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PRJEB1986: zebrafish developmental stages transcriptome

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Results for rx3

Z-value: 0.72

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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_107561540.145.6e-01Click!

Activity profile of rx3 motif

Sorted Z-values of rx3 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr25_-_10503043 2.24 ENSDART00000155404
cox8b
cytochrome c oxidase subunit 8b
chr11_+_30244356 2.23 ENSDART00000036050
ENSDART00000150080
rs1a
retinoschisin 1a
chr19_+_10339538 1.82 ENSDART00000151808
ENSDART00000151235
rcvrn3
recoverin 3
chr5_-_50992690 1.75 ENSDART00000149553
ENSDART00000097460
ENSDART00000192021
hmgcra
3-hydroxy-3-methylglutaryl-CoA reductase a
chr20_-_40755614 1.58 ENSDART00000061247
cx32.3
connexin 32.3
chr3_-_50443607 1.47 ENSDART00000074036
rcvrna
recoverin a
chr10_-_7756865 1.46 ENSDART00000114373
ENSDART00000125407
ENSDART00000016317
loxa
lysyl oxidase a
chr2_+_39021282 1.41 ENSDART00000056577
RBP1 (1 of many)
si:ch211-119o8.7
chr13_+_28701233 1.33 ENSDART00000135931
si:ch211-67n3.9
si:ch211-67n3.9
chr14_-_2933185 1.29 ENSDART00000161677
ENSDART00000162446
ENSDART00000109378
si:dkey-201i24.6
si:dkey-201i24.6
chr21_-_42100471 1.20 ENSDART00000166148
gabra1
gamma-aminobutyric acid (GABA) A receptor, alpha 1
chr22_+_28337204 1.08 ENSDART00000163352
impg2b
interphotoreceptor matrix proteoglycan 2b
chr22_+_28337429 0.92 ENSDART00000166177
impg2b
interphotoreceptor matrix proteoglycan 2b
chr23_-_19230627 0.91 ENSDART00000007122
guca1b
guanylate cyclase activator 1B
chr13_-_44630111 0.88 ENSDART00000110092
mdga1
MAM domain containing glycosylphosphatidylinositol anchor 1
chr14_+_40874608 0.88 ENSDART00000168448
si:ch211-106m9.1
si:ch211-106m9.1
chr10_-_13343831 0.84 ENSDART00000135941
il11ra
interleukin 11 receptor, alpha
chr11_+_38280454 0.83 ENSDART00000171496
CDK18
si:dkey-166c18.1
chr2_+_22702488 0.83 ENSDART00000076647
kif1ab
kinesin family member 1Ab
chr5_+_64732036 0.73 ENSDART00000073950
olfm1a
olfactomedin 1a
chr18_-_43884044 0.71 ENSDART00000087382
ddx6
DEAD (Asp-Glu-Ala-Asp) box helicase 6
chr17_-_200316 0.69 ENSDART00000190561
CABZ01083778.1

chr9_-_21912227 0.66 ENSDART00000145576
lmo7a
LIM domain 7a
chr4_-_4834347 0.64 ENSDART00000141803
coa6
cytochrome c oxidase assembly factor 6
chr1_-_50859053 0.64 ENSDART00000132779
ENSDART00000137648
si:dkeyp-123h10.2
si:dkeyp-123h10.2
chr3_-_61162750 0.63 ENSDART00000055064
pvalb8
parvalbumin 8
chr4_-_4834617 0.62 ENSDART00000141539
coa6
cytochrome c oxidase assembly factor 6
chr20_+_34717403 0.62 ENSDART00000034252
pnocb
prepronociceptin b
chr18_-_5598958 0.61 ENSDART00000161538
cyp1a
cytochrome P450, family 1, subfamily A
chr4_+_21129752 0.56 ENSDART00000169764
syt1a
synaptotagmin Ia
chr15_-_21877726 0.55 ENSDART00000127819
ENSDART00000145646
ENSDART00000100897
ENSDART00000144739
zgc:162608
zgc:162608
