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PRJDB7713: Age associated transcriptome analysis in 5 tissues of zebrafish

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Results for lmx1a

Z-value: 0.54

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Transcription factors associated with lmx1a

Gene Symbol Gene ID Gene Info
lmx1a
ENSDARG00000020354 LIM homeobox transcription factor 1, alpha

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
lmx1adr11_v1_chr20_+_33924235_33924236-0.347.1e-04Click!

Activity profile of lmx1a motif

Sorted Z-values of lmx1a motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr16_-_12173554 7.37 ENSDART00000110567
ENSDART00000155935
clstn3
calsyntenin 3
chr9_+_24159280 6.27 ENSDART00000184624
ENSDART00000178422
hecw2a
HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2a
chr3_+_62000822 6.10 ENSDART00000106680
rai1
retinoic acid induced 1
chr23_+_20563779 5.62 ENSDART00000146008
camkvl
CaM kinase-like vesicle-associated, like
chr13_+_11440389 5.06 ENSDART00000186463
zbtb18
zinc finger and BTB domain containing 18
chr16_-_28856112 4.81 ENSDART00000078543
syt11b
synaptotagmin XIb
chr22_-_12160283 4.70 ENSDART00000146785
ENSDART00000128176
tmem163b
transmembrane protein 163b
chr9_+_34641237 4.57 ENSDART00000133996
shox
short stature homeobox
chr13_-_29421331 4.00 ENSDART00000150228
chata
choline O-acetyltransferase a
chr3_+_39853788 3.84 ENSDART00000154869
cacna1ha
calcium channel, voltage-dependent, T type, alpha 1H subunit a
chr3_+_50312422 3.82 ENSDART00000157689
gas7a
growth arrest-specific 7a
chr24_+_24461341 3.63 ENSDART00000147658
bhlhe22
basic helix-loop-helix family, member e22
chr12_+_25600685 3.53 ENSDART00000077157
six3b
SIX homeobox 3b
chr5_-_21422390 3.44 ENSDART00000144198
tenm1
teneurin transmembrane protein 1
chr11_-_25733910 3.37 ENSDART00000171935
brpf3a
bromodomain and PHD finger containing, 3a
chr16_-_12173399 3.36 ENSDART00000142574
clstn3
calsyntenin 3
chr24_+_24461558 3.36 ENSDART00000182424
bhlhe22
basic helix-loop-helix family, member e22
chr1_+_6172786 3.25 ENSDART00000126468
prkag3a
protein kinase, AMP-activated, gamma 3a non-catalytic subunit
chr9_+_42063906 3.25 ENSDART00000048893
pcbp3
poly(rC) binding protein 3
chr16_-_16152199 3.19 ENSDART00000012718
fabp11b
fatty acid binding protein 11b
chr9_-_38398789 3.13 ENSDART00000188384
znf142
zinc finger protein 142
chr2_-_16217344 2.82 ENSDART00000152031
arhgef4
Rho guanine nucleotide exchange factor (GEF) 4
chr9_-_43538328 2.80 ENSDART00000140526
znf385b
zinc finger protein 385B
chr3_-_48716422 2.72 ENSDART00000164979
si:ch211-114m9.1
si:ch211-114m9.1
chr6_-_40029423 2.69 ENSDART00000103230
pfkfb4b
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4b
chr5_-_31901468 2.68 ENSDART00000147814
ENSDART00000141446
coro1cb
coronin, actin binding protein, 1Cb
chr17_-_16422654 2.64 ENSDART00000150149
tdp1
tyrosyl-DNA phosphodiesterase 1
chr22_-_13466246 2.56 ENSDART00000134035
cntnap5b
contactin associated protein-like 5b
chr9_+_24159725 2.53 ENSDART00000137756
hecw2a
HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2a
chr6_+_3004972 2.51 ENSDART00000186750
ENSDART00000183862
ENSDART00000191485
ENSDART00000171014
ptprfa
protein tyrosine phosphatase, receptor type, f, a
chr5_+_60590796 2.27 ENSDART00000159859
tmem132e
transmembrane protein 132E
chr2_+_2223837 2.12 ENSDART00000101038
ENSDART00000129354
tmie
transmembrane inner ear
chr16_+_2820340 2.11 ENSDART00000092299
ENSDART00000192931
ENSDART00000148512
si:dkey-288i20.2
si:dkey-288i20.2
chr15_-_22074315 1.81 ENSDART00000149830
drd2a
dopamine receptor D2a
chr24_-_38657683 1.72 ENSDART00000154843
si:ch1073-164k15.3
si:ch1073-164k15.3
chr17_-_40956035 1.62 ENSDART00000124715
si:dkey-16j16.4
si:dkey-16j16.4
chr10_-_5844915 1.60 ENSDART00000185929
ankrd55
ankyrin repeat domain 55
chr17_+_28533102 1.60 ENSDART00000156218
mdga2a
MAM domain containing glycosylphosphatidylinositol anchor 2a
chr24_+_17260001 1.55 ENSDART00000066765
bmi1a
bmi1 polycomb ring finger oncogene 1a
chr4_+_72723304 1.50 ENSDART00000186791
ENSDART00000158902
ENSDART00000191925
rab3ip
RAB3A interacting protein (rabin3)
chr10_-_11261565 1.46 ENSDART00000146727
ptbp3
polypyrimidine tract binding protein 3
chr21_+_25802190 1.38 ENSDART00000128987
nf2b
neurofibromin 2b (merlin)
chr18_+_46382484 1.34 ENSDART00000024202
ENSDART00000142790
daw1
dynein assembly factor with WDR repeat domains 1
chr15_+_9861973 1.34 ENSDART00000170945
si:dkey-13m3.2
si:dkey-13m3.2
chr1_+_10318089 1.30 ENSDART00000029774
pip4p1b
phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1b
chr1_+_51039558 1.23 ENSDART00000024743
dpy30
dpy-30 histone methyltransferase complex regulatory subunit
chr12_+_47122104 1.15 ENSDART00000184248
CABZ01088982.1

