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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for rx1+rx2

Z-value: 0.28

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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_5006119-0.262.9e-01Click!
rx2dr11_v1_chr2_-_55853943_55853943-0.184.7e-01Click!

Activity profile of rx1+rx2 motif

Sorted Z-values of rx1+rx2 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr5_+_37903790 0.51 ENSDART00000162470
tmprss4b
transmembrane protease, serine 4b
chr8_-_53044300 0.46 ENSDART00000191653
nr6a1a
nuclear receptor subfamily 6, group A, member 1a
chr20_+_29209767 0.39 ENSDART00000141252
katnbl1
katanin p80 subunit B-like 1
chr20_+_29209615 0.38 ENSDART00000062350
katnbl1
katanin p80 subunit B-like 1
chr11_-_39118882 0.37 ENSDART00000113185
ENSDART00000156526
ap5b1
adaptor-related protein complex 5, beta 1 subunit
chr20_+_29209926 0.37 ENSDART00000152949
ENSDART00000153016
katnbl1
katanin p80 subunit B-like 1
chr16_+_13818743 0.32 ENSDART00000090191
flcn
folliculin
chr16_+_13818500 0.32 ENSDART00000135245
flcn
folliculin
chr10_-_34002185 0.29 ENSDART00000046599
zar1l
zygote arrest 1-like
chr7_-_51727760 0.29 ENSDART00000174180
hdac8
histone deacetylase 8
chr24_-_25144441 0.28 ENSDART00000152104
phldb2b
pleckstrin homology-like domain, family B, member 2b
chr22_+_23359369 0.27 ENSDART00000170886
dennd1b
DENN/MADD domain containing 1B
chr8_-_53044089 0.25 ENSDART00000135982
nr6a1a
nuclear receptor subfamily 6, group A, member 1a
chr13_-_36798204 0.24 ENSDART00000012357
sav1
salvador family WW domain containing protein 1
chr4_-_16124417 0.24 ENSDART00000128079
ENSDART00000077664
atp2b1a
ATPase plasma membrane Ca2+ transporting 1a
chr19_-_25149598 0.23 ENSDART00000162917
ptp4a3
protein tyrosine phosphatase type IVA, member 3
chr8_-_39822917 0.23 ENSDART00000067843
zgc:162025
zgc:162025
chr10_-_2788668 0.23 ENSDART00000131749
ENSDART00000124356
ENSDART00000085031
ash2l
ash2 (absent, small, or homeotic)-like (Drosophila)
chr7_-_41746427 0.22 ENSDART00000174232
arl8
ADP-ribosylation factor-like 8
chr8_-_50888806 0.21 ENSDART00000053750
acsl2
acyl-CoA synthetase long chain family member 2
chr17_+_22587356 0.21 ENSDART00000157328
birc6
baculoviral IAP repeat containing 6
chr21_-_13661631 0.21 ENSDART00000184408
pnpla7a
patatin-like phospholipase domain containing 7a
chr24_+_19415124 0.20 ENSDART00000186931
sulf1
sulfatase 1
chr9_+_45493341 0.20 ENSDART00000145616
adarb1b
adenosine deaminase, RNA-specific, B1b
chr8_-_25034411 0.20 ENSDART00000135973
nfyal
nuclear transcription factor Y, alpha, like
chr21_-_30082414 0.20 ENSDART00000157307
ENSDART00000155188
ccnjl
cyclin J-like
chr25_+_30131055 0.19 ENSDART00000152705
api5
apoptosis inhibitor 5
chr16_-_31351419 0.19 ENSDART00000178298
ENSDART00000018091
mroh1
maestro heat-like repeat family member 1
chr5_-_68074592 0.18 ENSDART00000165052
ENSDART00000018792
spag7
sperm associated antigen 7
chr9_+_43799829 0.18 ENSDART00000186240
ube2e3
ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)
chr22_-_20924564 0.17 ENSDART00000100642
ENSDART00000032770
ell
elongation factor RNA polymerase II
chr16_-_27677930 0.16 ENSDART00000145991
tbrg4
transforming growth factor beta regulator 4
chr8_+_25079470 0.15 ENSDART00000000744
sypl2b
synaptophysin-like 2b
chr2_+_25315591 0.15 ENSDART00000161386
fndc3ba
fibronectin type III domain containing 3Ba
chr24_-_29586082 0.14 ENSDART00000136763
vav3a
vav 3 guanine nucleotide exchange factor a
chr6_-_40922971 0.14 ENSDART00000155363
sfi1
SFI1 centrin binding protein
chr16_-_30434279 0.13 ENSDART00000018504
zgc:77086
zgc:77086
chr11_+_2855430 0.13 ENSDART00000172837
kif21b
kinesin family member 21B
chr6_-_55399214 0.13 ENSDART00000168367
ctsa
cathepsin A
chr13_-_35808904 0.13 ENSDART00000171667
map3k4
mitogen-activated protein kinase kinase kinase 4
chr4_+_21129752 0.12 ENSDART00000169764
syt1a
synaptotagmin Ia
chr19_+_2631565 0.12 ENSDART00000171487
fam126a
family with sequence similarity 126, member A
chr21_-_15200556 0.11 ENSDART00000141809
sfswap
splicing factor SWAP
chr14_+_21820034 0.11 ENSDART00000122739
ctbp1
