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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for lmx1a

Z-value: 0.83

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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_33924236-0.931.4e-08Click!

Activity profile of lmx1a motif

Sorted Z-values of lmx1a motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr3_+_39853788 3.10 ENSDART00000154869
cacna1ha
calcium channel, voltage-dependent, T type, alpha 1H subunit a
chr8_+_43340995 3.00 ENSDART00000038566
rflna
refilin A
chr18_+_46382484 2.71 ENSDART00000024202
ENSDART00000142790
daw1
dynein assembly factor with WDR repeat domains 1
chr11_-_2838699 2.32 ENSDART00000066189
lhfpl5a
LHFPL tetraspan subfamily member 5a
chr24_-_26328721 2.30 ENSDART00000125468
apodb
apolipoprotein Db
chr11_-_25733910 2.03 ENSDART00000171935
brpf3a
bromodomain and PHD finger containing, 3a
chr22_-_24285432 1.96 ENSDART00000164083
si:ch211-117l17.4
si:ch211-117l17.4
chr25_-_16157776 1.93 ENSDART00000138453
si:dkey-80c24.5
si:dkey-80c24.5
chr18_-_17485419 1.84 ENSDART00000018764
foxl1
forkhead box L1
chr25_+_16189044 1.73 ENSDART00000143975
si:dkey-80c24.1
si:dkey-80c24.1
chr4_+_72723304 1.56 ENSDART00000186791
ENSDART00000158902
ENSDART00000191925
rab3ip
RAB3A interacting protein (rabin3)
chr16_-_28856112 1.42 ENSDART00000078543
syt11b
synaptotagmin XIb
chr7_-_58729894 1.39 ENSDART00000149347
chchd7
coiled-coil-helix-coiled-coil-helix domain containing 7
chr23_-_39666519 1.33 ENSDART00000110868
ENSDART00000190961
vwa1
von Willebrand factor A domain containing 1
chr16_-_12173554 1.31 ENSDART00000110567
ENSDART00000155935
clstn3
calsyntenin 3
chr24_-_38657683 1.29 ENSDART00000154843
si:ch1073-164k15.3
si:ch1073-164k15.3
chr12_+_25600685 1.26 ENSDART00000077157
six3b
SIX homeobox 3b
chr12_-_35830625 1.11 ENSDART00000180028
CU459056.1

