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PRJEB1986: zebrafish developmental stages transcriptome

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Results for lmx1a

Z-value: 0.46

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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_33924236-0.371.2e-01Click!

Activity profile of lmx1a motif

Sorted Z-values of lmx1a motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr17_-_16422654 0.74 ENSDART00000150149
tdp1
tyrosyl-DNA phosphodiesterase 1
chr3_-_26787430 0.54 ENSDART00000087047
rab40c
RAB40c, member RAS oncogene family
chr15_+_47440477 0.48 ENSDART00000002384
phox2a
paired-like homeobox 2a
chr13_+_11440389 0.47 ENSDART00000186463
zbtb18
zinc finger and BTB domain containing 18
chr15_+_9861973 0.42 ENSDART00000170945
si:dkey-13m3.2
si:dkey-13m3.2
chr6_-_12912606 0.41 ENSDART00000164640
ical1
islet cell autoantigen 1-like
chr22_-_14247276 0.41 ENSDART00000033332
si:ch211-246m6.5
si:ch211-246m6.5
chr2_-_30668580 0.40 ENSDART00000087270
ctnnd2b
catenin (cadherin-associated protein), delta 2b
chr17_+_20589553 0.38 ENSDART00000154447
si:ch73-288o11.4
si:ch73-288o11.4
chr24_-_38657683 0.37 ENSDART00000154843
si:ch1073-164k15.3
si:ch1073-164k15.3
chr2_+_36701322 0.37 ENSDART00000002510
golim4b
golgi integral membrane protein 4b
chr2_-_38363017 0.37 ENSDART00000088026
prmt5
protein arginine methyltransferase 5
chr12_+_25600685 0.37 ENSDART00000077157
six3b
SIX homeobox 3b
chr5_-_31901468 0.35 ENSDART00000147814
ENSDART00000141446
coro1cb
coronin, actin binding protein, 1Cb
chr4_-_5795309 0.33 ENSDART00000039987
pgm3
phosphoglucomutase 3
chr24_+_24461558 0.33 ENSDART00000182424
bhlhe22
basic helix-loop-helix family, member e22
chr5_+_60590796 0.32 ENSDART00000159859
tmem132e
transmembrane protein 132E
chr5_-_30715225 0.31 ENSDART00000016758
ftr82
finTRIM family, member 82
chr24_+_24461341 0.31 ENSDART00000147658
bhlhe22
basic helix-loop-helix family, member e22
chr9_-_27398369 0.29 ENSDART00000186499
tex30
testis expressed 30
chr7_-_61279523 0.29 ENSDART00000098610
rell1
RELT like 1
chr23_+_20640484 0.29 ENSDART00000054691
uba1
ubiquitin-like modifier activating enzyme 1
chr2_+_38373272 0.28 ENSDART00000113111
psmb5
proteasome subunit beta 5
chr20_-_45812144 0.28 ENSDART00000147897
ENSDART00000147637
fermt1
fermitin family member 1
chr7_-_38658411 0.28 ENSDART00000109463
ENSDART00000017155
npsn
nephrosin
chr18_+_46382484 0.28 ENSDART00000024202
ENSDART00000142790
daw1
dynein assembly factor with WDR repeat domains 1
chr1_-_669717 0.28 ENSDART00000160564
cyyr1
cysteine/tyrosine-rich 1
chr20_-_9095105 0.28 ENSDART00000140792
oma1
OMA1 zinc metallopeptidase
chr7_+_53879191 0.28 ENSDART00000164768
neo1a
neogenin 1a
chr24_+_17260001 0.27 ENSDART00000066765
bmi1a
bmi1 polycomb ring finger oncogene 1a
chr1_+_6172786 0.27 ENSDART00000126468
prkag3a
protein kinase, AMP-activated, gamma 3a non-catalytic subunit
chr12_-_35830625 0.25 ENSDART00000180028
CU459056.1