C-terminal binding protein 1
chr17_-_9950911 0.11 ENSDART00000105117
sptssa
serine palmitoyltransferase, small subunit A
chr7_+_24023653 0.11 ENSDART00000141165
tinf2
TERF1 (TRF1)-interacting nuclear factor 2
chr20_+_28803977 0.11 ENSDART00000153351
ENSDART00000038149
fntb
farnesyltransferase, CAAX box, beta
chr9_-_34937025 0.11 ENSDART00000137888
cdc16
cell division cycle 16 homolog (S. cerevisiae)
chr6_+_36839509 0.10 ENSDART00000190605
ENSDART00000104160
zgc:110788
zgc:110788
chr6_+_40922572 0.10 ENSDART00000133599
ENSDART00000002728
ENSDART00000145153
eif4enif1
eukaryotic translation initiation factor 4E nuclear import factor 1
chr8_+_7801060 0.10 ENSDART00000161618
tfe3a
transcription factor binding to IGHM enhancer 3a
chr24_-_18809433 0.10 ENSDART00000152009
arfgef1
ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)
chr4_+_25917915 0.09 ENSDART00000138603
vezt
vezatin, adherens junctions transmembrane protein
chr9_-_11676491 0.09 ENSDART00000022358
zc3h15
zinc finger CCCH-type containing 15
chr10_+_35358675 0.09 ENSDART00000193263
si:dkey-259j3.5
si:dkey-259j3.5
chr5_-_52010122 0.09 ENSDART00000073627
ENSDART00000163898
ENSDART00000051003
cdk7
cyclin-dependent kinase 7
chr4_+_9400012 0.09 ENSDART00000191960
tmtc1
transmembrane and tetratricopeptide repeat containing 1
chr13_+_4871886 0.08 ENSDART00000132301
micu1
mitochondrial calcium uptake 1
chr16_-_31622777 0.08 ENSDART00000137311
ENSDART00000002930
phf20l1
PHD finger protein 20 like 1
chr14_+_30795559 0.08 ENSDART00000006132
cfl1
cofilin 1
chr4_+_11723852 0.08 ENSDART00000028820
mkln1
muskelin 1, intracellular mediator containing kelch motifs
chr8_+_29742237 0.07 ENSDART00000133955
ENSDART00000020621
mapk4
mitogen-activated protein kinase 4
chr11_-_21528056 0.07 ENSDART00000181626
srgap2
SLIT-ROBO Rho GTPase activating protein 2
chr20_+_36812368 0.07 ENSDART00000062931
abracl
ABRA C-terminal like
chr16_-_51288178 0.07 ENSDART00000079864
zgc:173729
zgc:173729
chr16_-_32013913 0.06 ENSDART00000030282
ENSDART00000138701
gstk1
glutathione S-transferase kappa 1
chr16_-_11798994 0.06 ENSDART00000135408
cnfn
cornifelin
chr22_-_10055744 0.05 ENSDART00000143686
si:ch211-222k6.2
si:ch211-222k6.2
chr9_+_1313418 0.05 ENSDART00000191361
casp8l2
caspase 8, apoptosis-related cysteine peptidase, like 2
chr17_+_24318753 0.05 ENSDART00000064083
otx1
orthodenticle homeobox 1
chr23_+_16638639 0.04 ENSDART00000143545
snphb
syntaphilin b
chr20_-_29864390 0.04 ENSDART00000161834
ENSDART00000132278
rnf144ab
ring finger protein 144ab
chr7_+_6652967 0.03 ENSDART00000102681
pnp5a
purine nucleoside phosphorylase 5a
chr14_-_4556896 0.02 ENSDART00000044678
ENSDART00000192863
GABRA2
gamma-aminobutyric acid type A receptor alpha2 subunit
chr22_-_20011476 0.02 ENSDART00000093312
ENSDART00000093310
celf5a
cugbp, Elav-like family member 5a
chr17_+_20589553 0.02 ENSDART00000154447
si:ch73-288o11.4
si:ch73-288o11.4
chr21_-_45363871 0.02 ENSDART00000075443
ENSDART00000182078
ENSDART00000151106
PPP2CA
zgc:56064
chr22_+_19407531 0.01 ENSDART00000141060
si:dkey-78l4.2
si:dkey-78l4.2
chr18_+_21408794 0.01 ENSDART00000140161
necab2
N-terminal EF-hand calcium binding protein 2
chr15_+_5360407 0.01 ENSDART00000110420
or112-1
odorant receptor, family A, subfamily 112, member 1
chr8_-_12264486 0.01 ENSDART00000091612
ENSDART00000135812
dab2ipa
DAB2 interacting protein a
chr7_+_54642005 0.01 ENSDART00000171864
fgf19
fibroblast growth factor 19
chr16_+_23799622 0.01 ENSDART00000046922
rab13
RAB13, member RAS oncogene family
chr4_-_56954002 0.01 ENSDART00000160934
si:dkey-269o24.1
si:dkey-269o24.1
chr17_+_15983557 0.00 ENSDART00000190806
clmn
calmin
chr15_+_45640906 0.00 ENSDART00000149361
ENSDART00000149079
sagb
S-antigen; retina and pineal gland (arrestin) b
chr4_-_4387012 0.00 ENSDART00000191836
CU468826.3
Danio rerio U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1-like (LOC100331497), mRNA.
chr18_+_28106139 0.00 ENSDART00000089615
kiaa1549lb
KIAA1549-like b
chr7_-_33960170 0.00 ENSDART00000180766
skor1a
SKI family transcriptional corepressor 1a
chr5_+_58550795 0.00 ENSDART00000192282
pou2f3
POU class 2 homeobox 3

