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PRJNA195909:zebrafish embryo and larva development

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Results for lmx1a

Z-value: 0.73

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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_+_33922339_33922339-0.872.0e-03Click!

Activity profile of lmx1a motif

Sorted Z-values of lmx1a motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr24_-_26328721 1.59 ENSDART00000125468
apodb
apolipoprotein Db
chr12_+_25600685 1.48 ENSDART00000077157
six3b
SIX homeobox 3b
chr24_+_24461558 1.16 ENSDART00000182424
bhlhe22
basic helix-loop-helix family, member e22
chr16_-_16152199 1.13 ENSDART00000012718
fabp11b
fatty acid binding protein 11b
chr24_+_24461341 1.13 ENSDART00000147658
bhlhe22
basic helix-loop-helix family, member e22
chr7_+_7048245 1.08 ENSDART00000001649
actn3b
actinin alpha 3b
chr9_+_34641237 1.02 ENSDART00000133996
shox
short stature homeobox
chr16_-_28856112 0.99 ENSDART00000078543
syt11b
synaptotagmin XIb
chr12_-_35830625 0.99 ENSDART00000180028
CU459056.1

chr6_+_9130989 0.96 ENSDART00000162588
rgn
regucalcin
chr2_-_30668580 0.96 ENSDART00000087270
ctnnd2b
catenin (cadherin-associated protein), delta 2b
chr22_-_24285432 0.89 ENSDART00000164083
si:ch211-117l17.4
si:ch211-117l17.4
chr2_+_2223837 0.86 ENSDART00000101038
ENSDART00000129354
tmie
transmembrane inner ear
chr7_-_58729894 0.86 ENSDART00000149347
chchd7
coiled-coil-helix-coiled-coil-helix domain containing 7
chr8_-_14484599 0.85 ENSDART00000057644
lhx4
LIM homeobox 4
chr24_-_38657683 0.85 ENSDART00000154843
si:ch1073-164k15.3
si:ch1073-164k15.3
chr18_+_46382484 0.82 ENSDART00000024202
ENSDART00000142790
daw1
dynein assembly factor with WDR repeat domains 1
chr16_-_12173554 0.81 ENSDART00000110567
ENSDART00000155935
clstn3
calsyntenin 3
chr1_-_669717 0.76 ENSDART00000160564
cyyr1
cysteine/tyrosine-rich 1
chr7_-_38658411 0.75 ENSDART00000109463
ENSDART00000017155
npsn
nephrosin
chr4_+_72723304 0.74 ENSDART00000186791
ENSDART00000158902
ENSDART00000191925
rab3ip
RAB3A interacting protein (rabin3)
chr20_-_45812144 0.73 ENSDART00000147897
ENSDART00000147637
fermt1
fermitin family member 1
chr12_+_47122104 0.70 ENSDART00000184248
CABZ01088982.1

chr15_-_22074315 0.70 ENSDART00000149830
drd2a
dopamine receptor D2a
chr5_-_31901468 0.70 ENSDART00000147814
ENSDART00000141446
coro1cb
coronin, actin binding protein, 1Cb
chr15_+_9861973 0.69 ENSDART00000170945
si:dkey-13m3.2
si:dkey-13m3.2
chr15_+_47440477 0.67 ENSDART00000002384
phox2a
paired-like homeobox 2a
chr23_-_39666519 0.65 ENSDART00000110868
ENSDART00000190961
vwa1
von Willebrand factor A domain containing 1
chr8_-_12867434 0.60 ENSDART00000081657
slc2a6
solute carrier family 2 (facilitated glucose transporter), member 6
chr19_+_14573998 0.60 ENSDART00000022076
fam46bb
family with sequence similarity 46, member Bb
chr9_+_37152564 0.58 ENSDART00000189497
gli2a
GLI family zinc finger 2a
chr22_-_12160283 0.57 ENSDART00000146785
ENSDART00000128176
tmem163b
transmembrane protein 163b
chr1_+_6172786 0.57 ENSDART00000126468
prkag3a
protein kinase, AMP-activated, gamma 3a non-catalytic subunit
chr3_+_50312422 0.53 ENSDART00000157689
gas7a
growth arrest-specific 7a
chr24_-_40860603 0.52 ENSDART00000188032
CU633479.7

