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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for rx3

Z-value: 1.06

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Transcription factors associated with rx3

Gene Symbol Gene ID Gene Info
rx3
ENSDARG00000052893 retinal homeobox gene 3

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
rx3dr11_v1_chr21_+_10756154_10756154-0.897.4e-07Click!

Activity profile of rx3 motif

Sorted Z-values of rx3 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr10_-_21362071 4.64 ENSDART00000125167
avd
avidin
chr10_-_21362320 4.35 ENSDART00000189789
avd
avidin
chr9_-_35633827 4.26 ENSDART00000077745
zp2l1
zona pellucida glycoprotein 2, like 1
chr20_-_23426339 4.13 ENSDART00000004625
zar1
zygote arrest 1
chr18_-_40708537 4.00 ENSDART00000077577
si:ch211-132b12.8
si:ch211-132b12.8
chr21_+_25777425 3.60 ENSDART00000021620
cldnd
claudin d
chr8_+_45334255 3.42 ENSDART00000126848
ENSDART00000134161
ENSDART00000142322
ENSDART00000145011
ENSDART00000183560
pabpc1l
poly(A) binding protein, cytoplasmic 1-like
chr11_-_44801968 3.22 ENSDART00000161846
map1lc3c
microtubule-associated protein 1 light chain 3 gamma
chr1_-_18811517 3.05 ENSDART00000142026
si:dkey-167i21.2
si:dkey-167i21.2
chr10_-_34002185 3.02 ENSDART00000046599
zar1l
zygote arrest 1-like
chr2_+_6253246 2.95 ENSDART00000058256
ENSDART00000076700
zp3b
zona pellucida glycoprotein 3b
chr17_+_16046314 2.12 ENSDART00000154554
ENSDART00000154338
ENSDART00000155336
si:ch73-204p21.2
si:ch73-204p21.2
chr12_-_33357655 2.11 ENSDART00000066233
ENSDART00000148165
slc16a3
solute carrier family 16 (monocarboxylate transporter), member 3
chr2_-_15324837 1.93 ENSDART00000015655
tecrl2b
trans-2,3-enoyl-CoA reductase-like 2b
chr6_+_21001264 1.91 ENSDART00000044519
ENSDART00000151278
cx44.2
connexin 44.2
chr17_+_16046132 1.90 ENSDART00000155005
si:ch73-204p21.2
si:ch73-204p21.2
chr24_+_12835935 1.73 ENSDART00000114762
nanog
nanog homeobox
chr17_-_40956035 1.66 ENSDART00000124715
si:dkey-16j16.4
si:dkey-16j16.4
chr21_-_32060993 1.36 ENSDART00000131651
si:ch211-160j14.2
si:ch211-160j14.2
chr1_-_513762 1.35 ENSDART00000148162
ENSDART00000144606
trmt10c
tRNA methyltransferase 10C, mitochondrial RNase P subunit
chr14_+_34490445 1.29 ENSDART00000132193
ENSDART00000148044
wnt8a
wingless-type MMTV integration site family, member 8a
chr20_-_40758410 1.20 ENSDART00000183031
cx34.5
connexin 34.5
chr19_-_25119443 1.16 ENSDART00000148953
ptp4a3
protein tyrosine phosphatase type IVA, member 3
chr8_-_19467011 1.09 ENSDART00000162010
zgc:92140
zgc:92140
chr12_+_22580579 1.06 ENSDART00000171725
ENSDART00000192290
capgb
capping protein (actin filament), gelsolin-like b
chr13_+_38814521 1.03 ENSDART00000110976
col19a1
collagen, type XIX, alpha 1
chr19_-_8768564 1.02 ENSDART00000170416
si:ch73-350k19.1
si:ch73-350k19.1
chr10_+_43039947 1.00 ENSDART00000193434
atg10
ATG10 autophagy related 10 homolog (S. cerevisiae)
chr14_+_8940326 0.98 ENSDART00000159920
rps6kal
ribosomal protein S6 kinase a, like
chr17_+_37227936 0.95 ENSDART00000076009
