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PRJEB1986: zebrafish developmental stages transcriptome

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Results for six3a+six3b+six7_six1a+six2a+six2b+six5+six9_six1b

Z-value: 0.88

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Transcription factors associated with six3a+six3b+six7_six1a+six2a+six2b+six5+six9_six1b

Gene Symbol Gene ID Gene Info
ENSDARG00000054879 SIX homeobox 3b
ENSDARG00000058008 SIX homeobox 3a
ENSDARG00000070107 SIX homeobox 7
ENSDARG00000114971 SIX homeobox 3a
ENSDARG00000039304 SIX homeobox 1a
ENSDARG00000054878 SIX homeobox 2b
ENSDARG00000058004 SIX homeobox 2a
ENSDARG00000068406 SIX homeobox 5
ENSDARG00000068407 SIX homeobox 9
ENSDARG00000115214 SIX homeobox 2a
ENSDARG00000026473 SIX homeobox 1b

Activity profile of six3a+six3b+six7_six1a+six2a+six2b+six5+six9_six1b motif

Sorted Z-values of six3a+six3b+six7_six1a+six2a+six2b+six5+six9_six1b motif

Promoter Log-likelihood Transcript Gene Gene Info
chr6_+_41181869 7.47 ENSDART00000002046
opsin 1 (cone pigments), medium-wave-sensitive, 1
chr17_+_20607487 4.17 ENSDART00000154123
si:ch73-288o11.5
chr5_+_68112194 3.13 ENSDART00000162468

chr25_-_19068557 2.84 ENSDART00000184780
calcium channel, voltage-dependent, alpha 2/delta subunit 4b
chr23_-_39666519 2.73 ENSDART00000110868
ENSDART00000190961
von Willebrand factor A domain containing 1
chr1_-_24255149 2.65 ENSDART00000146960
LPS-responsive vesicle trafficking, beach and anchor containing
chr11_+_24002503 2.31 ENSDART00000164702
chitinase, acidic.2
chr7_-_71486162 2.20 ENSDART00000045253
aconitase 1, soluble
chr5_+_9377005 2.15 ENSDART00000124924
UDP glucuronosyltransferase 2 family, polypeptide A7
chr1_-_53259746 2.12 ENSDART00000134222
interleukin 15
chr21_+_11385031 1.87 ENSDART00000040598
carboxyl ester lipase, tandem duplicate 2
chr4_-_27398385 1.72 ENSDART00000142117
ENSDART00000150553
ENSDART00000182746
family with sequence similarity 19 (chemokine (C-C motif)-like), member A5a
chr11_+_3575963 1.71 ENSDART00000077305
si:dkey-33m11.8
chr1_+_37752171 1.64 ENSDART00000183247
ENSDART00000189756
ENSDART00000139448
si:ch211-15e22.3
chr9_+_46644633 1.60 ENSDART00000160285
solute carrier family 4 (anion exchanger), member 3
chr13_-_47800342 1.53 ENSDART00000121817
fibulin 7
chr6_-_48087152 1.53 ENSDART00000180614
solute carrier family 2 (facilitated glucose transporter), member 1b
chr6_+_41186320 1.42 ENSDART00000025241
opsin 1 (cone pigments), medium-wave-sensitive, 2
chr20_-_34127415 1.39 ENSDART00000010028
prostaglandin-endoperoxide synthase 2b
chr4_-_27301356 1.33 ENSDART00000100444
family with sequence similarity 19 (chemokine (C-C motif)-like), member A5a
chr23_+_39481537 1.28 ENSDART00000187222
microtubule associated monooxygenase, calponin and LIM domain containing 1
chr11_-_24016761 1.20 ENSDART00000153601
ENSDART00000067817
ENSDART00000170531
chitinase, acidic.3
chr19_+_34230108 1.17 ENSDART00000141950
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12
chr5_-_12823876 1.17 ENSDART00000019461
purinergic receptor P2X, ligand-gated ion channel, 2
chr15_+_17446796 1.15 ENSDART00000157189
sorting nexin 19b
chr1_+_532766 1.10 ENSDART00000179731
ENSDART00000060944
mitochondrial ribosomal protein L39
chr13_-_40120252 1.06 ENSDART00000157852
cartilage acidic protein 1b
chr17_-_44776224 1.06 ENSDART00000156195
zinc finger, DHHC-type containing 22
chr1_+_7538909 1.00 ENSDART00000148276
myosin, light polypeptide 3, skeletal muscle
chr7_-_47381146 0.97 ENSDART00000185596