chr24_+_17260329 1.15 ENSDART00000129554
bmi1a
bmi1 polycomb ring finger oncogene 1a
chr3_-_26787430 1.07 ENSDART00000087047
rab40c
RAB40c, member RAS oncogene family
chr8_+_50953776 1.06 ENSDART00000013870
zgc:56596
zgc:56596
chr3_-_26806032 1.02 ENSDART00000143710
pigq
phosphatidylinositol glycan anchor biosynthesis, class Q
chr17_+_22577472 0.98 ENSDART00000045099
yipf4
Yip1 domain family, member 4
chr2_-_30668580 0.97 ENSDART00000087270
ctnnd2b
catenin (cadherin-associated protein), delta 2b
chr20_-_45812144 0.95 ENSDART00000147897
ENSDART00000147637
fermt1
fermitin family member 1
chr8_+_26007308 0.85 ENSDART00000191423
xpc
xeroderma pigmentosum, complementation group C
chr18_-_17485419 0.83 ENSDART00000018764
foxl1
forkhead box L1
chr17_-_200316 0.82 ENSDART00000190561
CABZ01083778.1

chr6_-_12912606 0.77 ENSDART00000164640
ical1
islet cell autoantigen 1-like
chr1_-_51038885 0.77 ENSDART00000035150
spast
spastin
chr22_-_8725768 0.75 ENSDART00000189873
ENSDART00000181819
si:ch73-27e22.1
si:ch73-27e22.8
si:ch73-27e22.1
si:ch73-27e22.8
chr15_+_47440477 0.68 ENSDART00000002384
phox2a
paired-like homeobox 2a
chr10_-_11261386 0.67 ENSDART00000189946
ptbp3
polypyrimidine tract binding protein 3
chr1_-_50438247 0.59 ENSDART00000114098
dkk2
dickkopf WNT signaling pathway inhibitor 2
chr7_+_7696665 0.56 ENSDART00000091099
ino80b
INO80 complex subunit B
chr19_+_32158010 0.48 ENSDART00000005255
mrpl53
mitochondrial ribosomal protein L53
chr22_-_19552796 0.44 ENSDART00000148088
ENSDART00000105485
si:dkey-78l4.14
si:dkey-78l4.14
chr8_-_30979494 0.43 ENSDART00000138959
si:ch211-251j10.3
si:ch211-251j10.3
chr20_+_52389858 0.41 ENSDART00000185863
ENSDART00000166651
arhgap39
Rho GTPase activating protein 39
chr1_-_669717 0.39 ENSDART00000160564
cyyr1
cysteine/tyrosine-rich 1
chr15_-_43284021 0.35 ENSDART00000041677
serpine2
serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2
chr7_-_38658411 0.32 ENSDART00000109463
ENSDART00000017155
npsn
nephrosin
chr23_-_16485190 0.31 ENSDART00000155038
si:dkeyp-100a5.4
si:dkeyp-100a5.4
chr24_-_40860603 0.26 ENSDART00000188032
CU633479.7

chr18_+_8320165 0.23 ENSDART00000092053
chkb
choline kinase beta
chr3_+_14259115 0.20 ENSDART00000154470
si:ch211-108d22.1
si:ch211-108d22.1
chr23_+_17878969 0.17 ENSDART00000154934
ENSDART00000154140
ENSDART00000156331
si:ch73-390p7.2
si:ch73-390p7.2
chr4_-_5795309 0.17 ENSDART00000039987
pgm3
phosphoglucomutase 3
chr19_+_14573998 0.17 ENSDART00000022076
fam46bb
family with sequence similarity 46, member Bb
chr24_+_21540842 0.14 ENSDART00000091529
wasf3b
WAS protein family, member 3b
chr19_+_46158078 0.11 ENSDART00000183933
ENSDART00000164055
cap2
CAP, adenylate cyclase-associated protein, 2 (yeast)
chr15_+_32798333 0.11 ENSDART00000162370
ENSDART00000166525
spartb
spartin b
chr21_-_25801956 0.05 ENSDART00000101219
mettl27
methyltransferase like 27
chr25_+_34915576 0.02 ENSDART00000073441
sntb2
syntrophin, beta 2

Network of associatons between targets according to the STRING database.

