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PRJEB1986: zebrafish developmental stages transcriptome

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Results for rx1+rx2

Z-value: 0.36

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Transcription factors associated with rx1+rx2

Gene Symbol Gene ID Gene Info
rx2
ENSDARG00000040321 retinal homeobox gene 2
rx1
ENSDARG00000071684 retinal homeobox gene 1

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
rx1dr11_v1_chr22_-_5006119_50061190.493.4e-02Click!
rx2dr11_v1_chr2_-_55853943_558539430.381.1e-01Click!

Activity profile of rx1+rx2 motif

Sorted Z-values of rx1+rx2 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr4_+_306036 0.77 ENSDART00000103659
msgn1
mesogenin 1
chr8_-_16697615 0.62 ENSDART00000187929
rpe65b
retinal pigment epithelium-specific protein 65b
chr3_-_53533128 0.60 ENSDART00000183591
notch3
notch 3
chr4_-_9891874 0.59 ENSDART00000067193
adm2a
adrenomedullin 2a
chr9_-_34937025 0.57 ENSDART00000137888
cdc16
cell division cycle 16 homolog (S. cerevisiae)
chr8_-_50888806 0.52 ENSDART00000053750
acsl2
acyl-CoA synthetase long chain family member 2
chr24_+_19415124 0.52 ENSDART00000186931
sulf1
sulfatase 1
chr21_-_15200556 0.48 ENSDART00000141809
sfswap
splicing factor SWAP
chr25_+_30131055 0.44 ENSDART00000152705
api5
apoptosis inhibitor 5
chr11_-_21528056 0.44 ENSDART00000181626
srgap2
SLIT-ROBO Rho GTPase activating protein 2
chr11_-_39118882 0.42 ENSDART00000113185
ENSDART00000156526
ap5b1
adaptor-related protein complex 5, beta 1 subunit
chr24_+_38301080 0.42 ENSDART00000105672
mybpc2b
myosin binding protein C, fast type b
chr20_+_29209615 0.41 ENSDART00000062350
katnbl1
katanin p80 subunit B-like 1
chr14_+_21820034 0.40 ENSDART00000122739
ctbp1
C-terminal binding protein 1
chr15_+_23799461 0.39 ENSDART00000154885
si:ch211-167j9.4
si:ch211-167j9.4
chr25_+_11008419 0.38 ENSDART00000156589
mhc1lia
major histocompatibility complex class I LIA
chr1_+_21731382 0.37 ENSDART00000054395
pax5
paired box 5
chr23_+_43255328 0.36 ENSDART00000102712
tgm2a
transglutaminase 2, C polypeptide A
chr8_+_26059677 0.35 ENSDART00000009178
impdh2
IMP (inosine 5'-monophosphate) dehydrogenase 2
chr18_+_17827149 0.35 ENSDART00000190237
ENSDART00000189345
ZNF423
si:ch211-216l23.1
chr4_+_6032640 0.34 ENSDART00000157487
tfec
transcription factor EC
chr3_-_26017831 0.33 ENSDART00000179982
hmox1a
heme oxygenase 1a
chr8_+_18010978 0.32 ENSDART00000039887
ENSDART00000144532
ssbp3b
single stranded DNA binding protein 3b
chr10_-_2788668 0.32 ENSDART00000131749
ENSDART00000124356
ENSDART00000085031
ash2l
ash2 (absent, small, or homeotic)-like (Drosophila)
chr14_-_4170654 0.31 ENSDART00000188347
si:dkey-185e18.7
si:dkey-185e18.7
chr16_+_23799622 0.30 ENSDART00000046922
rab13
RAB13, member RAS oncogene family
chr21_-_30082414 0.30 ENSDART00000157307
ENSDART00000155188
ccnjl
cyclin J-like
chr13_-_35808904 0.30 ENSDART00000171667
map3k4
mitogen-activated protein kinase kinase kinase 4
chr4_+_11723852 0.30 ENSDART00000028820
mkln1
muskelin 1, intracellular mediator containing kelch motifs
chr8_-_39822917 0.30 ENSDART00000067843
zgc:162025
zgc:162025
chr18_+_9171778 0.29 ENSDART00000101192
sema3d
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D
chr7_-_41746427 0.29 ENSDART00000174232
arl8
ADP-ribosylation factor-like 8
chr16_-_30434279 0.29 ENSDART00000018504
zgc:77086
zgc:77086
chr9_+_43799829 0.29 ENSDART00000186240
ube2e3
ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)
chr16_-_27677930 0.28 ENSDART00000145991
tbrg4
transforming growth factor beta regulator 4
chr11_+_16153207 0.28 ENSDART00000192356
tada3l
transcriptional adaptor 3 (NGG1 homolog, yeast)-like
chr7_+_24023653 0.28 ENSDART00000141165
tinf2
TERF1 (TRF1)-interacting nuclear factor 2
chr20_+_36812368 0.28 ENSDART00000062931
abracl
ABRA C-terminal like
chr8_+_18010568 0.27 ENSDART00000121984
ssbp3b
single stranded DNA binding protein 3b
chr8_+_25079470 0.27 ENSDART00000000744
sypl2b
synaptophysin-like 2b
chr20_-_37813863 0.26 ENSDART00000147529
batf3
basic leucine zipper transcription factor, ATF-like 3
chr17_+_24318753 0.26 ENSDART00000064083
otx1
orthodenticle homeobox 1
chr19_+_2631565 0.25 ENSDART00000171487
fam126a
family with sequence similarity 126, member A
chr20_+_29209767 0.24 ENSDART00000141252
katnbl1
katanin p80 subunit B-like 1
chr2_+_25315591 0.24 ENSDART00000161386
fndc3ba
fibronectin type III domain containing 3Ba
chr9_-_11676491 0.24 ENSDART00000022358
zc3h15
zinc finger CCCH-type containing 15
chr22_+_2260497 0.23 ENSDART00000142890
si:dkey-4c15.9
si:dkey-4c15.9
chr5_-_12219572 0.23 ENSDART00000167834
nos1
nitric oxide synthase 1 (neuronal)
chr8_+_29742237 0.23 ENSDART00000133955
ENSDART00000020621
mapk4
mitogen-activated protein kinase 4
chr10_-_34002185 0.23 ENSDART00000046599
zar1l
zygote arrest 1-like
chr25_+_20715950 0.22 ENSDART00000180223
ergic2
ERGIC and golgi 2
chr19_-_5669122 0.21 ENSDART00000112211
si:ch211-264f5.2
si:ch211-264f5.2
chr8_+_18011522 0.21 ENSDART00000136756
ssbp3b
single stranded DNA binding protein 3b
chr6_+_36839509 0.20 ENSDART00000190605
ENSDART00000104160
zgc:110788
zgc:110788
chr6_-_40922971 0.20 ENSDART00000155363
sfi1
SFI1 centrin binding protein
chr11_+_16152316 0.20 ENSDART00000081054
tada3l
transcriptional adaptor 3 (NGG1 homolog, yeast)-like
chr20_-_9095105 0.20 ENSDART00000140792
oma1
OMA1 zinc metallopeptidase
chr20_+_29209926 0.20 ENSDART00000152949
ENSDART00000153016
katnbl1
katanin p80 subunit B-like 1
chr23_+_12134839 0.20 ENSDART00000128551
ENSDART00000141204
ttll9
tubulin tyrosine ligase-like family, member 9
chr11_-_16152400 0.19 ENSDART00000123665
arpc4l
actin related protein 2/3 complex, subunit 4, like
chr8_+_29986265 0.18 ENSDART00000148258
ptch1
patched 1
chr4_+_47636303 0.18 ENSDART00000167272
ENSDART00000166961
BX324142.1