chr16_-_12173399 0.49 ENSDART00000142574
clstn3
calsyntenin 3
chr3_+_14259115 0.49 ENSDART00000154470
si:ch211-108d22.1
si:ch211-108d22.1
chr8_+_43340995 0.48 ENSDART00000038566
rflna
refilin A
chr14_-_451555 0.45 ENSDART00000190906
FAT4
FAT atypical cadherin 4
chr2_+_36701322 0.42 ENSDART00000002510
golim4b
golgi integral membrane protein 4b
chr24_+_21540842 0.42 ENSDART00000091529
wasf3b
WAS protein family, member 3b
chr22_-_19552796 0.38 ENSDART00000148088
ENSDART00000105485
si:dkey-78l4.14
si:dkey-78l4.14
chr20_+_52389858 0.37 ENSDART00000185863
ENSDART00000166651
arhgap39
Rho GTPase activating protein 39
chr19_+_32158010 0.35 ENSDART00000005255
mrpl53
mitochondrial ribosomal protein L53
chr9_+_24159280 0.35 ENSDART00000184624
ENSDART00000178422
hecw2a
HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2a
chr13_-_29421331 0.33 ENSDART00000150228
chata
choline O-acetyltransferase a
chr4_+_57881965 0.32 ENSDART00000162234
si:dkeyp-44b5.4
si:dkeyp-44b5.4
chr6_+_3004972 0.29 ENSDART00000186750
ENSDART00000183862
ENSDART00000191485
ENSDART00000171014
ptprfa
protein tyrosine phosphatase, receptor type, f, a
chr23_-_16485190 0.29 ENSDART00000155038
si:dkeyp-100a5.4
si:dkeyp-100a5.4
chr18_-_17485419 0.27 ENSDART00000018764
foxl1
forkhead box L1
chr8_-_12867128 0.26 ENSDART00000142201
slc2a6
solute carrier family 2 (facilitated glucose transporter), member 6
chr5_-_30715225 0.22 ENSDART00000016758
ftr82
finTRIM family, member 82
chr10_+_16584382 0.22 ENSDART00000112039
CR790388.1

chr17_-_23616626 0.19 ENSDART00000104730
ifit14
interferon-induced protein with tetratricopeptide repeats 14
chr22_-_8725768 0.19 ENSDART00000189873
ENSDART00000181819
si:ch73-27e22.1
si:ch73-27e22.8
si:ch73-27e22.1
si:ch73-27e22.8
chr8_-_30979494 0.18 ENSDART00000138959
si:ch211-251j10.3
si:ch211-251j10.3
chr4_+_45484774 0.18 ENSDART00000150573
si:dkey-256i11.6
si:dkey-256i11.6
chr11_-_2838699 0.18 ENSDART00000066189
lhfpl5a
LHFPL tetraspan subfamily member 5a
chr21_+_25802190 0.17 ENSDART00000128987
nf2b
neurofibromin 2b (merlin)
chr2_-_16217344 0.16 ENSDART00000152031
arhgef4
Rho guanine nucleotide exchange factor (GEF) 4
chr1_+_51039558 0.16 ENSDART00000024743
dpy30
dpy-30 histone methyltransferase complex regulatory subunit
chr17_-_45040813 0.16 ENSDART00000075514
entpd5a
ectonucleoside triphosphate diphosphohydrolase 5a
chr25_+_16189044 0.15 ENSDART00000143975
si:dkey-80c24.1
si:dkey-80c24.1
chr20_+_6035427 0.15 ENSDART00000054086
tshr
thyroid stimulating hormone receptor
chr25_-_16157776 0.12 ENSDART00000138453
si:dkey-80c24.5
si:dkey-80c24.5
chr9_+_24159725 0.12 ENSDART00000137756
hecw2a
HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2a
chr10_-_5844915 0.12 ENSDART00000185929
ankrd55
ankyrin repeat domain 55
chr23_+_17878969 0.12 ENSDART00000154934
ENSDART00000154140
ENSDART00000156331
si:ch73-390p7.2
si:ch73-390p7.2
chr20_-_9095105 0.10 ENSDART00000140792
oma1
OMA1 zinc metallopeptidase
chr22_+_19552987 0.09 ENSDART00000105315
hsd11b1la
hydroxysteroid (11-beta) dehydrogenase 1-like a
chr2_+_38373272 0.07 ENSDART00000113111
psmb5
proteasome subunit beta 5
chr3_-_24093144 0.05 ENSDART00000103982
nfe2l1a
nuclear factor, erythroid 2-like 1a
chr19_+_46158078 0.04 ENSDART00000183933
ENSDART00000164055
cap2
CAP, adenylate cyclase-associated protein, 2 (yeast)
chr1_-_50438247 0.03 ENSDART00000114098
dkk2
dickkopf WNT signaling pathway inhibitor 2
chr17_+_30369396 0.03 ENSDART00000076611
greb1
growth regulation by estrogen in breast cancer 1

