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PRJNA195909:zebrafish embryo and larva development

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Results for raraa+rarab

Z-value: 0.78

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Transcription factors associated with raraa+rarab

Gene Symbol Gene ID Gene Info
rarab
ENSDARG00000034893 retinoic acid receptor, alpha b
raraa
ENSDARG00000056783 retinoic acid receptor, alpha a
rarab
ENSDARG00000111757 retinoic acid receptor, alpha b

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
rarabdr11_v1_chr3_-_33175583_33175583-0.971.2e-05Click!
raraadr11_v1_chr12_+_11080776_110807760.791.1e-02Click!

Activity profile of raraa+rarab motif

Sorted Z-values of raraa+rarab motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr21_+_28445052 2.79 ENSDART00000077871
pygma
phosphorylase, glycogen, muscle A
chr19_+_19762183 1.26 ENSDART00000163611
ENSDART00000187604
hoxa3a
homeobox A3a
chr13_+_24834199 1.14 ENSDART00000101274
zgc:153981
zgc:153981
chr1_+_59538755 1.11 ENSDART00000166354
sp6
Sp6 transcription factor
chr14_-_51855047 1.01 ENSDART00000088912
cplx1
complexin 1
chr6_-_8277221 1.00 ENSDART00000053869
slc44a2
solute carrier family 44 (choline transporter), member 2
chr17_+_53311618 0.95 ENSDART00000166517
asb2b
ankyrin repeat and SOCS box containing 2b
chr5_-_64823750 0.94 ENSDART00000140305
lix1
limb and CNS expressed 1
chr2_+_52847049 0.94 ENSDART00000121980
creb3l3b
cAMP responsive element binding protein 3-like 3b
chr22_+_38173960 0.92 ENSDART00000010537
cp
ceruloplasmin
chr8_+_37168570 0.86 ENSDART00000098636
csf1b
colony stimulating factor 1b (macrophage)
chr4_-_191736 0.76 ENSDART00000169187
ENSDART00000192054
ptpro
protein tyrosine phosphatase, receptor type, O
chr4_+_1530287 0.75 ENSDART00000067446
slc38a4
solute carrier family 38, member 4
chr14_-_2001386 0.74 ENSDART00000170346
ENSDART00000163975
pcdh2g5
protocadherin 2 gamma 5
chr14_-_36862745 0.73 ENSDART00000109293
rnf130
ring finger protein 130
chr22_+_30009926 0.73 ENSDART00000142529
si:dkey-286j15.1
si:dkey-286j15.1
chr14_-_52552875 0.66 ENSDART00000170107
ppp2r2ba
protein phosphatase 2, regulatory subunit B, beta a
chr17_+_14886828 0.66 ENSDART00000010507
ENSDART00000131052
ptger2a
prostaglandin E receptor 2a (subtype EP2)
chr5_+_64856666 0.57 ENSDART00000050863
zgc:101858
zgc:101858
chr16_+_7242610 0.55 ENSDART00000081477
sri
sorcin
chr2_+_3696038 0.51 ENSDART00000150499
ENSDART00000136906
ENSDART00000164152
ENSDART00000128514
ENSDART00000108964
egfra
epidermal growth factor receptor a (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)
chr4_+_3980247 0.49 ENSDART00000049194
gpr37b
G protein-coupled receptor 37b
chr22_+_20208185 0.46 ENSDART00000142748
si:dkey-110c1.7
si:dkey-110c1.7
chr16_-_22194400 0.46 ENSDART00000186042