chr25_+_34915576 0.25 ENSDART00000073441
sntb2
syntrophin, beta 2
chr4_+_57881965 0.25 ENSDART00000162234
si:dkeyp-44b5.4
si:dkeyp-44b5.4
chr1_-_51038885 0.25 ENSDART00000035150
spast
spastin
chr6_-_40029423 0.25 ENSDART00000103230
pfkfb4b
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4b
chr9_+_37152564 0.24 ENSDART00000189497
gli2a
GLI family zinc finger 2a
chr24_+_17260329 0.23 ENSDART00000129554
bmi1a
bmi1 polycomb ring finger oncogene 1a
chr17_+_30369396 0.22 ENSDART00000076611
greb1
growth regulation by estrogen in breast cancer 1
chr21_+_42717424 0.21 ENSDART00000166936
ENSDART00000172135
sh3pxd2b
SH3 and PX domains 2B
chr16_-_16152199 0.21 ENSDART00000012718
fabp11b
fatty acid binding protein 11b
chr4_+_77943184 0.21 ENSDART00000159094
pacsin2
protein kinase C and casein kinase substrate in neurons 2
chr8_-_14484599 0.20 ENSDART00000057644
lhx4
LIM homeobox 4
chr7_+_21272833 0.20 ENSDART00000052942
serpinh2
serine (or cysteine) peptidase inhibitor, clade H, member 2
chr3_-_26806032 0.20 ENSDART00000143710
pigq
phosphatidylinositol glycan anchor biosynthesis, class Q
chr21_+_25802190 0.19 ENSDART00000128987
nf2b
neurofibromin 2b (merlin)
chr2_-_16217344 0.18 ENSDART00000152031
arhgef4
Rho guanine nucleotide exchange factor (GEF) 4
chr14_+_44794936 0.18 ENSDART00000128881
zgc:195212
zgc:195212
chr1_+_35985813 0.17 ENSDART00000179634
ENSDART00000139636
ENSDART00000175902
zgc:152968
zgc:152968
chr3_+_14259115 0.17 ENSDART00000154470
si:ch211-108d22.1
si:ch211-108d22.1
chr22_-_24285432 0.17 ENSDART00000164083
si:ch211-117l17.4
si:ch211-117l17.4
chr23_-_18567088 0.17 ENSDART00000192371
sephs2
selenophosphate synthetase 2
chr18_+_8320165 0.17 ENSDART00000092053
chkb
choline kinase beta
chr8_+_50953776 0.16 ENSDART00000013870
zgc:56596
zgc:56596
chr2_+_2223837 0.16 ENSDART00000101038
ENSDART00000129354
tmie
transmembrane inner ear
chr15_+_32798333 0.16 ENSDART00000162370
ENSDART00000166525
spartb
spartin b
chr24_+_21540842 0.16 ENSDART00000091529
wasf3b
WAS protein family, member 3b
chr16_-_46567344 0.15 ENSDART00000127721
si:dkey-152b24.7
si:dkey-152b24.7
chr20_+_6035427 0.15 ENSDART00000054086
tshr
thyroid stimulating hormone receptor
chr10_-_5844915 0.15 ENSDART00000185929
ankrd55
ankyrin repeat domain 55
chr17_+_22577472 0.14 ENSDART00000045099
yipf4
Yip1 domain family, member 4
chr7_+_7696665 0.13 ENSDART00000091099
ino80b
INO80 complex subunit B
chr8_+_43340995 0.13 ENSDART00000038566
rflna
refilin A
chr9_-_38398789 0.13 ENSDART00000188384
znf142
zinc finger protein 142
chr15_-_43284021 0.12 ENSDART00000041677
serpine2
serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2
chr4_+_25692277 0.12 ENSDART00000047113
acot18
acyl-CoA thioesterase 18
chr4_+_72723304 0.12 ENSDART00000186791
ENSDART00000158902
ENSDART00000191925
rab3ip
RAB3A interacting protein (rabin3)
chr21_-_25801956 0.11 ENSDART00000101219
mettl27
methyltransferase like 27
chr18_-_17485419 0.11 ENSDART00000018764
foxl1
forkhead box L1
chr24_-_40860603 0.10 ENSDART00000188032
CU633479.7