chr23_-_1348933 0.54 ENSDART00000168981
CABZ01078120.1

chr21_-_22827548 0.53 ENSDART00000079161
angptl5
angiopoietin-like 5
chr10_+_42423318 0.52 ENSDART00000134282
npy8ar
neuropeptide Y receptor Y8a
chr5_+_64732270 0.47 ENSDART00000134241
olfm1a
olfactomedin 1a
chr11_-_44801968 0.47 ENSDART00000161846
map1lc3c
microtubule-associated protein 1 light chain 3 gamma
chr12_+_24342303 0.46 ENSDART00000111239
nrxn1a
neurexin 1a
chr12_-_6880694 0.45 ENSDART00000171846
pcdh15b
protocadherin-related 15b
chr8_+_7801060 0.43 ENSDART00000161618
tfe3a
transcription factor binding to IGHM enhancer 3a
chr9_+_50001746 0.42 ENSDART00000058892
slc38a11
solute carrier family 38, member 11
chr22_-_7129631 0.41 ENSDART00000171359
asic1b
acid-sensing (proton-gated) ion channel 1b
chr6_+_24398907 0.41 ENSDART00000167482
tgfbr3
transforming growth factor, beta receptor III
chr24_-_39518599 0.41 ENSDART00000145606
ENSDART00000031486
lyrm1
LYR motif containing 1
chr22_+_5176693 0.41 ENSDART00000160927
cers1
ceramide synthase 1
chr8_+_20776654 0.40 ENSDART00000135850
nfic
nuclear factor I/C
chr10_+_21867307 0.37 ENSDART00000126629
cbln17
cerebellin 17
chr4_-_20292821 0.36 ENSDART00000136069
ENSDART00000192504
cacna2d4a
calcium channel, voltage-dependent, alpha 2/delta subunit 4a
chr7_-_23768234 0.36 ENSDART00000173981
si:ch211-200p22.4
si:ch211-200p22.4
chr24_+_13316737 0.36 ENSDART00000191658
SBSPON
somatomedin B and thrombospondin type 1 domain containing
chr16_+_46111849 0.35 ENSDART00000172232
sv2a
synaptic vesicle glycoprotein 2A
chr25_-_27621268 0.35 ENSDART00000146205
ENSDART00000073511
hyal6
hyaluronoglucosaminidase 6
chr3_-_23406964 0.35 ENSDART00000114723
rapgefl1
Rap guanine nucleotide exchange factor (GEF)-like 1
chr22_-_21897203 0.34 ENSDART00000158501
ENSDART00000105566
ENSDART00000136795
gna11a
guanine nucleotide binding protein (G protein), alpha 11a (Gq class)
chr11_-_42554290 0.34 ENSDART00000130573
atp6ap1la
ATPase H+ transporting accessory protein 1 like a
chr5_-_67629263 0.33 ENSDART00000133753
zbtb20
zinc finger and BTB domain containing 20
chr22_+_5176255 0.32 ENSDART00000092647
cers1
ceramide synthase 1
chr17_-_40956035 0.32 ENSDART00000124715
si:dkey-16j16.4
si:dkey-16j16.4
chr15_-_22074315 0.31 ENSDART00000149830
drd2a
dopamine receptor D2a
chr10_-_32494304 0.30 ENSDART00000028161
uvrag
UV radiation resistance associated gene
chr20_+_28861629 0.30 ENSDART00000187274
ENSDART00000047826
slc10a1
solute carrier family 10 (sodium/bile acid cotransporter), member 1
chr1_-_513762 0.29 ENSDART00000148162
ENSDART00000144606
trmt10c
tRNA methyltransferase 10C, mitochondrial RNase P subunit
chr4_+_3980247 0.29 ENSDART00000049194
gpr37b
G protein-coupled receptor 37b
chr14_-_858985 0.28 ENSDART00000148687
ENSDART00000149375
slc34a1a
solute carrier family 34 (type II sodium/phosphate cotransporter), member 1a
chr13_+_38814521 0.28 ENSDART00000110976
col19a1
collagen, type XIX, alpha 1
chr14_+_30795559 0.28 ENSDART00000006132