chr5_-_30615901 0.96 ENSDART00000147769
si:ch211-117m20.5
chr10_+_23520952 0.93 ENSDART00000125317
zmp:0000000937
chr10_-_20706109 0.93 ENSDART00000124751
Kv channel interacting protein 3b, calsenilin
chr4_+_14826299 0.92 ENSDART00000067035
shisa like 1a
chr12_+_13742778 0.91 ENSDART00000111401
ENSDART00000190552
protein phosphatase 1, regulatory subunit 16A
chr12_+_13742953 0.89 ENSDART00000152257
protein phosphatase 1, regulatory subunit 16A
chr9_-_22076368 0.87 ENSDART00000128486
crystallin, gamma M2a
chr7_-_38183331 0.85 ENSDART00000149382
ATP-binding cassette, sub-family C (CFTR/MRP), member 12
chr20_-_45709990 0.79 ENSDART00000027482
glycerophosphocholine phosphodiesterase 1
chr15_-_36352983 0.77 ENSDART00000059786
si:dkey-23k10.5
chr16_+_50755133 0.77 ENSDART00000029283
zgc:110372
chr16_+_41060161 0.77 ENSDART00000141130
SREBF chaperone
chr24_+_30435164 0.71 ENSDART00000193877
dihydropyrimidine dehydrogenase a, tandem duplicate 1
chr10_-_42898220 0.70 ENSDART00000099270

chr13_-_18122333 0.67 ENSDART00000128748
WASH complex subunit 2C
chr11_-_44194132 0.67 ENSDART00000182954
ENSDART00000111271

chr14_+_26805388 0.66 ENSDART00000044389
ENSDART00000173126
kelch-like family member 4
chr8_+_23745167 0.66 ENSDART00000149352
si:ch211-163l21.11
chr1_-_21901589 0.65 ENSDART00000140553
FERM and PDZ domain containing 1a
chr5_+_64732036 0.65 ENSDART00000073950
olfactomedin 1a
chr21_+_18405585 0.63 ENSDART00000139318
si:dkey-1d7.3
chr6_-_40899618 0.61 ENSDART00000153949
ENSDART00000021969
zgc:172271
chr20_+_22067337 0.58 ENSDART00000152636
clock circadian regulator a
chr13_+_9678427 0.58 ENSDART00000153907
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Ga
chr7_-_72423666 0.58 ENSDART00000191214
rabphilin 3A homolog (mouse), b
chr3_-_5067585 0.52 ENSDART00000169609
thyrotrophic embryonic factor b
chr13_-_2215213 0.51 ENSDART00000129773
muscular LMNA-interacting protein
chr25_+_192116 0.50 ENSDART00000153983
zgc:114188
chr16_-_383664 0.49 ENSDART00000051693
iroquois homeobox 4a
chr10_+_21718468 0.47 ENSDART00000126622
protocadherin 1 gamma b 9
chr8_-_26961779 0.47 ENSDART00000099214
solute carrier family 16 (monocarboxylate transporter), member 1b
chr20_-_39735952 0.44 ENSDART00000101049
ENSDART00000137485
ENSDART00000062402
tumor protein D52-like 1
chr10_+_35468978 0.43 ENSDART00000131984
pleckstrin homology-like domain, family B, member 2a
chr10_-_32610776 0.43 ENSDART00000017436
monoacylglycerol O-acyltransferase 2
chr16_-_44512882 0.43 ENSDART00000191241

chr11_+_24339377 0.42 ENSDART00000133679
ENSDART00000135435
ENSDART00000017973
ENSDART00000131365
ENSDART00000186418
RNA binding motif protein 39a
chr12_-_35095414 0.40 ENSDART00000153229
si:dkey-21e13.3
chr19_+_12237945 0.39 ENSDART00000190034
grainyhead-like transcription factor 2b
chr5_+_37903790 0.39 ENSDART00000162470
transmembrane protease, serine 4b
chr2_-_52020049 0.37 ENSDART00000128198
ENSDART00000135331
sodium channel, voltage gated, type XII, alpha a
chr24_-_21588914 0.36 ENSDART00000152054
G protein-coupled receptor 12
chr2_-_50298337 0.35 ENSDART00000155125
contactin associated protein like 2b
chr23_+_3721042 0.35 ENSDART00000143323
small integral membrane protein 29
chr7_+_63325819 0.32 ENSDART00000085612
ENSDART00000161436
protocadherin 7b
chr13_+_25412307 0.31 ENSDART00000175339
calcium homeostasis modulator 1
chr15_+_40792667 0.31 ENSDART00000193186
ENSDART00000184559
FAT atypical cadherin 3a
chr18_+_44080948 0.30 ENSDART00000191036