hadhab
hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha b
chr8_-_25034411 0.94 ENSDART00000135973
nfyal
nuclear transcription factor Y, alpha, like
chr6_+_40922572 0.93 ENSDART00000133599
ENSDART00000002728
ENSDART00000145153
eif4enif1
eukaryotic translation initiation factor 4E nuclear import factor 1
chr5_+_60590796 0.88 ENSDART00000159859
tmem132e
transmembrane protein 132E
chr17_+_19630272 0.87 ENSDART00000104895
rgs7a
regulator of G protein signaling 7a
chr24_-_25144441 0.85 ENSDART00000152104
phldb2b
pleckstrin homology-like domain, family B, member 2b
chr1_+_35985813 0.84 ENSDART00000179634
ENSDART00000139636
ENSDART00000175902
zgc:152968
zgc:152968
chr20_-_37813863 0.79 ENSDART00000147529
batf3
basic leucine zipper transcription factor, ATF-like 3
chr25_-_27621268 0.78 ENSDART00000146205
ENSDART00000073511
hyal6
hyaluronoglucosaminidase 6
chr6_-_12172424 0.77 ENSDART00000109344
tanc1a
tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1a
chr10_-_32494499 0.70 ENSDART00000129395
uvrag
UV radiation resistance associated gene
chr14_+_30795559 0.70 ENSDART00000006132
cfl1
cofilin 1
chr9_+_43799829 0.69 ENSDART00000186240
ube2e3
ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)
chr1_+_513986 0.69 ENSDART00000109083
ENSDART00000081945
txnl4b
thioredoxin-like 4B
chr6_-_40922971 0.67 ENSDART00000155363
sfi1
SFI1 centrin binding protein
chr22_-_21897203 0.66 ENSDART00000158501
ENSDART00000105566
ENSDART00000136795
gna11a
guanine nucleotide binding protein (G protein), alpha 11a (Gq class)
chr17_+_24821627 0.66 ENSDART00000112389
wdr43
WD repeat domain 43
chr16_-_42056137 0.66 ENSDART00000102798
zp3d.2
zona pellucida glycoprotein 3d tandem duplicate 2
chr24_+_19415124 0.65 ENSDART00000186931
sulf1
sulfatase 1
chr2_-_21820697 0.59 ENSDART00000135230
chd7
chromodomain helicase DNA binding protein 7
chr10_-_32494304 0.59 ENSDART00000028161
uvrag
UV radiation resistance associated gene
chr7_-_30174882 0.57 ENSDART00000110409
frmd5
FERM domain containing 5
chr13_+_22480496 0.55 ENSDART00000136863
ENSDART00000131870
ENSDART00000078720
ENSDART00000078740
ENSDART00000139218
ldb3a
LIM domain binding 3a
chr4_-_4834617 0.53 ENSDART00000141539
coa6
cytochrome c oxidase assembly factor 6
chr13_+_22479988 0.53 ENSDART00000188182
ENSDART00000192972
ENSDART00000178372
ldb3a
LIM domain binding 3a
chr2_+_40294313 0.52 ENSDART00000037292
epha4b
eph receptor A4b
chr9_-_3934963 0.52 ENSDART00000062336
ubr3
ubiquitin protein ligase E3 component n-recognin 3
chr23_-_17003533 0.50 ENSDART00000080545
dnmt3bb.2
DNA (cytosine-5-)-methyltransferase 3 beta, duplicate b.2
chr9_+_50001746 0.50 ENSDART00000058892
slc38a11
solute carrier family 38, member 11
chr4_-_4834347 0.48 ENSDART00000141803
coa6
cytochrome c oxidase assembly factor 6
chr24_-_39518599 0.47 ENSDART00000145606
ENSDART00000031486
lyrm1
LYR motif containing 1
chr20_+_28803977 0.46 ENSDART00000153351
ENSDART00000038149
fntb
farnesyltransferase, CAAX box, beta
chr17_+_8799661 0.45 ENSDART00000105326
tonsl
tonsoku-like, DNA repair protein
