage-gated calcium channel activity(GO:1901387)
0.0 0.1 GO:0006699 bile acid biosynthetic process(GO:0006699) bile acid metabolic process(GO:0008206)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.2 GO:0033185 dolichol-phosphate-mannose synthase complex(GO:0033185)
0.0 0.3 GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1)(GO:0045261)
0.0 0.5 GO:0000795 synaptonemal complex(GO:0000795)
0.0 0.3 GO:0071007 U2-type catalytic step 2 spliceosome(GO:0071007)
0.0 0.3 GO:0008250 oligosaccharyltransferase complex(GO:0008250)
0.0 0.5 GO:0035861 site of double-strand break(GO:0035861)
0.0 0.1 GO:0030991 intraciliary transport particle A(GO:0030991)
0.0 0.2 GO:0034993 microtubule organizing center attachment site(GO:0034992) LINC complex(GO:0034993)
0.0 0.2 GO:0097038 perinuclear endoplasmic reticulum(GO:0097038)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 0.5 GO:0071568 UFM1 transferase activity(GO:0071568)
0.1 0.3 GO:0030623 U5 snRNA binding(GO:0030623)
0.1 0.2 GO:0048030 disaccharide binding(GO:0048030)
0.0 0.2 GO:0030626 U12 snRNA binding(GO:0030626)
0.0 0.3 GO:0016286 small conductance calcium-activated potassium channel activity(GO:0016286)
0.0 0.3 GO:0046933 proton-transporting ATP synthase activity, rotational mechanism(GO:0046933)
0.0 0.2 GO:0043495 protein anchor(GO:0043495)
0.0 0.2 GO:0016868 intramolecular transferase activity, phosphotransferases(GO:0016868)
0.0 0.4 GO:0070006 metalloaminopeptidase activity(GO:0070006)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
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 0.7 REACTOME BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN Genes involved in Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
0.0 0.2 REACTOME GLYCOGEN BREAKDOWN GLYCOGENOLYSIS Genes involved in Glycogen breakdown (glycogenolysis)