chr17_+_24821627 0.18 ENSDART00000112389
wdr43
WD repeat domain 43
chr7_-_33960170 0.18 ENSDART00000180766
skor1a
SKI family transcriptional corepressor 1a
chr13_-_36798204 0.16 ENSDART00000012357
sav1
salvador family WW domain containing protein 1
chr16_+_35379720 0.16 ENSDART00000170497
si:dkey-34d22.2
si:dkey-34d22.2
chr17_+_20589553 0.15 ENSDART00000154447
si:ch73-288o11.4
si:ch73-288o11.4
chr19_-_25149598 0.15 ENSDART00000162917
ptp4a3
protein tyrosine phosphatase type IVA, member 3
chr8_-_24332284 0.15 ENSDART00000163241
pimr142
Pim proto-oncogene, serine/threonine kinase, related 142
chr5_-_25733745 0.15 ENSDART00000051566
zgc:101016
zgc:101016
chr8_+_28695914 0.14 ENSDART00000033386
ocstamp
osteoclast stimulatory transmembrane protein
chr6_-_7720332 0.14 ENSDART00000135945
rpsa
ribosomal protein SA
chr20_-_29864390 0.14 ENSDART00000161834
ENSDART00000132278
rnf144ab
ring finger protein 144ab
chr16_-_54971277 0.14 ENSDART00000113358
wdtc1
WD and tetratricopeptide repeats 1
chr1_+_35985813 0.13 ENSDART00000179634
ENSDART00000139636
ENSDART00000175902
zgc:152968
zgc:152968
chr21_+_45223194 0.13 ENSDART00000150902
si:ch73-269m14.3
si:ch73-269m14.3
chr7_+_6652967 0.13 ENSDART00000102681
pnp5a
purine nucleoside phosphorylase 5a
chr8_-_24366726 0.13 ENSDART00000182351
ENSDART00000187099
ENSDART00000181534
CR450805.1