cfl1
cofilin 1
chr24_-_31425799 0.27 ENSDART00000157998
cngb3.1
cyclic nucleotide gated channel beta 3, tandem duplicate 1
chr18_-_2433011 0.26 ENSDART00000181922
ENSDART00000193276
CR769778.1

chr6_-_6487876 0.26 ENSDART00000137642
cep170ab
centrosomal protein 170Ab
chr16_+_33902006 0.24 ENSDART00000161807
ENSDART00000159474
gnl2
guanine nucleotide binding protein-like 2 (nucleolar)
chr8_-_24252933 0.24 ENSDART00000057624
zgc:110353
zgc:110353
chr11_-_30158191 0.24 ENSDART00000155278
ENSDART00000156121
scml2
Scm polycomb group protein like 2
chr1_+_18811679 0.23 ENSDART00000078610
slc25a51a
solute carrier family 25, member 51a
chr20_+_28861435 0.23 ENSDART00000142678
slc10a1
solute carrier family 10 (sodium/bile acid cotransporter), member 1
chr22_+_18477934 0.22 ENSDART00000132684
cilp2
cartilage intermediate layer protein 2
chr25_-_13842618 0.22 ENSDART00000160258
mapk8ip1a
mitogen-activated protein kinase 8 interacting protein 1a
chr17_+_19630272 0.21 ENSDART00000104895
rgs7a
regulator of G protein signaling 7a
chr15_-_14552101 0.21 ENSDART00000171169
numbl
numb homolog (Drosophila)-like
chr19_-_30524952 0.20 ENSDART00000103506
hpcal4
hippocalcin like 4
chr1_-_18811517 0.20 ENSDART00000142026
si:dkey-167i21.2
si:dkey-167i21.2
chr9_+_22485343 0.20 ENSDART00000146028
dgkg
diacylglycerol kinase, gamma
chr10_-_32494499 0.19 ENSDART00000129395
uvrag
UV radiation resistance associated gene
chr8_+_6410933 0.19 ENSDART00000168789
lrrtm4l2
leucine rich repeat transmembrane neuronal 4 like 2
chr9_-_50001606 0.18 ENSDART00000161648
ENSDART00000168514
scn1a
sodium channel, voltage-gated, type I, alpha
chr12_+_48803098 0.17 ENSDART00000074768
ppifb
peptidylprolyl isomerase Fb
chr2_+_40294313 0.17 ENSDART00000037292
epha4b
eph receptor A4b
chr7_+_34592526 0.17 ENSDART00000173959
fhod1
formin homology 2 domain containing 1
chr8_+_25034544 0.16 ENSDART00000123300
ngrn
neugrin, neurite outgrowth associated
chr21_-_35419486 0.16 ENSDART00000138529
si:dkeyp-23e4.3
si:dkeyp-23e4.3
chr14_+_36521005 0.15 ENSDART00000192286
TENM3
si:dkey-237h12.3
chr24_-_35282568 0.14 ENSDART00000167406
ENSDART00000088609
sntg1
syntrophin, gamma 1
chr13_-_31017960 0.14 ENSDART00000145287
wdfy4
WDFY family member 4
chr1_-_17715493 0.13 ENSDART00000133027
si:dkey-256e7.8
si:dkey-256e7.8
chr21_+_32820175 0.13 ENSDART00000076903
adra2db
adrenergic, alpha-2D-, receptor b
chr24_-_4782052 0.13 ENSDART00000149911
agtr1b
angiotensin II receptor, type 1b
chr11_-_29768054 0.13 ENSDART00000079117
plekha3
pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3
chr18_+_2228737 0.12 ENSDART00000165301
rab27a
RAB27A, member RAS oncogene family
chr22_-_10121880 0.12 ENSDART00000002348
rdh5
retinol dehydrogenase 5 (11-cis/9-cis)
chr22_-_8725768 0.11 ENSDART00000189873
ENSDART00000181819
si:ch73-27e22.1
si:ch73-27e22.8
si:ch73-27e22.1
si:ch73-27e22.8
chr20_+_28803977 0.11 ENSDART00000153351
ENSDART00000038149
fntb
farnesyltransferase, CAAX box, beta