il6r
interleukin 6 receptor
chr23_+_25305431 0.43 ENSDART00000143291
RPL41
si:dkey-151g10.6
chr18_+_8340886 0.41 ENSDART00000081132
cpt1b
carnitine palmitoyltransferase 1B (muscle)
chr24_+_21973929 0.40 ENSDART00000042495
sat1b
spermidine/spermine N1-acetyltransferase 1b
chr12_+_2677303 0.38 ENSDART00000093113
antxr1c
anthrax toxin receptor 1c
chr17_+_14711765 0.37 ENSDART00000012889
cx28.6
connexin 28.6
chr21_-_32284532 0.35 ENSDART00000190676
clk4b
CDC-like kinase 4b
chr21_-_43482426 0.34 ENSDART00000192901
ankrd46a
ankyrin repeat domain 46a
chr17_+_33340675 0.32 ENSDART00000184396
ENSDART00000077553
xdh
xanthine dehydrogenase
chr23_+_25822742 0.32 ENSDART00000184436
r3hdml
R3H domain containing-like
chr24_-_36727922 0.29 ENSDART00000135142
si:ch73-334d15.1
si:ch73-334d15.1
chr23_-_3703569 0.28 ENSDART00000143731
pacsin1a
protein kinase C and casein kinase substrate in neurons 1a
chr25_+_1549838 0.26 ENSDART00000115001
avpr1aa
arginine vasopressin receptor 1Aa
chr14_+_94946 0.24 ENSDART00000165766
ENSDART00000163778
mcm7
minichromosome maintenance complex component 7
chr3_+_57268363 0.23 ENSDART00000180725
TMEM235 (1 of many)
transmembrane protein 235
chr11_+_25111846 0.22 ENSDART00000128705
ENSDART00000190058
ndrg3a
ndrg family member 3a
chr2_+_58841181 0.22 ENSDART00000164102
cirbpa
cold inducible RNA binding protein a
chr17_+_53311243 0.17 ENSDART00000160241
ENSDART00000160009
ENSDART00000162239
asb2b
ankyrin repeat and SOCS box containing 2b
chr11_-_34147205 0.17 ENSDART00000173216
atp13a3
ATPase 13A3
chr22_+_21324398 0.17 ENSDART00000168509
shc2
SHC (Src homology 2 domain containing) transforming protein 2
chr18_+_3338228 0.13 ENSDART00000161520
gdpd4a
glycerophosphodiester phosphodiesterase domain containing 4a
chr1_+_59154521 0.12 ENSDART00000130089
ENSDART00000152456
soul5l
heme-binding protein soul5, like
chr18_-_36066087 0.12 ENSDART00000059352
ENSDART00000145177
exosc5
exosome component 5
chr18_+_7073130 0.11 ENSDART00000101216
ENSDART00000148947
si:dkey-88e18.2
si:dkey-88e18.2
chr18_+_19842569 0.10 ENSDART00000147470
iqch
IQ motif containing H
chr17_+_46739693 0.09 ENSDART00000097810
pimr22
Pim proto-oncogene, serine/threonine kinase, related 22
chr4_+_73215536 0.08 ENSDART00000174290
LO018260.2
Danio rerio protein NLRC3-like (LOC101883187), mRNA.
chr22_-_31788170 0.06 ENSDART00000170925
pimr207
Pim proto-oncogene, serine/threonine kinase, related 207
chr15_+_1199407 0.05 ENSDART00000163827
mfsd1
major facilitator superfamily domain containing 1
chr8_-_28342313 0.03 ENSDART00000005583
kdm5bb
lysine (K)-specific demethylase 5Bb
chr2_-_55317035 0.02 ENSDART00000169382
ENSDART00000097874
tpm4b
tropomyosin 4b
chr14_+_36497250 0.01 ENSDART00000184727
TENM3
si:dkey-237h12.3
chr3_+_5297493 0.01 ENSDART00000138596
si:ch211-150d5.3
si:ch211-150d5.3