chr5_-_52010122 0.13 ENSDART00000073627
ENSDART00000163898
ENSDART00000051003
cdk7
cyclin-dependent kinase 7
chr6_-_55399214 0.13 ENSDART00000168367
ctsa
cathepsin A
chr17_-_9950911 0.13 ENSDART00000105117
sptssa
serine palmitoyltransferase, small subunit A
chr2_+_6255434 0.13 ENSDART00000139429
zp3b
zona pellucida glycoprotein 3b
chr24_+_37640626 0.13 ENSDART00000008047
wdr24
WD repeat domain 24
chr1_+_6161930 0.12 ENSDART00000037036
cnppd1
cyclin Pas1/PHO80 domain containing 1
chr8_-_24502997 0.12 ENSDART00000184801
ENSDART00000179794
BX296549.1

chr24_-_25144441 0.12 ENSDART00000152104
phldb2b
pleckstrin homology-like domain, family B, member 2b
chr21_-_45363871 0.12 ENSDART00000075443
ENSDART00000182078
ENSDART00000151106
PPP2CA
zgc:56064
chr7_-_40630698 0.12 ENSDART00000134547
ube3c
ubiquitin protein ligase E3C
chr13_-_36663358 0.10 ENSDART00000085319
sos2
son of sevenless homolog 2 (Drosophila)
chr21_-_13661631 0.10 ENSDART00000184408
pnpla7a
patatin-like phospholipase domain containing 7a
chr8_-_53044300 0.09 ENSDART00000191653
nr6a1a
nuclear receptor subfamily 6, group A, member 1a
chr6_+_40922572 0.09 ENSDART00000133599
ENSDART00000002728
ENSDART00000145153
eif4enif1
eukaryotic translation initiation factor 4E nuclear import factor 1
chr18_-_40708537 0.09 ENSDART00000077577
si:ch211-132b12.8
si:ch211-132b12.8
chr16_+_13818743 0.09 ENSDART00000090191
flcn
folliculin
chr1_+_6162090 0.08 ENSDART00000188295
cnppd1
cyclin Pas1/PHO80 domain containing 1
chr6_+_7421898 0.08 ENSDART00000043946
ccdc65
coiled-coil domain containing 65
chr7_+_34453185 0.08 ENSDART00000173875
ENSDART00000173921
ENSDART00000173995
si:cabz01009626.1
si:cabz01009626.1
chr21_-_2341937 0.08 ENSDART00000158459
zgc:193790
zgc:193790
chr4_+_9400012 0.07 ENSDART00000191960
tmtc1
transmembrane and tetratricopeptide repeat containing 1
chr22_-_20924564 0.07 ENSDART00000100642
ENSDART00000032770
ell
elongation factor RNA polymerase II
chr17_+_22587356 0.07 ENSDART00000157328
birc6
baculoviral IAP repeat containing 6
chr9_+_21165484 0.07 ENSDART00000177286
si:rp71-68n21.9
si:rp71-68n21.9
chr4_-_56954002 0.06 ENSDART00000160934
si:dkey-269o24.1
si:dkey-269o24.1
chr17_-_53329704 0.06 ENSDART00000193895
exd1
exonuclease 3'-5' domain containing 1
chr17_-_49978986 0.05 ENSDART00000154728
col12a1a
collagen, type XII, alpha 1a
chr22_-_10055744 0.05 ENSDART00000143686
si:ch211-222k6.2
si:ch211-222k6.2
chr8_-_53044089 0.05 ENSDART00000135982
nr6a1a
nuclear receptor subfamily 6, group A, member 1a
chr21_-_43015383 0.05 ENSDART00000065097
dpysl3
dihydropyrimidinase-like 3
chr13_+_4871886 0.05 ENSDART00000132301
micu1
mitochondrial calcium uptake 1
chr10_-_40421050 0.04 ENSDART00000141834
ENSDART00000164847
taar20w
trace amine associated receptor 20w
chr8_-_18010735 0.04 ENSDART00000125014
acot11b
acyl-CoA thioesterase 11b
chr7_+_46368520 0.03 ENSDART00000192821
znf536
zinc finger protein 536
chr14_-_413273 0.03 ENSDART00000163976
ENSDART00000179907
FAT4
FAT atypical cadherin 4
chr8_-_25034411 0.02 ENSDART00000135973
nfyal
nuclear transcription factor Y, alpha, like
chr7_+_26173751 0.01 ENSDART00000065131
si:ch211-196f2.7
si:ch211-196f2.7
chr22_+_23359369 0.01 ENSDART00000170886
dennd1b
DENN/MADD domain containing 1B
chr22_+_5123479 0.01 ENSDART00000111822
ENSDART00000081910
loxl5a
lysyl oxidase-like 5a
chr25_+_34938317 0.00 ENSDART00000042678
vps4a
vacuolar protein sorting 4a homolog A (S. cerevisiae)
chr23_-_15216654 0.00 ENSDART00000131649
sulf2b
sulfatase 2b
chr19_+_42983613 0.00 ENSDART00000033724
fabp3
fatty acid binding protein 3, muscle and heart
chr21_-_33995710 0.00 ENSDART00000100508
ENSDART00000179622
ebf1b
early B cell factor 1b