chr4_+_45484774 0.10 ENSDART00000150573
si:dkey-256i11.6
si:dkey-256i11.6
chr23_-_16485190 0.09 ENSDART00000155038
si:dkeyp-100a5.4
si:dkeyp-100a5.4
chr4_-_64336270 0.09 ENSDART00000131672
znf1147
zinc finger protein 1147
chr25_+_34915762 0.08 ENSDART00000191776
sntb2
syntrophin, beta 2
chr8_+_26007308 0.08 ENSDART00000191423
xpc
xeroderma pigmentosum, complementation group C
chr10_-_11261386 0.07 ENSDART00000189946
ptbp3
polypyrimidine tract binding protein 3
chr22_-_17653143 0.07 ENSDART00000089171
hmha1b
histocompatibility (minor) HA-1 b
chr19_-_14970813 0.06 ENSDART00000184312
CR394532.2

chr16_+_23303859 0.06 ENSDART00000006093
slc50a1
solute carrier family 50 (sugar efflux transporter), member 1
chr22_-_17652914 0.06 ENSDART00000138483
si:ch73-243b8.4
si:ch73-243b8.4
chr25_-_16157776 0.05 ENSDART00000138453
si:dkey-80c24.5
si:dkey-80c24.5
chr25_+_16189044 0.05 ENSDART00000143975
si:dkey-80c24.1
si:dkey-80c24.1
chr22_-_19552796 0.05 ENSDART00000148088
ENSDART00000105485
si:dkey-78l4.14
si:dkey-78l4.14
chr8_-_53044300 0.05 ENSDART00000191653
nr6a1a
nuclear receptor subfamily 6, group A, member 1a
chr16_-_28856112 0.05 ENSDART00000078543
syt11b
synaptotagmin XIb
chr7_-_58729894 0.05 ENSDART00000149347
chchd7
coiled-coil-helix-coiled-coil-helix domain containing 7
chr5_+_33498253 0.05 ENSDART00000140993
ms4a17c.2
membrane-spanning 4-domains, subfamily A, member 17c.2
chr7_+_7048245 0.03 ENSDART00000001649
actn3b
actinin alpha 3b
chr6_+_9130989 0.03 ENSDART00000162588
rgn
regucalcin
chr17_-_45040813 0.03 ENSDART00000075514
entpd5a
ectonucleoside triphosphate diphosphohydrolase 5a
chr5_-_23843636 0.03 ENSDART00000193280
GBGT1 (1 of many)
si:ch211-135f11.5
chr19_+_14573998 0.00 ENSDART00000022076
fam46bb
family with sequence similarity 46, member Bb