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
0.1 0.6 GO:0030511 positive regulation of transforming growth factor beta receptor signaling pathway(GO:0030511) positive regulation of cellular response to transforming growth factor beta stimulus(GO:1903846)
0.1 0.2 GO:1903292 protein localization to Golgi membrane(GO:1903292)
0.0 0.2 GO:0034505 tooth mineralization(GO:0034505)
0.0 0.2 GO:0097065 anterior head development(GO:0097065)
0.0 0.3 GO:0070933 histone H4 deacetylation(GO:0070933)
0.0 0.2 GO:0042795 snRNA transcription from RNA polymerase II promoter(GO:0042795)
0.0 0.1 GO:0018343 protein farnesylation(GO:0018343)
0.0 0.1 GO:0030043 actin filament fragmentation(GO:0030043)
0.0 0.2 GO:2000290 smoothened signaling pathway involved in ventral spinal cord patterning(GO:0021910) regulation of myotome development(GO:2000290)
0.0 0.2 GO:0044528 regulation of mitochondrial mRNA stability(GO:0044528)
0.0 0.1 GO:0000395 mRNA 5'-splice site recognition(GO:0000395)
0.0 0.2 GO:0006382 adenosine to inosine editing(GO:0006382)
0.0 0.2 GO:0070979 protein K11-linked ubiquitination(GO:0070979)
0.0 0.1 GO:0051561 positive regulation of mitochondrial calcium ion concentration(GO:0051561)
0.0 0.1 GO:2001223 negative regulation of neuron migration(GO:2001223)
0.0 0.1 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)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.1 GO:0005965 protein farnesyltransferase complex(GO:0005965)
0.0 0.1 GO:0042584 chromaffin granule membrane(GO:0042584)
0.0 0.2 GO:0016602 CCAAT-binding factor complex(GO:0016602)
0.0 0.2 GO:0048188 Set1C/COMPASS complex(GO:0048188)
0.0 0.3 GO:0045180 basal cortex(GO:0045180)
0.0 0.1 GO:0017059 serine C-palmitoyltransferase complex(GO:0017059) endoplasmic reticulum palmitoyltransferase complex(GO:0031211)
0.0 0.4 GO:0030119 AP-type membrane coat adaptor complex(GO:0030119)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.1 GO:0004660 protein farnesyltransferase activity(GO:0004660)
0.0 0.1 GO:0004185 serine-type carboxypeptidase activity(GO:0004185)
0.0 0.3 GO:0031078 histone deacetylase activity (H3-K14 specific)(GO:0031078) NAD-dependent histone deacetylase activity (H3-K14 specific)(GO:0032041)
0.0 0.2 GO:0047676 arachidonate-CoA ligase activity(GO:0047676)
0.0 0.2 GO:0003726 double-stranded RNA adenosine deaminase activity(GO:0003726)
0.0 0.1 GO:0004758 serine C-palmitoyltransferase activity(GO:0004758) C-palmitoyltransferase activity(GO:0016454)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.2 REACTOME SIGNALING BY HIPPO Genes involved in Signaling by Hippo