Network of associatons between targets according to the STRING database.

First level regulatory network of rx1+rx2

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 0.8 GO:0048340 paraxial mesoderm morphogenesis(GO:0048340) paraxial mesoderm formation(GO:0048341)
0.2 0.6 GO:0098725 somatic stem cell population maintenance(GO:0035019) symmetric cell division(GO:0098725)
0.2 0.6 GO:0016109 tetraterpenoid metabolic process(GO:0016108) tetraterpenoid biosynthetic process(GO:0016109) carotenoid metabolic process(GO:0016116) carotenoid biosynthetic process(GO:0016117) xanthophyll metabolic process(GO:0016122) xanthophyll biosynthetic process(GO:0016123) zeaxanthin metabolic process(GO:1901825) zeaxanthin biosynthetic process(GO:1901827)
0.1 0.3 GO:0007585 respiratory gaseous exchange(GO:0007585) regulation of respiratory gaseous exchange(GO:0043576)
0.1 0.4 GO:2001223 negative regulation of neuron migration(GO:2001223)
0.1 0.5 GO:0000395 mRNA 5'-splice site recognition(GO:0000395)
0.1 0.2 GO:0098923 retrograde trans-synaptic signaling by soluble gas(GO:0098923) retrograde trans-synaptic signaling by nitric oxide(GO:0098924)
0.1 0.3 GO:0048210 Golgi vesicle fusion to target membrane(GO:0048210)
0.1 0.3 GO:1903292 protein localization to Golgi membrane(GO:1903292)
0.1 0.5 GO:0021910 smoothened signaling pathway involved in ventral spinal cord patterning(GO:0021910) regulation of myotome development(GO:2000290)
0.1 0.3 GO:0007508 larval development(GO:0002164) larval heart development(GO:0007508)
0.0 0.3 GO:0097065 anterior head development(GO:0097065)
0.0 0.6 GO:1901970 positive regulation of mitotic metaphase/anaphase transition(GO:0045842) positive regulation of mitotic sister chromatid separation(GO:1901970) positive regulation of metaphase/anaphase transition of cell cycle(GO:1902101)
0.0 0.4 GO:0060005 reflex(GO:0060004) vestibular reflex(GO:0060005) vestibular receptor cell differentiation(GO:0060114) vestibular receptor cell development(GO:0060118)
0.0 0.4 GO:0006177 GMP biosynthetic process(GO:0006177) GMP metabolic process(GO:0046037)
0.0 0.3 GO:0044528 regulation of mitochondrial mRNA stability(GO:0044528)
0.0 0.1 GO:0045922 negative regulation of fatty acid metabolic process(GO:0045922)
0.0 0.3 GO:0070979 protein K11-linked ubiquitination(GO:0070979)
0.0 0.3 GO:0061484 hematopoietic stem cell homeostasis(GO:0061484)
0.0 0.2 GO:1990845 adaptive thermogenesis(GO:1990845)
0.0 0.5 GO:0035338 long-chain fatty-acyl-CoA biosynthetic process(GO:0035338)
0.0 0.2 GO:0048635 negative regulation of muscle organ development(GO:0048635)
0.0 0.3 GO:1904356 regulation of telomere maintenance via telomere lengthening(GO:1904356)
0.0 0.4 GO:0018149 peptide cross-linking(GO:0018149)
0.0 0.5 GO:0043967 histone H4 acetylation(GO:0043967)
0.0 0.3 GO:0003406 retinal pigment epithelium development(GO:0003406)
0.0 0.3 GO:0051568 histone H3-K4 methylation(GO:0051568)
0.0 0.1 GO:0042795 snRNA transcription from RNA polymerase II promoter(GO:0042795)
0.0 0.1 GO:0003352 regulation of cilium movement(GO:0003352)