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
0.3 1.0 GO:0042364 L-ascorbic acid metabolic process(GO:0019852) water-soluble vitamin biosynthetic process(GO:0042364)
0.2 2.1 GO:0021631 optic nerve morphogenesis(GO:0021631)
0.2 0.5 GO:1900157 negative regulation of chondrocyte differentiation(GO:0032331) negative regulation of cartilage development(GO:0061037) negative regulation of chondrocyte development(GO:0061182) regulation of bone mineralization involved in bone maturation(GO:1900157) negative regulation of bone mineralization involved in bone maturation(GO:1900158) negative regulation of bone development(GO:1903011)
0.1 1.3 GO:0051965 positive regulation of synapse assembly(GO:0051965)
0.1 0.3 GO:1900620 acetylcholine biosynthetic process(GO:0008292) acetate ester biosynthetic process(GO:1900620)
0.1 0.9 GO:0021521 ventral spinal cord interneuron specification(GO:0021521) cell fate specification involved in pattern specification(GO:0060573)
0.1 0.2 GO:0070589 cell wall biogenesis(GO:0042546) cell wall macromolecule biosynthetic process(GO:0044038) cellular component macromolecule biosynthetic process(GO:0070589)
0.1 0.7 GO:0021703 locus ceruleus development(GO:0021703)
0.1 0.5 GO:2000650 negative regulation of sodium ion transmembrane transporter activity(GO:2000650)
0.0 0.7 GO:0051481 negative regulation of cytosolic calcium ion concentration(GO:0051481) negative regulation of synaptic transmission, glutamatergic(GO:0051967)
0.0 1.6 GO:0007568 aging(GO:0007568)
0.0 0.9 GO:0060088 auditory receptor cell stereocilium organization(GO:0060088)
0.0 0.8 GO:0001539 cilium or flagellum-dependent cell motility(GO:0001539) cilium-dependent cell motility(GO:0060285)
0.0 0.3 GO:0097374 sensory neuron axon guidance(GO:0097374)
0.0 1.0 GO:0014059 dopamine secretion(GO:0014046) regulation of dopamine secretion(GO:0014059)
0.0 0.4 GO:0051127 positive regulation of actin nucleation(GO:0051127) positive regulation of Arp2/3 complex-mediated actin nucleation(GO:2000601)
0.0 1.2 GO:0030282 bone mineralization(GO:0030282)
0.0 0.6 GO:0060997 dendritic spine morphogenesis(GO:0060997)
0.0 0.6 GO:0006829 zinc II ion transport(GO:0006829)
0.0 0.2 GO:0006348 chromatin silencing at telomere(GO:0006348)
0.0 0.6 GO:0042149 cellular response to glucose starvation(GO:0042149)
0.0 0.5 GO:0051904 melanosome transport(GO:0032402) pigment granule transport(GO:0051904)
0.0 0.1 GO:1990845 adaptive thermogenesis(GO:1990845)
0.0 0.1 GO:0030816 activation of adenylate cyclase activity(GO:0007190) positive regulation of cAMP metabolic process(GO:0030816) positive regulation of cAMP biosynthetic process(GO:0030819) positive regulation of adenylate cyclase activity(GO:0045762)
0.0 0.2 GO:0060122 inner ear receptor stereocilium organization(GO:0060122)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 0.7 GO:0070319 Golgi to plasma membrane transport vesicle(GO:0070319)
0.0 0.6 GO:0031588 nucleotide-activated protein kinase complex(GO:0031588)
0.0 0.6 GO:0030285 integral component of synaptic vesicle membrane(GO:0030285) intrinsic component of synaptic vesicle membrane(GO:0098563)
0.0 0.4 GO:0031209 SCAR complex(GO:0031209)
0.0 0.7 GO:0098978 glutamatergic synapse(GO:0098978)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.9 GO:0055056 D-glucose transmembrane transporter activity(GO:0055056)
0.1 0.5 GO:0031005 filamin binding(GO:0031005)
0.0 0.7 GO:0001591 dopamine neurotransmitter receptor activity, coupled via Gi/Go(GO:0001591)
0.0 0.4 GO:0071933 Arp2/3 complex binding(GO:0071933)
0.0 0.3 GO:0016413 O-acetyltransferase activity(GO:0016413)
0.0 1.0 GO:0001786 phosphatidylserine binding(GO:0001786)
0.0 0.6 GO:0016208 AMP binding(GO:0016208)
0.0 0.7 GO:0005178 integrin binding(GO:0005178)
0.0 0.0 GO:0008179 adenylate cyclase binding(GO:0008179)
0.0 0.1 GO:0016500 protein-hormone receptor activity(GO:0016500)

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.9 REACTOME FACILITATIVE NA INDEPENDENT GLUCOSE TRANSPORTERS Genes involved in Facilitative Na+-independent glucose transporters
0.0 0.1 REACTOME HORMONE LIGAND BINDING RECEPTORS Genes involved in Hormone ligand-binding receptors