chr16_-_12173399 1.08 ENSDART00000142574
clstn3
calsyntenin 3
chr10_-_5844915 1.08 ENSDART00000185929
ankrd55
ankyrin repeat domain 55
chr21_-_25801956 1.07 ENSDART00000101219
mettl27
methyltransferase like 27
chr5_-_30715225 1.04 ENSDART00000016758
ftr82
finTRIM family, member 82
chr15_+_9861973 1.03 ENSDART00000170945
si:dkey-13m3.2
si:dkey-13m3.2
chr25_+_34915576 1.02 ENSDART00000073441
sntb2
syntrophin, beta 2
chr1_-_669717 0.95 ENSDART00000160564
cyyr1
cysteine/tyrosine-rich 1
chr25_+_34915762 0.91 ENSDART00000191776
sntb2
syntrophin, beta 2
chr2_-_30668580 0.90 ENSDART00000087270
ctnnd2b
catenin (cadherin-associated protein), delta 2b
chr10_-_31015535 0.89 ENSDART00000146116
panx3
pannexin 3
chr7_+_7048245 0.81 ENSDART00000001649
actn3b
actinin alpha 3b
chr22_-_12160283 0.78 ENSDART00000146785
ENSDART00000128176
tmem163b
transmembrane protein 163b
chr20_-_9095105 0.74 ENSDART00000140792
oma1
OMA1 zinc metallopeptidase
chr6_+_9130989 0.72 ENSDART00000162588
rgn
regucalcin
chr12_-_6880694 0.72 ENSDART00000171846
pcdh15b
protocadherin-related 15b
chr20_-_45812144 0.66 ENSDART00000147897
ENSDART00000147637
fermt1
fermitin family member 1
chr14_+_44794936 0.66 ENSDART00000128881
zgc:195212
zgc:195212
chr4_+_57881965 0.64 ENSDART00000162234
si:dkeyp-44b5.4
si:dkeyp-44b5.4
chr23_-_16485190 0.64 ENSDART00000155038
si:dkeyp-100a5.4
si:dkeyp-100a5.4
chr7_-_38658411 0.60 ENSDART00000109463
ENSDART00000017155
npsn
nephrosin
chr15_-_22074315 0.59 ENSDART00000149830
drd2a
dopamine receptor D2a
chr9_-_9415000 0.57 ENSDART00000146210
si:ch211-214p13.9
si:ch211-214p13.9
chr2_+_42072231 0.54 ENSDART00000084517
vcpip1
valosin containing protein (p97)/p47 complex interacting protein 1
chr22_+_19552987 0.54 ENSDART00000105315
hsd11b1la
hydroxysteroid (11-beta) dehydrogenase 1-like a
chr9_+_34641237 0.53 ENSDART00000133996
shox
short stature homeobox
chr2_-_16217344 0.49 ENSDART00000152031
arhgef4
Rho guanine nucleotide exchange factor (GEF) 4
chr1_+_10318089 0.48 ENSDART00000029774
pip4p1b
phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1b
chr20_+_6035427 0.48 ENSDART00000054086
tshr
thyroid stimulating hormone receptor
chr2_+_38373272 0.45 ENSDART00000113111
psmb5
proteasome subunit beta 5
chr22_-_19552796 0.42 ENSDART00000148088
ENSDART00000105485
si:dkey-78l4.14
si:dkey-78l4.14
chr9_+_37152564 0.41 ENSDART00000189497
gli2a
GLI family zinc finger 2a
chr19_+_32158010 0.40 ENSDART00000005255
mrpl53
mitochondrial ribosomal protein L53
chr2_+_2223837 0.38 ENSDART00000101038
ENSDART00000129354
tmie
transmembrane inner ear
chr9_+_42063906 0.37 ENSDART00000048893
pcbp3
poly(rC) binding protein 3
chr10_-_11261565 0.37 ENSDART00000146727
ptbp3
polypyrimidine tract binding protein 3
chr6_-_43677125 0.36 ENSDART00000150128
foxp1b
forkhead box P1b
chr5_-_21422390 0.35 ENSDART00000144198
tenm1
teneurin transmembrane protein 1
chr24_-_40860603 0.35 ENSDART00000188032
CU633479.7

chr19_+_14573998 0.35 ENSDART00000022076
fam46bb
family with sequence similarity 46, member Bb
chr4_+_77943184 0.30 ENSDART00000159094
pacsin2
protein kinase C and casein kinase substrate in neurons 2
chr10_-_11261386 0.29 ENSDART00000189946
ptbp3
polypyrimidine tract binding protein 3
chr3_-_48716422 0.28 ENSDART00000164979
si:ch211-114m9.1
si:ch211-114m9.1
chr6_+_3004972 0.28 ENSDART00000186750
ENSDART00000183862
ENSDART00000191485
ENSDART00000171014
ptprfa
protein tyrosine phosphatase, receptor type, f, a
chr20_+_52389858 0.24 ENSDART00000185863
ENSDART00000166651
arhgap39
Rho GTPase activating protein 39
chr23_+_17878969 0.24 ENSDART00000154934
ENSDART00000154140
ENSDART00000156331
si:ch73-390p7.2
si:ch73-390p7.2
chr16_+_23303859 0.23 ENSDART00000006093
slc50a1
solute carrier family 50 (sugar efflux transporter), member 1
chr8_-_14484599 0.22 ENSDART00000057644
lhx4
LIM homeobox 4
chr15_+_47440477 0.22 ENSDART00000002384
phox2a
paired-like homeobox 2a
chr4_+_45484774 0.21 ENSDART00000150573
si:dkey-256i11.6
si:dkey-256i11.6
chr19_+_5480327 0.19 ENSDART00000148794
jupb
junction plakoglobin b
chr16_-_46567344 0.18 ENSDART00000127721
si:dkey-152b24.7
si:dkey-152b24.7
chr18_+_2228737 0.18 ENSDART00000165301
rab27a
RAB27A, member RAS oncogene family
chr3_-_24093144 0.18 ENSDART00000103982
nfe2l1a
nuclear factor, erythroid 2-like 1a
chr1_+_6172786 0.18 ENSDART00000126468
prkag3a
protein kinase, AMP-activated, gamma 3a non-catalytic subunit
chr15_+_32798333 0.18 ENSDART00000162370
ENSDART00000166525
spartb
spartin b
chr10_+_16584382 0.16 ENSDART00000112039
CR790388.1