chr15_+_5360407 0.11 ENSDART00000110420
or112-1
odorant receptor, family A, subfamily 112, member 1
chr14_-_7207961 0.10 ENSDART00000167994
ENSDART00000166532
stox2b
storkhead box 2b
chr5_-_27438812 0.10 ENSDART00000078755
drd7
dopamine receptor D7
chr14_+_23717165 0.09 ENSDART00000006373
ndfip1
Nedd4 family interacting protein 1
chr19_-_42391383 0.08 ENSDART00000110075
ENSDART00000087002
plekho1a
pleckstrin homology domain containing, family O member 1a
chr4_-_19982119 0.08 ENSDART00000169248
drd4-rs
dopamine receptor D4 related sequence
chr13_+_38430466 0.08 ENSDART00000132691
adgrb3
adhesion G protein-coupled receptor B3
chr6_-_40352215 0.07 ENSDART00000103992
ttll3
tubulin tyrosine ligase-like family, member 3
chr12_+_31744217 0.07 ENSDART00000190361
RNF157
si:dkey-49c17.3
chr10_-_33297864 0.06 ENSDART00000163360
PRDM15
PR/SET domain 15
chr14_-_8940499 0.05 ENSDART00000129030
zgc:153681
zgc:153681
chr21_+_25777425 0.03 ENSDART00000021620
cldnd
claudin d
chr21_-_32060993 0.03 ENSDART00000131651
si:ch211-160j14.2
si:ch211-160j14.2
chr19_-_8768564 0.03 ENSDART00000170416
si:ch73-350k19.1
si:ch73-350k19.1
chr2_-_15324837 0.02 ENSDART00000015655
tecrl2b
trans-2,3-enoyl-CoA reductase-like 2b
chr14_+_8940326 0.02 ENSDART00000159920
rps6kal
ribosomal protein S6 kinase a, like
chr9_+_22364997 0.01 ENSDART00000188054
ENSDART00000046116
crygs3
crystallin, gamma S3
chr11_+_31864921 0.01 ENSDART00000180252
diaph3
diaphanous-related formin 3
chr17_+_10593398 0.01 ENSDART00000168897
ENSDART00000193989
ENSDART00000191664
ENSDART00000167188
mapkbp1
mitogen-activated protein kinase binding protein 1

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
0.3 3.3 GO:0036368 cone photoresponse recovery(GO:0036368)
0.2 1.2 GO:0070208 protein heterotrimerization(GO:0070208)
0.1 1.2 GO:0061075 positive regulation of neural retina development(GO:0061075) positive regulation of retina development in camera-type eye(GO:1902868)
0.1 0.5 GO:0010872 regulation of cholesterol esterification(GO:0010872) positive regulation of cholesterol esterification(GO:0010873)
0.1 0.3 GO:0030043 actin filament fragmentation(GO:0030043)
0.1 1.7 GO:0015936 coenzyme A metabolic process(GO:0015936)
0.1 0.7 GO:0034063 stress granule assembly(GO:0034063)
0.1 1.5 GO:0018057 peptidyl-lysine oxidation(GO:0018057)
0.1 1.3 GO:0008535 respiratory chain complex IV assembly(GO:0008535)
0.1 0.2 GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)(GO:0000448)
0.1 0.4 GO:0070206 protein trimerization(GO:0070206)
0.1 0.3 GO:0090646 mitochondrial tRNA processing(GO:0090646)
0.0 0.3 GO:0044341 sodium-dependent phosphate transport(GO:0044341)
0.0 0.4 GO:0045670 regulation of osteoclast differentiation(GO:0045670)
0.0 0.5 GO:0050962 detection of light stimulus involved in visual perception(GO:0050908) detection of light stimulus involved in sensory perception(GO:0050962)
0.0 0.5 GO:0015721 bile acid and bile salt transport(GO:0015721)