Network of associatons between targets according to the STRING database.

First level regulatory network of raraa+rarab

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
0.9 2.8 GO:0052575 carbohydrate localization(GO:0052575) carbohydrate storage(GO:0052576)
0.2 1.0 GO:0015871 choline transport(GO:0015871)
0.2 1.3 GO:0060017 parathyroid gland development(GO:0060017)
0.1 0.7 GO:0071380 response to prostaglandin E(GO:0034695) cellular response to prostaglandin E stimulus(GO:0071380)
0.1 0.3 GO:0006145 purine nucleobase catabolic process(GO:0006145)
0.1 0.4 GO:0006598 polyamine catabolic process(GO:0006598) putrescine catabolic process(GO:0009447)
0.1 0.5 GO:0016081 synaptic vesicle docking(GO:0016081) presynaptic dense core granule exocytosis(GO:0099525)
0.0 0.9 GO:0006825 copper ion transport(GO:0006825)
0.0 0.4 GO:1901998 toxin transport(GO:1901998)
0.0 1.1 GO:0055003 cardiac myofibril assembly(GO:0055003)
0.0 0.5 GO:0061154 endothelial tube morphogenesis(GO:0061154) blood vessel lumenization(GO:0072554)
0.0 0.9 GO:0097352 autophagosome maturation(GO:0097352)
0.0 0.3 GO:0001992 regulation of systemic arterial blood pressure by vasopressin(GO:0001992)
0.0 0.4 GO:0009437 carnitine metabolic process(GO:0009437)
0.0 0.9 GO:0030968 endoplasmic reticulum unfolded protein response(GO:0030968)
0.0 0.8 GO:0021587 cerebellum morphogenesis(GO:0021587)
0.0 0.1 GO:0071051 polyadenylation-dependent snoRNA 3'-end processing(GO:0071051)
0.0 0.7 GO:0003333 amino acid transmembrane transport(GO:0003333)
0.0 0.3 GO:0097320 membrane tubulation(GO:0097320)
0.0 0.2 GO:0048026 positive regulation of mRNA splicing, via spliceosome(GO:0048026)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.5 GO:0009925 basal plasma membrane(GO:0009925)
0.0 0.7 GO:0000159 protein phosphatase type 2A complex(GO:0000159)
0.0 0.5 GO:0043195 terminal bouton(GO:0043195)
0.0 0.1 GO:0000177 nuclear exosome (RNase complex)(GO:0000176) cytoplasmic exosome (RNase complex)(GO:0000177)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.6 2.8 GO:0008184 phosphorylase activity(GO:0004645) glycogen phosphorylase activity(GO:0008184)
0.2 1.0 GO:0015220 choline transmembrane transporter activity(GO:0015220)
0.2 0.5 GO:0005006 epidermal growth factor-activated receptor activity(GO:0005006)
0.1 0.7 GO:0004957 prostaglandin E receptor activity(GO:0004957)
0.1 0.9 GO:0016724 ferroxidase activity(GO:0004322) oxidoreductase activity, oxidizing metal ions, oxygen as acceptor(GO:0016724)
0.1 0.4 GO:0004095 carnitine O-palmitoyltransferase activity(GO:0004095) O-palmitoyltransferase activity(GO:0016416)
0.1 0.4 GO:0019809 spermidine binding(GO:0019809)
0.1 0.9 GO:0035497 cAMP response element binding(GO:0035497)
0.0 0.3 GO:0016725 oxidoreductase activity, acting on CH or CH2 groups(GO:0016725)
0.0 0.3 GO:0005000 vasopressin receptor activity(GO:0005000)
0.0 0.1 GO:0043140 ATP-dependent 3'-5' DNA helicase activity(GO:0043140) single-stranded DNA-dependent ATP-dependent 3'-5' DNA helicase activity(GO:1990518)
0.0 1.1 GO:0008138 protein tyrosine/serine/threonine phosphatase activity(GO:0008138)
0.0 0.5 GO:0017075 syntaxin-1 binding(GO:0017075)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.5 SA MMP CYTOKINE CONNECTION Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix.
0.0 0.9 PID HIF1 TFPATHWAY HIF-1-alpha transcription factor network
0.0 0.8 PID KIT PATHWAY Signaling events mediated by Stem cell factor receptor (c-Kit)
0.0 0.2 PID VEGFR1 PATHWAY VEGFR1 specific signals
0.0 0.4 PID HNF3B PATHWAY FOXA2 and FOXA3 transcription factor networks

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.3 REACTOME PURINE CATABOLISM Genes involved in Purine catabolism
0.1 1.0 REACTOME SYNTHESIS OF PC Genes involved in Synthesis of PC
0.1 0.9 REACTOME IRON UPTAKE AND TRANSPORT Genes involved in Iron uptake and transport
0.0 0.5 REACTOME IL 6 SIGNALING Genes involved in Interleukin-6 signaling
0.0 0.7 REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE Genes involved in Amino acid transport across the plasma membrane
0.0 0.4 REACTOME ACTIVATED AMPK STIMULATES FATTY ACID OXIDATION IN MUSCLE Genes involved in Activated AMPK stimulates fatty-acid oxidation in muscle
0.0 0.2 REACTOME SIGNAL ATTENUATION Genes involved in Signal attenuation
0.0 0.1 REACTOME MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE Genes involved in mRNA Decay by 3' to 5' Exoribonuclease