chr8_+_25034544 0.45 ENSDART00000123300
ngrn
neugrin, neurite outgrowth associated
chr9_-_50001606 0.44 ENSDART00000161648
ENSDART00000168514
scn1a
sodium channel, voltage-gated, type I, alpha
chr10_-_13343831 0.42 ENSDART00000135941
il11ra
interleukin 11 receptor, alpha
chr15_-_9272328 0.42 ENSDART00000172114
calm2a
calmodulin 2a (phosphorylase kinase, delta)
chr2_+_50608099 0.40 ENSDART00000185805
ENSDART00000111135
neurod6b
neuronal differentiation 6b
chr13_-_31017960 0.38 ENSDART00000145287
wdfy4
WDFY family member 4
chr20_-_9436521 0.38 ENSDART00000133000
zgc:101840
zgc:101840
chr16_+_27383717 0.37 ENSDART00000132329
ENSDART00000136256
stx17
syntaxin 17
chr22_-_20166660 0.37 ENSDART00000085913
ENSDART00000188241
btbd2a
BTB (POZ) domain containing 2a
chr17_+_8799451 0.36 ENSDART00000189814
ENSDART00000191577
tonsl
tonsoku-like, DNA repair protein
chr8_-_50888806 0.34 ENSDART00000053750
acsl2
acyl-CoA synthetase long chain family member 2
chr20_-_45060241 0.33 ENSDART00000185227
klhl29
kelch-like family member 29
chr24_-_25004553 0.33 ENSDART00000080997
ENSDART00000136860
zdhhc20b
zinc finger, DHHC-type containing 20b
chr3_-_61162750 0.33 ENSDART00000055064
pvalb8
parvalbumin 8
chr10_-_33297864 0.26 ENSDART00000163360
PRDM15
PR/SET domain 15
chr1_-_26444075 0.26 ENSDART00000125690
ints12
integrator complex subunit 12
chr4_+_3980247 0.26 ENSDART00000049194
gpr37b
G protein-coupled receptor 37b
chr13_+_38430466 0.24 ENSDART00000132691
adgrb3
adhesion G protein-coupled receptor B3
chr3_+_32365811 0.23 ENSDART00000155967
ap2a1
adaptor-related protein complex 2, alpha 1 subunit
chr22_-_7129631 0.23 ENSDART00000171359
asic1b
acid-sensing (proton-gated) ion channel 1b
chr11_+_31864921 0.21 ENSDART00000180252
diaph3
diaphanous-related formin 3
chr15_+_31344472 0.21 ENSDART00000146695
ENSDART00000159182
ENSDART00000060125
or107-1
odorant receptor, family D, subfamily 107, member 1
chr15_-_2184638 0.21 ENSDART00000135460
shox2
short stature homeobox 2
chr9_+_22485343 0.20 ENSDART00000146028
dgkg
diacylglycerol kinase, gamma
chr14_+_36521005 0.17 ENSDART00000192286
TENM3
si:dkey-237h12.3
chr24_+_39518774 0.15 ENSDART00000132939
dcun1d3
defective in cullin neddylation 1 domain containing 3
chr16_+_42471455 0.15 ENSDART00000166640
si:ch211-215k15.5
si:ch211-215k15.5
chr3_+_23692462 0.14 ENSDART00000145934
hoxb7a
homeobox B7a
chr11_+_33312601 0.14 ENSDART00000188024
cntnap5l
contactin associated protein-like 5 like
chr22_+_28337204 0.14 ENSDART00000163352
impg2b
interphotoreceptor matrix proteoglycan 2b
chr12_+_48803098 0.14 ENSDART00000074768
ppifb
peptidylprolyl isomerase Fb
chr13_-_25819825 0.13 ENSDART00000077612
rel
v-rel avian reticuloendotheliosis viral oncogene homolog
chr15_-_5178899 0.12 ENSDART00000132148
or126-4
odorant receptor, family E, subfamily 126, member 4
chr8_+_7801060 0.11 ENSDART00000161618
tfe3a
transcription factor binding to IGHM enhancer 3a
chr14_-_7207961 0.11 ENSDART00000167994
ENSDART00000166532
stox2b
storkhead box 2b
chr23_-_1348933 0.11 ENSDART00000168981
CABZ01078120.1