0.0 0.5 GO:0035493 SNARE complex assembly(GO:0035493)
0.0 0.7 GO:0060158 phospholipase C-activating dopamine receptor signaling pathway(GO:0060158)
0.0 2.2 GO:0006119 oxidative phosphorylation(GO:0006119)
0.0 0.1 GO:0018343 protein farnesylation(GO:0018343)
0.0 0.4 GO:0030214 hyaluronan catabolic process(GO:0030214)
0.0 0.1 GO:0071881 adenylate cyclase-inhibiting adrenergic receptor signaling pathway(GO:0071881)
0.0 0.6 GO:0048791 calcium ion-regulated exocytosis of neurotransmitter(GO:0048791)
0.0 0.5 GO:0006995 cellular response to nitrogen starvation(GO:0006995) cellular response to nitrogen levels(GO:0043562)
0.0 0.4 GO:0046549 retinal cone cell development(GO:0046549)
0.0 0.1 GO:0042362 fat-soluble vitamin biosynthetic process(GO:0042362)
0.0 0.1 GO:0035627 ceramide transport(GO:0035627)
0.0 0.2 GO:0070301 cellular response to hydrogen peroxide(GO:0070301)
0.0 0.1 GO:0016322 neuron remodeling(GO:0016322)
0.0 3.0 GO:0007601 visual perception(GO:0007601)
0.0 0.4 GO:0016185 synaptic vesicle budding from presynaptic endocytic zone membrane(GO:0016185)
0.0 0.2 GO:0031641 regulation of myelination(GO:0031641)
0.0 1.1 GO:0007218 neuropeptide signaling pathway(GO:0007218)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 2.0 GO:0033165 interphotoreceptor matrix(GO:0033165)
0.1 2.2 GO:0045277 respiratory chain complex IV(GO:0045277)
0.1 0.6 GO:0042584 chromaffin granule membrane(GO:0042584)
0.1 0.3 GO:0033181 plasma membrane proton-transporting V-type ATPase complex(GO:0033181)
0.0 0.5 GO:0042627 chylomicron(GO:0042627)
0.0 1.7 GO:0005778 peroxisomal membrane(GO:0005778) microbody membrane(GO:0031903)
0.0 0.3 GO:0042645 nucleoid(GO:0009295) mitochondrial nucleoid(GO:0042645)
0.0 1.2 GO:1902710 GABA receptor complex(GO:1902710) GABA-A receptor complex(GO:1902711)
0.0 0.4 GO:0098894 presynaptic endocytic zone(GO:0098833) presynaptic endocytic zone membrane(GO:0098835) extrinsic component of presynaptic membrane(GO:0098888) extrinsic component of presynaptic endocytic zone(GO:0098894)
0.0 0.1 GO:0005965 protein farnesyltransferase complex(GO:0005965)
0.0 0.5 GO:0032420 stereocilium(GO:0032420)
0.0 0.1 GO:0043083 synaptic cleft(GO:0043083)
0.0 0.6 GO:0043679 axon terminus(GO:0043679)
0.0 0.3 GO:0005903 brush border(GO:0005903)
0.0 0.5 GO:0010494 cytoplasmic stress granule(GO:0010494)
0.0 0.5 GO:0000421 autophagosome membrane(GO:0000421)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.9 GO:0008048 calcium sensitive guanylate cyclase activator activity(GO:0008048)
0.1 0.5 GO:0060228 phosphatidylcholine-sterol O-acyltransferase activator activity(GO:0060228)
0.1 0.6 GO:0070330 aromatase activity(GO:0070330)
0.1 0.5 GO:0008508 bile acid:sodium symporter activity(GO:0008508)
0.1 1.2 GO:0022851 benzodiazepine receptor activity(GO:0008503) GABA-gated chloride ion channel activity(GO:0022851)
0.1 1.5 GO:0004720 protein-lysine 6-oxidase activity(GO:0004720)
0.1 0.4 GO:0044736 acid-sensing ion channel activity(GO:0044736)