chr16_-_50157187 0.28 ENSDART00000155162
NIMA-related kinase 10
chr24_-_18809433 0.28 ENSDART00000152009
ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)
chr4_-_5317006 0.27 ENSDART00000150867
si:ch211-214j24.15
chr16_+_29630965 0.27 ENSDART00000185820
ENSDART00000192105
ENSDART00000153683
ENSDART00000186713
si:ch211-203d17.1
chr2_-_24270062 0.26 ENSDART00000192445
myosin heavy chain 7
chr3_+_1724941 0.25 ENSDART00000193402

chr13_+_9678262 0.25 ENSDART00000111365
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Ga
chr23_-_4019928 0.24 ENSDART00000021062
solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8
chr16_-_23797570 0.22 ENSDART00000077834
ribosomal protein S27, isoform 2
chr5_-_24112175 0.22 ENSDART00000131595
si:ch211-114c12.5
chr6_+_52947186 0.22 ENSDART00000155831
ubiquitin-like modifier activating enzyme 7
chr8_+_7801060 0.21 ENSDART00000161618
transcription factor binding to IGHM enhancer 3a
chr5_+_13326765 0.21 ENSDART00000090851
YdjC chitooligosaccharide deacetylase homolog
chr23_-_4019699 0.21 ENSDART00000159780
solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8
chr19_-_15434813 0.20 ENSDART00000019843
finTRIM family, member 55
chr25_+_3788074 0.20 ENSDART00000154008
chitinase domain containing 1
chr10_+_23441488 0.19 ENSDART00000100783
si:ch73-122g19.1
chr3_-_34084387 0.17 ENSDART00000155365
immunoglobulin heavy variable 4-3
chr6_+_52947699 0.17 ENSDART00000180913
ubiquitin-like modifier activating enzyme 7
chr11_+_1602916 0.16 ENSDART00000184434
ENSDART00000112597
ENSDART00000192165
si:dkey-40c23.2
si:dkey-40c23.3
chr20_-_45058041 0.15 ENSDART00000124298
kelch-like family member 29
chr22_+_2778600 0.14 ENSDART00000134028
si:dkey-20i20.9
chr20_-_44460789 0.12 ENSDART00000085442
methylmalonyl CoA mutase
chr4_-_13502549 0.12 ENSDART00000140366
si:ch211-266a5.12
chr15_+_3246475 0.12 ENSDART00000189565

chr4_+_74396786 0.12 ENSDART00000127501
ENSDART00000174347
zmp:0000001020
chr12_+_28854963 0.12 ENSDART00000153227
nuclear factor, erythroid 2-like 1b
chr25_+_10947743 0.12 ENSDART00000073381
major histocompatibility complex class I LFA
chr15_-_38218320 0.11 ENSDART00000152363
ras homolog family member Ga
chr17_-_6600899 0.10 ENSDART00000154074
ENSDART00000180912
si:ch211-189e2.2
chr17_+_4408809 0.10 ENSDART00000113401
si:zfos-364h11.1
chr4_+_22613625 0.10 ENSDART00000131161
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C
chr5_-_26247973 0.10 ENSDART00000098527
endoplasmic reticulum aminopeptidase 1b
chr7_-_36113098 0.09 ENSDART00000064913
fat mass and obesity associated
chr4_+_73672430 0.08 ENSDART00000174310
ENSDART00000150505
si:dkey-262g12.7
chr14_+_1355857 0.07 ENSDART00000188008
Bardet-Biedl syndrome 12
chr7_-_59515569 0.05 ENSDART00000163343
ENSDART00000165457
ENSDART00000163745
SLX1 homolog B, structure-specific endonuclease subunit
chr4_+_19127973 0.04 ENSDART00000136611
si:dkey-21o22.2
chr12_+_19030391 0.03 ENSDART00000153927
si:ch73-139e5.2
chr25_+_18953756 0.03 ENSDART00000154291
thymine DNA glycosylase, tandem duplicate 2
chr1_+_11691722 0.03 ENSDART00000134531
eukaryotic translation initiation factor 3, subunit Bb
chr6_-_40352215 0.02 ENSDART00000103992
tubulin tyrosine ligase-like family, member 3
chr25_-_18953322 0.02 ENSDART00000155927
si:ch211-68a17.7
chr21_-_43094210 0.01 ENSDART00000144747
si:ch73-68b22.2
chr7_+_2244859 0.01 ENSDART00000114242
ENSDART00000064292
si:ch211-285c6.4
chr21_-_13972745 0.01 ENSDART00000143874
AT-hook transcription factor
chr21_-_7940043 0.01 ENSDART00000099733
ENSDART00000136671
coagulation factor II (thrombin) receptor-like 1, tandem duplicate 1
chr8_+_20440297 0.01 ENSDART00000189486
MAP kinase interacting serine/threonine kinase 2b
chr4_-_7811925 0.01 ENSDART00000103070
cyclin-dependent kinase 17
chr2_+_26240631 0.00 ENSDART00000129895
paralemmin 1b

Network of associatons between targets according to the STRING database.