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
0.1 0.7 GO:0000012 single strand break repair(GO:0000012)
0.1 0.3 GO:1900745 positive regulation of p38MAPK cascade(GO:1900745)
0.1 0.4 GO:0034969 histone arginine methylation(GO:0034969)
0.1 0.2 GO:0034214 protein hexamerization(GO:0034214) mitotic spindle disassembly(GO:0051228) spindle disassembly(GO:0051230)
0.1 0.2 GO:0048618 post-embryonic foregut morphogenesis(GO:0048618)
0.0 0.4 GO:0021631 optic nerve morphogenesis(GO:0021631)
0.0 0.5 GO:0021703 locus ceruleus development(GO:0021703)
0.0 0.1 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)
0.0 0.5 GO:0036353 histone H2A-K119 monoubiquitination(GO:0036353)
0.0 0.3 GO:1990845 adaptive thermogenesis(GO:1990845)
0.0 0.2 GO:0071800 podosome assembly(GO:0071800)
0.0 0.3 GO:0035677 posterior lateral line neuromast hair cell development(GO:0035677)
0.0 0.3 GO:0006048 UDP-N-acetylglucosamine biosynthetic process(GO:0006048)
0.0 0.2 GO:0042138 meiotic DNA double-strand break formation(GO:0042138)
0.0 0.2 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 0.2 GO:0021521 ventral spinal cord interneuron specification(GO:0021521) cell fate specification involved in pattern specification(GO:0060573)
0.0 0.2 GO:0071816 tail-anchored membrane protein insertion into ER membrane(GO:0071816)
0.0 0.2 GO:0006003 fructose 2,6-bisphosphate metabolic process(GO:0006003)
0.0 0.3 GO:0060285 cilium or flagellum-dependent cell motility(GO:0001539) cilium-dependent cell motility(GO:0060285)
0.0 0.2 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:2000601 positive regulation of actin nucleation(GO:0051127) positive regulation of Arp2/3 complex-mediated actin nucleation(GO:2000601)
0.0 0.0 GO:0019852 L-ascorbic acid metabolic process(GO:0019852) water-soluble vitamin biosynthetic process(GO:0042364)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.2 GO:0000506 glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex(GO:0000506)
0.0 0.1 GO:0070319 Golgi to plasma membrane transport vesicle(GO:0070319)
0.0 0.2 GO:0071818 BAT3 complex(GO:0071818)
0.0 0.3 GO:0031588 nucleotide-activated protein kinase complex(GO:0031588)
0.0 0.5 GO:0035102 PRC1 complex(GO:0035102)
0.0 0.2 GO:0002102 podosome(GO:0002102)
0.0 0.3 GO:0090665 dystrophin-associated glycoprotein complex(GO:0016010) glycoprotein complex(GO:0090665)
0.0 0.3 GO:0005839 proteasome core complex(GO:0005839)
0.0 0.2 GO:0031209 SCAR complex(GO:0031209)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 0.7 GO:0070259 tyrosyl-DNA phosphodiesterase activity(GO:0070259)
0.1 0.4 GO:0035243 protein-arginine omega-N symmetric methyltransferase activity(GO:0035243)
0.1 0.2 GO:0048487 beta-tubulin binding(GO:0048487)
0.0 0.3 GO:0004839 ubiquitin activating enzyme activity(GO:0004839)
0.0 0.1 GO:0031005 filamin binding(GO:0031005)
0.0 0.2 GO:0017176 phosphatidylinositol N-acetylglucosaminyltransferase activity(GO:0017176)
0.0 0.3 GO:0016868 intramolecular transferase activity, phosphotransferases(GO:0016868)
0.0 0.2 GO:0016176 superoxide-generating NADPH oxidase activity(GO:0016175) superoxide-generating NADPH oxidase activator activity(GO:0016176)
0.0 0.5 GO:1990841 promoter-specific chromatin binding(GO:1990841)
0.0 0.2 GO:0071933 Arp2/3 complex binding(GO:0071933)
0.0 0.2 GO:0003873 6-phosphofructo-2-kinase activity(GO:0003873)
0.0 0.3 GO:0004298 threonine-type endopeptidase activity(GO:0004298) threonine-type peptidase activity(GO:0070003)
0.0 0.2 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
0.0 0.7 REACTOME DOUBLE STRAND BREAK REPAIR Genes involved in Double-Strand Break Repair
0.0 0.3 REACTOME SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS Genes involved in Synthesis of substrates in N-glycan biosythesis
0.0 0.2 REACTOME HORMONE LIGAND BINDING RECEPTORS Genes involved in Hormone ligand-binding receptors
0.0 0.2 REACTOME SYNTHESIS OF PE Genes involved in Synthesis of PE
0.0 0.2 REACTOME SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI Genes involved in Synthesis of glycosylphosphatidylinositol (GPI)