chr21_+_25802190 0.14 ENSDART00000128987
nf2b
neurofibromin 2b (merlin)
chr22_-_8725768 0.10 ENSDART00000189873
ENSDART00000181819
si:ch73-27e22.1
si:ch73-27e22.8
si:ch73-27e22.1
si:ch73-27e22.8
chr22_-_13466246 0.10 ENSDART00000134035
cntnap5b
contactin associated protein-like 5b
chr17_-_23616626 0.09 ENSDART00000104730
ifit14
interferon-induced protein with tetratricopeptide repeats 14
chr2_+_36701322 0.09 ENSDART00000002510
golim4b
golgi integral membrane protein 4b
chr5_-_31901468 0.07 ENSDART00000147814
ENSDART00000141446
coro1cb
coronin, actin binding protein, 1Cb
chr24_+_21540842 0.06 ENSDART00000091529
wasf3b
WAS protein family, member 3b
chr8_-_30979494 0.05 ENSDART00000138959
si:ch211-251j10.3
si:ch211-251j10.3
chr20_-_46128590 0.05 ENSDART00000123744
taar1b
trace amine associated receptor 1b
chr14_-_451555 0.04 ENSDART00000190906
FAT4
FAT atypical cadherin 4
chr13_+_10945337 0.03 ENSDART00000091845
abcg5
ATP-binding cassette, sub-family G (WHITE), member 5
chr8_-_12867434 0.03 ENSDART00000081657
slc2a6
solute carrier family 2 (facilitated glucose transporter), member 6
chr16_-_16761164 0.03 ENSDART00000135872
si:dkey-27n14.1
si:dkey-27n14.1
chr12_+_47122104 0.03 ENSDART00000184248
CABZ01088982.1