chr8_+_6410933 0.11 ENSDART00000168789
lrrtm4l2
leucine rich repeat transmembrane neuronal 4 like 2
chr21_-_15200556 0.10 ENSDART00000141809
sfswap
splicing factor SWAP
chr22_+_28337429 0.10 ENSDART00000166177
impg2b
interphotoreceptor matrix proteoglycan 2b
chr3_-_50443607 0.10 ENSDART00000074036
rcvrna
recoverin a
chr7_-_23768234 0.09 ENSDART00000173981
si:ch211-200p22.4
si:ch211-200p22.4
chr19_+_2631565 0.08 ENSDART00000171487
fam126a
family with sequence similarity 126, member A
chr17_-_200316 0.08 ENSDART00000190561
CABZ01083778.1

chr20_-_29864390 0.08 ENSDART00000161834
ENSDART00000132278
rnf144ab
ring finger protein 144ab
chr7_+_34592526 0.08 ENSDART00000173959
fhod1
formin homology 2 domain containing 1
chr8_-_39822917 0.06 ENSDART00000067843
zgc:162025
zgc:162025
chr18_-_5598958 0.06 ENSDART00000161538
cyp1a
cytochrome P450, family 1, subfamily A
chr19_-_30524952 0.06 ENSDART00000103506
hpcal4
hippocalcin like 4
chr11_-_29563437 0.05 ENSDART00000163958
arhgef10la
Rho guanine nucleotide exchange factor (GEF) 10-like a
chr21_+_28478663 0.04 ENSDART00000077887
ENSDART00000134150
slc22a6l
solute carrier family 22 (organic anion transporter), member 6, like
chr15_-_16177603 0.02 ENSDART00000156352
si:ch211-259g3.4
si:ch211-259g3.4
chr17_-_20717845 0.01 ENSDART00000150037
ank3b
ankyrin 3b
chr14_-_32016615 0.00 ENSDART00000105761
zic3
zic family member 3 heterotaxy 1 (odd-paired homolog, Drosophila)

Network of associatons between targets according to the STRING database.