0.1 2.2 GO:0016676 cytochrome-c oxidase activity(GO:0004129) heme-copper terminal oxidase activity(GO:0015002) oxidoreductase activity, acting on a heme group of donors(GO:0016675) oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor(GO:0016676)
0.1 0.3 GO:0052905 tRNA (guanine(9)-N(1))-methyltransferase activity(GO:0052905)
0.1 0.4 GO:0050431 transforming growth factor beta binding(GO:0050431)
0.1 2.0 GO:0005540 hyaluronic acid binding(GO:0005540)
0.0 0.7 GO:0050291 sphingosine N-acyltransferase activity(GO:0050291)
0.0 0.6 GO:0031628 opioid receptor binding(GO:0031628)
0.0 0.3 GO:0005436 sodium:phosphate symporter activity(GO:0005436)
0.0 0.3 GO:0031826 type 2A serotonin receptor binding(GO:0031826)
0.0 0.1 GO:0001588 dopamine neurotransmitter receptor activity, coupled via Gs(GO:0001588)
0.0 0.1 GO:0001596 angiotensin type I receptor activity(GO:0001596) angiotensin type II receptor activity(GO:0004945)
0.0 0.5 GO:0004983 neuropeptide Y receptor activity(GO:0004983)
0.0 0.1 GO:0004660 protein farnesyltransferase activity(GO:0004660)
0.0 0.4 GO:0001591 dopamine neurotransmitter receptor activity, coupled via Gi/Go(GO:0001591)
0.0 0.4 GO:0005545 1-phosphatidylinositol binding(GO:0005545)
0.0 0.4 GO:0004415 hyalurononglucosaminidase activity(GO:0004415)
0.0 0.1 GO:1902387 ceramide transporter activity(GO:0035620) ceramide 1-phosphate binding(GO:1902387) ceramide 1-phosphate transporter activity(GO:1902388)
0.0 0.8 GO:0008574 ATP-dependent microtubule motor activity, plus-end-directed(GO:0008574)
0.0 0.1 GO:0070735 protein-glycine ligase activity(GO:0070735) tubulin-glycine ligase activity(GO:0070738)
0.0 1.3 GO:0050661 NADP binding(GO:0050661)
0.0 0.1 GO:0004938 alpha2-adrenergic receptor activity(GO:0004938)
0.0 0.3 GO:0005223 intracellular cyclic nucleotide activated cation channel activity(GO:0005221) intracellular cAMP activated cation channel activity(GO:0005222) intracellular cGMP activated cation channel activity(GO:0005223) cyclic nucleotide-gated ion channel activity(GO:0043855)
0.0 0.1 GO:0050699 WW domain binding(GO:0050699)
0.0 0.6 GO:0001786 phosphatidylserine binding(GO:0001786)
0.0 0.2 GO:0016018 cyclosporin A binding(GO:0016018)
0.0 0.2 GO:0005005 transmembrane-ephrin receptor activity(GO:0005005)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 1.0 PID CONE PATHWAY Visual signal transduction: Cones
0.0 0.3 SA FAS SIGNALING The TNF-type receptor Fas induces apoptosis on ligand binding.
0.0 0.5 PID HNF3A PATHWAY FOXA1 transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.5 REACTOME RECYCLING OF BILE ACIDS AND SALTS Genes involved in Recycling of bile acids and salts
0.1 1.2 REACTOME GABA A RECEPTOR ACTIVATION Genes involved in GABA A receptor activation
0.0 0.7 REACTOME MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE Genes involved in mRNA Decay by 5' to 3' Exoribonuclease
0.0 0.3 REACTOME SEMA3A PAK DEPENDENT AXON REPULSION Genes involved in Sema3A PAK dependent Axon repulsion