0.0 0.2 GO:0018095 protein polyglutamylation(GO:0018095)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.5 GO:0005671 Ada2/Gcn5/Ada3 transcription activator complex(GO:0005671)
0.0 0.3 GO:0032593 insulin-responsive compartment(GO:0032593)
0.0 0.6 GO:0005680 anaphase-promoting complex(GO:0005680)
0.0 0.4 GO:0044327 dendritic spine head(GO:0044327) phagocytic vesicle(GO:0045335)
0.0 0.3 GO:0070187 telosome(GO:0070187)
0.0 0.3 GO:0048188 Set1C/COMPASS complex(GO:0048188)
0.0 0.1 GO:0017059 serine C-palmitoyltransferase complex(GO:0017059) endoplasmic reticulum palmitoyltransferase complex(GO:0031211)
0.0 0.1 GO:1990923 PET complex(GO:1990923)
0.0 0.1 GO:0005675 holo TFIIH complex(GO:0005675)
0.0 0.4 GO:0030119 AP-type membrane coat adaptor complex(GO:0030119)
0.0 0.5 GO:0000307 cyclin-dependent protein kinase holoenzyme complex(GO:0000307)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 0.6 GO:0050251 retinol isomerase activity(GO:0050251) all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity(GO:0052885)
0.1 0.4 GO:0003938 IMP dehydrogenase activity(GO:0003938)
0.1 0.3 GO:0004392 heme oxygenase (decyclizing) activity(GO:0004392)
0.0 0.5 GO:0047676 arachidonate-CoA ligase activity(GO:0047676)
0.0 0.2 GO:0097108 hedgehog family protein binding(GO:0097108)
0.0 0.2 GO:0004517 nitric-oxide synthase activity(GO:0004517)
0.0 0.5 GO:0008449 N-acetylglucosamine-6-sulfatase activity(GO:0008449)
0.0 0.1 GO:0004185 serine-type carboxypeptidase activity(GO:0004185)
0.0 0.6 GO:0005112 Notch binding(GO:0005112)
0.0 0.3 GO:0038191 neuropilin binding(GO:0038191)
0.0 0.4 GO:0031267 small GTPase binding(GO:0031267)
0.0 0.4 GO:0003810 protein-glutamine gamma-glutamyltransferase activity(GO:0003810)
0.0 0.1 GO:0016454 serine C-palmitoyltransferase activity(GO:0004758) C-palmitoyltransferase activity(GO:0016454)
0.0 0.1 GO:0004731 purine-nucleoside phosphorylase activity(GO:0004731)
0.0 0.2 GO:0070739 protein-glutamic acid ligase activity(GO:0070739) tubulin-glutamic acid ligase activity(GO:0070740)
0.0 0.1 GO:0035804 structural constituent of egg coat(GO:0035804)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.3 PID TCR CALCIUM PATHWAY Calcium signaling in the CD4+ TCR pathway
0.0 1.0 PID NOTCH PATHWAY Notch signaling pathway
0.0 0.1 SA G2 AND M PHASES Cdc25 activates the cdc2/cyclin B complex to induce the G2/M transition.
0.0 0.3 PID P38 MKK3 6PATHWAY p38 MAPK signaling pathway
0.0 0.7 PID CMYB PATHWAY C-MYB transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.6 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 0.6 REACTOME CONVERSION FROM APC C CDC20 TO APC C CDH1 IN LATE ANAPHASE Genes involved in Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase
0.0 0.4 REACTOME PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS Genes involved in Purine ribonucleoside monophosphate biosynthesis
0.0 0.3 REACTOME PACKAGING OF TELOMERE ENDS Genes involved in Packaging Of Telomere Ends
0.0 0.5 REACTOME SIGNALING BY ROBO RECEPTOR Genes involved in Signaling by Robo receptor
0.0 0.2 REACTOME LATENT INFECTION OF HOMO SAPIENS WITH MYCOBACTERIUM TUBERCULOSIS Genes involved in Latent infection of Homo sapiens with Mycobacterium tuberculosis