First level regulatory network of rx3

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
0.7 3.6 GO:0016338 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules(GO:0016338)
0.4 1.3 GO:0072111 spinal cord anterior/posterior patterning(GO:0021512) cell proliferation involved in pronephros development(GO:0039015) cell proliferation involved in kidney development(GO:0072111)
0.3 1.3 GO:0090646 mitochondrial tRNA processing(GO:0090646)
0.2 0.7 GO:0030043 actin filament fragmentation(GO:0030043)
0.2 3.6 GO:0007339 binding of sperm to zona pellucida(GO:0007339) egg coat formation(GO:0035803) regulation of acrosome reaction(GO:0060046) positive regulation of acrosome reaction(GO:2000344)
0.2 1.0 GO:0006978 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator(GO:0006978) DNA damage response, signal transduction resulting in transcription(GO:0042772)
0.2 3.2 GO:0043562 cellular response to nitrogen starvation(GO:0006995) cellular response to nitrogen levels(GO:0043562)
0.1 0.5 GO:0018343 protein farnesylation(GO:0018343)
0.1 0.5 GO:0071596 ubiquitin-dependent protein catabolic process via the N-end rule pathway(GO:0071596)
0.1 0.5 GO:0032776 DNA methylation on cytosine(GO:0032776)
0.1 1.3 GO:0035493 SNARE complex assembly(GO:0035493)
0.1 0.7 GO:2000290 smoothened signaling pathway involved in ventral spinal cord patterning(GO:0021910) regulation of myotome development(GO:2000290)
0.1 0.9 GO:0035677 posterior lateral line neuromast hair cell development(GO:0035677)
0.1 0.7 GO:0070979 protein K11-linked ubiquitination(GO:0070979)
0.1 0.8 GO:0030214 hyaluronan catabolic process(GO:0030214)
0.1 1.9 GO:0042761 very long-chain fatty acid biosynthetic process(GO:0042761)
0.1 0.4 GO:0048681 negative regulation of axon regeneration(GO:0048681) negative regulation of neuron projection regeneration(GO:0070571)
0.1 1.0 GO:0008535 respiratory chain complex IV assembly(GO:0008535)
0.0 0.2 GO:0016322 neuron remodeling(GO:0016322)
0.0 0.6 GO:0009303 rRNA transcription(GO:0009303) swim bladder maturation(GO:0048796) swim bladder inflation(GO:0048798)
0.0 5.1 GO:0017148 negative regulation of translation(GO:0017148)
0.0 0.8 GO:0031297 replication fork processing(GO:0031297)
0.0 0.3 GO:0035338 long-chain fatty-acyl-CoA biosynthetic process(GO:0035338)
0.0 1.1 GO:0051014 actin filament severing(GO:0051014)
0.0 1.4 GO:0060968 regulation of gene silencing(GO:0060968)
0.0 0.2 GO:0070207 protein homotrimerization(GO:0070207)
0.0 0.1 GO:0070301 cellular response to hydrogen peroxide(GO:0070301)
0.0 1.0 GO:0006635 fatty acid beta-oxidation(GO:0006635)
0.0 1.6 GO:0015718 monocarboxylic acid transport(GO:0015718)
0.0 0.1 GO:0097065 anterior head development(GO:0097065)
0.0 0.1 GO:0000395 mRNA 5'-splice site recognition(GO:0000395)
0.0 1.3 GO:0006497 protein lipidation(GO:0006497)
0.0 0.7 GO:0001508 action potential(GO:0001508)
0.0 0.4 GO:0097352 autophagosome maturation(GO:0097352)
0.0 0.2 GO:0051443 protein neddylation(GO:0045116) positive regulation of ubiquitin-protein transferase activity(GO:0051443)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 1.3 GO:0097189 apoptotic body(GO:0097189)
0.2 1.3 GO:0009295 nucleoid(GO:0009295) mitochondrial nucleoid(GO:0042645)
0.1 0.8 GO:0005662 DNA replication factor A complex(GO:0005662)
0.1 0.5 GO:0005965 protein farnesyltransferase complex(GO:0005965)
0.1 3.6 GO:0000421 autophagosome membrane(GO:0000421)
0.1 0.9 GO:0016602 CCAAT-binding factor complex(GO:0016602)