First level regulatory network of lmx1a

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
1.3 4.0 GO:0008292 acetylcholine biosynthetic process(GO:0008292) acetate ester biosynthetic process(GO:1900620)
1.2 10.7 GO:0051965 positive regulation of synapse assembly(GO:0051965)
1.1 8.8 GO:2000650 negative regulation of sodium ion transmembrane transporter activity(GO:2000650)
0.7 2.7 GO:0099563 modification of synaptic structure(GO:0099563)
0.5 1.6 GO:0021611 facial nerve formation(GO:0021611)
0.5 2.6 GO:0000012 single strand break repair(GO:0000012)
0.3 2.5 GO:0097374 sensory neuron axon guidance(GO:0097374)
0.3 0.8 GO:0034214 protein hexamerization(GO:0034214) mitotic spindle disassembly(GO:0051228) spindle disassembly(GO:0051230)
0.2 3.4 GO:0044154 histone H3-K14 acetylation(GO:0044154)
0.2 2.3 GO:0021631 optic nerve morphogenesis(GO:0021631)
0.2 3.8 GO:0086010 membrane depolarization during action potential(GO:0086010)
0.2 2.3 GO:0035677 posterior lateral line neuromast hair cell development(GO:0035677)
0.2 2.7 GO:0036353 histone H2A-K119 monoubiquitination(GO:0036353)
0.2 2.7 GO:0006003 fructose 2,6-bisphosphate metabolic process(GO:0006003)
0.2 4.7 GO:0006829 zinc II ion transport(GO:0006829)
0.1 6.6 GO:0014059 dopamine secretion(GO:0014046) regulation of dopamine secretion(GO:0014059)
0.1 1.2 GO:0006348 chromatin silencing at telomere(GO:0006348)
0.1 6.1 GO:0032922 circadian regulation of gene expression(GO:0032922)
0.1 2.1 GO:0060088 auditory receptor cell stereocilium organization(GO:0060088)
0.1 1.1 GO:0071816 tail-anchored membrane protein insertion into ER membrane(GO:0071816)
0.1 3.4 GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules(GO:0007157)
0.1 3.2 GO:0042149 cellular response to glucose starvation(GO:0042149)
0.1 2.8 GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator(GO:0072332)
0.1 1.3 GO:0060285 cilium or flagellum-dependent cell motility(GO:0001539) cilium-dependent cell motility(GO:0060285)
0.1 5.4 GO:0033339 pectoral fin development(GO:0033339)
0.1 0.7 GO:0021703 locus ceruleus development(GO:0021703)
0.1 1.6 GO:0003323 type B pancreatic cell development(GO:0003323)
0.0 1.0 GO:0060997 dendritic spine morphogenesis(GO:0060997)
0.0 0.9 GO:0006298 mismatch repair(GO:0006298)
0.0 1.0 GO:0006506 GPI anchor biosynthetic process(GO:0006506)
0.0 1.3 GO:0046856 phosphatidylinositol dephosphorylation(GO:0046856)
0.0 5.6 GO:0018105 peptidyl-serine phosphorylation(GO:0018105)
0.0 0.7 GO:0032402 melanosome transport(GO:0032402) pigment granule transport(GO:0051904)
0.0 4.0 GO:0030041 actin filament polymerization(GO:0030041)
0.0 0.2 GO:0006048 UDP-N-acetylglucosamine biosynthetic process(GO:0006048)
0.0 2.1 GO:0043484 regulation of RNA splicing(GO:0043484)
0.0 1.0 GO:0007229 integrin-mediated signaling pathway(GO:0007229)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 1.5 GO:0070319 Golgi to plasma membrane transport vesicle(GO:0070319)
0.3 4.7 GO:0030285 integral component of synaptic vesicle membrane(GO:0030285) intrinsic component of synaptic vesicle membrane(GO:0098563)
0.3 3.2 GO:0031588 nucleotide-activated protein kinase complex(GO:0031588)
0.2 3.4 GO:0070775 H3 histone acetyltransferase complex(GO:0070775) MOZ/MORF histone acetyltransferase complex(GO:0070776)
0.2 1.0 GO:0000506 glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex(GO:0000506)
0.2 3.8 GO:0034706 voltage-gated sodium channel complex(GO:0001518) sodium channel complex(GO:0034706)
0.2 1.1 GO:0071818 BAT3 complex(GO:0071818)
0.1 2.7 GO:0035102 PRC1 complex(GO:0035102)
0.1 0.9 GO:0000109 nucleotide-excision repair complex(GO:0000109)