chr24_+_17260001 0.02 ENSDART00000066765
bmi1a
bmi1 polycomb ring finger oncogene 1a
chr16_+_2820340 0.01 ENSDART00000092299
ENSDART00000192931
ENSDART00000148512
si:dkey-288i20.2
si:dkey-288i20.2
chr1_-_50438247 0.01 ENSDART00000114098
dkk2
dickkopf WNT signaling pathway inhibitor 2
chr1_+_51039558 0.01 ENSDART00000024743
dpy30
dpy-30 histone methyltransferase complex regulatory subunit
chr9_-_38398789 0.01 ENSDART00000188384
znf142
zinc finger protein 142
chr5_-_23843636 0.00 ENSDART00000193280
GBGT1 (1 of many)
si:ch211-135f11.5
chr7_+_21272833 0.00 ENSDART00000052942
serpinh2
serine (or cysteine) peptidase inhibitor, clade H, member 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
1.0 3.0 GO:0032331 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)
0.3 2.4 GO:0051965 positive regulation of synapse assembly(GO:0051965)
0.2 0.7 GO:0019852 L-ascorbic acid metabolic process(GO:0019852) water-soluble vitamin biosynthetic process(GO:0042364)
0.2 3.1 GO:0086010 membrane depolarization during action potential(GO:0086010)
0.2 1.7 GO:0021631 optic nerve morphogenesis(GO:0021631)
0.1 2.0 GO:0044154 histone H3-K14 acetylation(GO:0044154)
0.1 2.7 GO:0001539 cilium or flagellum-dependent cell motility(GO:0001539) cilium-dependent cell motility(GO:0060285)
0.1 0.5 GO:0048313 organelle inheritance(GO:0048308) Golgi inheritance(GO:0048313)
0.1 0.9 GO:0032732 positive regulation of interleukin-1 production(GO:0032732)
0.1 0.7 GO:1990845 adaptive thermogenesis(GO:1990845)
0.1 0.7 GO:0042138 meiotic DNA double-strand break formation(GO:0042138)
0.1 2.7 GO:0060122 inner ear receptor stereocilium organization(GO:0060122)
0.1 2.3 GO:0007568 aging(GO:0007568)
0.1 0.3 GO:0099563 modification of synaptic structure(GO:0099563)
0.1 0.7 GO:0050908 detection of light stimulus involved in visual perception(GO:0050908) detection of light stimulus involved in sensory perception(GO:0050962)
0.0 1.7 GO:0051904 melanosome transport(GO:0032402) pigment granule transport(GO:0051904)
0.0 2.0 GO:0014059 dopamine secretion(GO:0014046) regulation of dopamine secretion(GO:0014059)
0.0 1.8 GO:0035138 pectoral fin morphogenesis(GO:0035138)
0.0 1.1 GO:0003323 type B pancreatic cell development(GO:0003323)
0.0 0.2 GO:0002159 desmosome assembly(GO:0002159)
0.0 0.5 GO:0007190 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 0.3 GO:0097374 sensory neuron axon guidance(GO:0097374)
0.0 0.9 GO:0060997 dendritic spine morphogenesis(GO:0060997)
0.0 0.1 GO:0070589 cell wall biogenesis(GO:0042546) cell wall macromolecule biosynthetic process(GO:0044038) cellular component macromolecule biosynthetic process(GO:0070589)
0.0 0.3 GO:0070836 membrane raft assembly(GO:0001765) plasma membrane raft assembly(GO:0044854) plasma membrane raft organization(GO:0044857) caveola assembly(GO:0070836)
0.0 0.8 GO:0006829 zinc II ion transport(GO:0006829)
0.0 0.6 GO:0030183 B cell differentiation(GO:0030183)
0.0 0.2 GO:0060573 ventral spinal cord interneuron specification(GO:0021521) cell fate specification involved in pattern specification(GO:0060573)
0.0 0.2 GO:0021703 locus ceruleus development(GO:0021703)
0.0 0.5 GO:0010499 proteasomal ubiquitin-independent protein catabolic process(GO:0010499)
0.0 0.5 GO:0033339 pectoral fin development(GO:0033339)
0.0 0.4 GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules(GO:0007157)
0.0 3.7 GO:0046777 protein autophosphorylation(GO:0046777)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 1.6 GO:0070319 Golgi to plasma membrane transport vesicle(GO:0070319)
0.1 0.6 GO:0019815 B cell receptor complex(GO:0019815)
0.1 3.1 GO:0001518 voltage-gated sodium channel complex(GO:0001518) sodium channel complex(GO:0034706)
0.1 2.0 GO:0070775 H3 histone acetyltransferase complex(GO:0070775) MOZ/MORF histone acetyltransferase complex(GO:0070776)
0.1 1.9 GO:0016010 dystrophin-associated glycoprotein complex(GO:0016010) glycoprotein complex(GO:0090665)
0.1 0.8 GO:0030285 integral component of synaptic vesicle membrane(GO:0030285) intrinsic component of synaptic vesicle membrane(GO:0098563)
0.0 3.0 GO:0032432 actin filament bundle(GO:0032432)
0.0 0.9 GO:0005921 gap junction(GO:0005921)
0.0 0.7 GO:0032420 stereocilium(GO:0032420)
0.0 0.5 GO:0005839 proteasome core complex(GO:0005839)
0.0 0.2 GO:0031588 nucleotide-activated protein kinase complex(GO:0031588)
0.0 0.6 GO:0098978 glutamatergic synapse(GO:0098978)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.7 3.0 GO:0031005 filamin binding(GO:0031005)
0.4 3.1 GO:0008332 low voltage-gated calcium channel activity(GO:0008332)
0.1 2.0 GO:0010484 H3 histone acetyltransferase activity(GO:0010484) histone acetyltransferase activity (H3-K23 specific)(GO:0043994)
0.1 0.5 GO:0034597 phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity(GO:0034597)
0.0 0.6 GO:0001591 dopamine neurotransmitter receptor activity, coupled via Gi/Go(GO:0001591)
0.0 0.5 GO:0016500 protein-hormone receptor activity(GO:0016500)
0.0 0.9 GO:0022829 wide pore channel activity(GO:0022829)
0.0 1.4 GO:0001786 phosphatidylserine binding(GO:0001786)
0.0 0.5 GO:0004298 threonine-type endopeptidase activity(GO:0004298) threonine-type peptidase activity(GO:0070003)
0.0 0.2 GO:0045294 alpha-catenin binding(GO:0045294)
0.0 0.5 GO:0016229 steroid dehydrogenase activity(GO:0016229)
0.0 0.7 GO:0005178 integrin binding(GO:0005178)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.5 PID ARF6 PATHWAY Arf6 signaling events

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.5 REACTOME HORMONE LIGAND BINDING RECEPTORS Genes involved in Hormone ligand-binding receptors
0.0 0.5 REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES Genes involved in Cross-presentation of soluble exogenous antigens (endosomes)
0.0 0.5 REACTOME NRAGE SIGNALS DEATH THROUGH JNK Genes involved in NRAGE signals death through JNK