0.1 2.7 GO:0010494 cytoplasmic stress granule(GO:0010494)
0.0 0.2 GO:0043083 synaptic cleft(GO:0043083)
0.0 0.7 GO:0005682 U5 snRNP(GO:0005682)
0.0 0.2 GO:0033165 interphotoreceptor matrix(GO:0033165)
0.0 0.9 GO:0045180 basal cortex(GO:0045180)
0.0 3.2 GO:0070160 bicellular tight junction(GO:0005923) occluding junction(GO:0070160)
0.0 0.2 GO:0030122 AP-2 adaptor complex(GO:0030122)
0.0 1.1 GO:0031941 filamentous actin(GO:0031941)
0.0 1.1 GO:0001726 ruffle(GO:0001726)
0.0 0.3 GO:0032039 integrator complex(GO:0032039)
0.0 4.3 GO:0031012 extracellular matrix(GO:0031012)
0.0 0.7 GO:0005834 heterotrimeric G-protein complex(GO:0005834)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.8 9.0 GO:0009374 biotin binding(GO:0009374)
0.3 1.3 GO:0052905 tRNA (guanine(9)-N(1))-methyltransferase activity(GO:0052905)
0.3 1.0 GO:0019777 Atg12 transferase activity(GO:0019777)
0.3 1.0 GO:0016509 long-chain-3-hydroxyacyl-CoA dehydrogenase activity(GO:0016509)
0.3 2.9 GO:0035804 structural constituent of egg coat(GO:0035804)
0.2 3.4 GO:0008266 poly(U) RNA binding(GO:0008266)
0.2 2.1 GO:0015129 lactate transmembrane transporter activity(GO:0015129)
0.1 0.5 GO:0004660 protein farnesyltransferase activity(GO:0004660)
0.1 0.7 GO:0032190 acrosin binding(GO:0032190)
0.1 1.0 GO:0004711 ribosomal protein S6 kinase activity(GO:0004711)
0.1 0.7 GO:0031826 type 2A serotonin receptor binding(GO:0031826)
0.1 0.8 GO:0004415 hyalurononglucosaminidase activity(GO:0004415)
0.1 1.1 GO:0051371 muscle alpha-actinin binding(GO:0051371) alpha-actinin binding(GO:0051393)
0.0 0.2 GO:0044736 acid-sensing ion channel activity(GO:0044736)
0.0 3.2 GO:0031625 ubiquitin protein ligase binding(GO:0031625)
0.0 0.5 GO:0003886 DNA (cytosine-5-)-methyltransferase activity(GO:0003886)
0.0 0.7 GO:0008449 N-acetylglucosamine-6-sulfatase activity(GO:0008449)
0.0 0.3 GO:0047676 arachidonate-CoA ligase activity(GO:0047676)
0.0 0.5 GO:0005005 transmembrane-ephrin receptor activity(GO:0005005)
0.0 1.1 GO:0005109 frizzled binding(GO:0005109)
0.0 1.9 GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors(GO:0016627)
0.0 7.4 GO:0044822 mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.0 5.4 GO:0042802 identical protein binding(GO:0042802)
0.0 0.7 GO:0061631 ubiquitin conjugating enzyme activity(GO:0061631)
0.0 0.2 GO:0035615 clathrin adaptor activity(GO:0035615) endocytic adaptor activity(GO:0098748)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.7 SA FAS SIGNALING The TNF-type receptor Fas induces apoptosis on ligand binding.
0.1 0.8 PID TCR CALCIUM PATHWAY Calcium signaling in the CD4+ TCR pathway
0.0 1.2 PID PRL SIGNALING EVENTS PATHWAY Signaling events mediated by PRL
0.0 0.8 ST TUMOR NECROSIS FACTOR PATHWAY Tumor Necrosis Factor Pathway.
0.0 1.0 NABA COLLAGENS Genes encoding collagen proteins
0.0 0.6 PID WNT NONCANONICAL PATHWAY Noncanonical Wnt signaling pathway
0.0 1.3 WNT SIGNALING Genes related to Wnt-mediated signal transduction
0.0 0.2 PID ARF 3PATHWAY Arf1 pathway

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 2.1 REACTOME BILE SALT AND ORGANIC ANION SLC TRANSPORTERS Genes involved in Bile salt and organic anion SLC transporters
0.1 0.7 REACTOME SEMA3A PAK DEPENDENT AXON REPULSION Genes involved in Sema3A PAK dependent Axon repulsion
0.0 0.2 REACTOME RETROGRADE NEUROTROPHIN SIGNALLING Genes involved in Retrograde neurotrophin signalling
0.0 1.0 REACTOME COLLAGEN FORMATION Genes involved in Collagen formation