0.1 1.2 GO:0048188 Set1C/COMPASS complex(GO:0048188)
0.0 2.7 GO:0044309 dendritic spine(GO:0043197) neuron spine(GO:0044309)
0.0 1.8 GO:0098978 glutamatergic synapse(GO:0098978)
0.0 10.7 GO:0045211 postsynaptic membrane(GO:0045211)
0.0 0.6 GO:0031011 Ino80 complex(GO:0031011) DNA helicase complex(GO:0033202)
0.0 3.8 GO:0005884 actin filament(GO:0005884)
0.0 5.9 GO:0070382 exocytic vesicle(GO:0070382)
0.0 1.0 GO:0014069 postsynaptic density(GO:0014069) postsynaptic specialization(GO:0099572)
0.0 1.6 GO:0031225 anchored component of membrane(GO:0031225)
0.0 1.3 GO:0031902 late endosome membrane(GO:0031902)
0.0 0.8 GO:0030496 midbody(GO:0030496)
0.0 9.5 GO:0043005 neuron projection(GO:0043005)
0.0 0.5 GO:0005762 organellar large ribosomal subunit(GO:0000315) mitochondrial large ribosomal subunit(GO:0005762)
0.0 3.5 GO:0005667 transcription factor complex(GO:0005667)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.9 2.6 GO:0070259 tyrosyl-DNA phosphodiesterase activity(GO:0070259)
0.5 3.8 GO:0008332 low voltage-gated calcium channel activity(GO:0008332)
0.3 4.0 GO:0016413 O-acetyltransferase activity(GO:0016413)
0.2 3.4 GO:0043994 H3 histone acetyltransferase activity(GO:0010484) histone acetyltransferase activity (H3-K23 specific)(GO:0043994)
0.2 2.7 GO:0003873 6-phosphofructo-2-kinase activity(GO:0003873)
0.2 0.8 GO:0048487 beta-tubulin binding(GO:0048487)
0.2 1.3 GO:0034597 phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity(GO:0034597)
0.1 1.0 GO:0017176 phosphatidylinositol N-acetylglucosaminyltransferase activity(GO:0017176)
0.1 1.8 GO:0001591 dopamine neurotransmitter receptor activity, coupled via Gi/Go(GO:0001591)
0.1 0.6 GO:0039706 co-receptor binding(GO:0039706)
0.1 5.6 GO:0004683 calmodulin-dependent protein kinase activity(GO:0004683)
0.1 3.2 GO:0016208 AMP binding(GO:0016208)
0.1 2.7 GO:1990841 promoter-specific chromatin binding(GO:1990841)
0.1 4.8 GO:0001786 phosphatidylserine binding(GO:0001786)
0.0 0.1 GO:0008179 adenylate cyclase binding(GO:0008179)
0.0 5.2 GO:0050839 cell adhesion molecule binding(GO:0050839)
0.0 0.9 GO:0003684 damaged DNA binding(GO:0003684)
0.0 8.8 GO:0061630 ubiquitin protein ligase activity(GO:0061630)
0.0 6.5 GO:0051015 actin filament binding(GO:0051015)
0.0 0.1 GO:0071933 Arp2/3 complex binding(GO:0071933)
0.0 5.2 GO:0003729 mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.0 0.2 GO:0016868 intramolecular transferase activity, phosphotransferases(GO:0016868)
0.0 4.8 GO:0005085 guanyl-nucleotide exchange factor activity(GO:0005085)
0.0 2.5 GO:0004725 protein tyrosine phosphatase activity(GO:0004725)
0.0 6.3 GO:0046983 protein dimerization activity(GO:0046983)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 2.8 PID MET PATHWAY Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met)
0.0 0.6 ST WNT BETA CATENIN PATHWAY Wnt/beta-catenin Pathway

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 2.6 REACTOME DOUBLE STRAND BREAK REPAIR Genes involved in Double-Strand Break Repair
0.1 2.8 REACTOME NRAGE SIGNALS DEATH THROUGH JNK Genes involved in NRAGE signals death through JNK
0.1 1.0 REACTOME SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI Genes involved in Synthesis of glycosylphosphatidylinositol (GPI)
0.0 0.9 REACTOME FORMATION OF INCISION COMPLEX IN GG NER Genes involved in Formation of incision complex in GG-NER
0.0 0.2 REACTOME SYNTHESIS OF PE Genes involved in Synthesis of PE
0.0 0.2 REACTOME SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS Genes involved in Synthesis of substrates in N-glycan biosythesis