First level regulatory network of six3a+six3b+six7_six1a+six2a+six2b+six5+six9_six1b

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
0.6 2.2 GO:0010039 response to iron ion(GO:0010039)
0.4 1.3 GO:0019417 sulfur oxidation(GO:0019417)
0.3 1.4 GO:0019371 cyclooxygenase pathway(GO:0019371)
0.3 3.5 GO:0006032 chitin catabolic process(GO:0006032)
0.2 8.9 GO:0018298 protein-chromophore linkage(GO:0018298)
0.2 2.8 GO:0046549 retinal cone cell development(GO:0046549)
0.2 1.9 GO:0097090 presynaptic membrane organization(GO:0097090) postsynaptic membrane assembly(GO:0097104) presynaptic membrane assembly(GO:0097105)
0.2 2.1 GO:0042531 positive regulation of tyrosine phosphorylation of STAT protein(GO:0042531)
0.1 0.7 GO:0006212 uracil catabolic process(GO:0006212) uracil metabolic process(GO:0019860)
0.1 0.4 GO:0006651 diacylglycerol biosynthetic process(GO:0006651)
0.1 1.6 GO:0086001 cardiac muscle cell action potential(GO:0086001)
0.1 1.2 GO:0033198 response to ATP(GO:0033198)
0.1 0.6 GO:0061075 positive regulation of neural retina development(GO:0061075) positive regulation of retina development in camera-type eye(GO:1902868)
0.1 0.4 GO:0099612 protein localization to juxtaparanode region of axon(GO:0071205) protein localization to axon(GO:0099612)
0.1 0.8 GO:0071501 response to sterol depletion(GO:0006991) SREBP signaling pathway(GO:0032933) cellular response to sterol depletion(GO:0071501)
0.0 0.3 GO:0055005 ventricular cardiac myofibril assembly(GO:0055005)
0.0 0.8 GO:0046475 glycerophospholipid catabolic process(GO:0046475)
0.0 0.1 GO:0042245 RNA repair(GO:0042245)
0.0 0.4 GO:0060561 apoptotic process involved in morphogenesis(GO:0060561)
0.0 0.5 GO:0048923 posterior lateral line neuromast hair cell differentiation(GO:0048923)
0.0 1.1 GO:0018230 peptidyl-L-cysteine S-palmitoylation(GO:0018230) peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine(GO:0018231)
0.0 0.4 GO:0086010 membrane depolarization during action potential(GO:0086010)
0.0 0.6 GO:0009648 photoperiodism(GO:0009648)
0.0 0.4 GO:2001235 positive regulation of apoptotic signaling pathway(GO:2001235)
0.0 0.6 GO:0006826 iron ion transport(GO:0006826)
0.0 0.2 GO:0045670 regulation of osteoclast differentiation(GO:0045670)
0.0 0.5 GO:0071482 cellular response to light stimulus(GO:0071482)
0.0 0.9 GO:1902668 negative regulation of axon extension involved in axon guidance(GO:0048843) negative regulation of axon guidance(GO:1902668)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 8.9 GO:0001750 photoreceptor outer segment(GO:0001750)
0.1 0.6 GO:1990513 CLOCK-BMAL transcription complex(GO:1990513)
0.1 1.2 GO:0031229 integral component of nuclear inner membrane(GO:0005639) intrinsic component of nuclear inner membrane(GO:0031229) nuclear membrane part(GO:0044453)
0.0 0.4 GO:0033010 paranodal junction(GO:0033010)
0.0 2.8 GO:0005891 voltage-gated calcium channel complex(GO:0005891)
0.0 0.4 GO:0034706 voltage-gated sodium channel complex(GO:0001518) sodium channel complex(GO:0034706)
0.0 0.8 GO:0012507 ER to Golgi transport vesicle membrane(GO:0012507)
0.0 0.4 GO:0045180 basal cortex(GO:0045180)
0.0 0.5 GO:0016605 PML body(GO:0016605)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.7 2.2 GO:0003994 aconitate hydratase activity(GO:0003994)
0.6 1.9 GO:0004771 sterol esterase activity(GO:0004771)
0.5 1.8 GO:0017020 myosin phosphatase regulator activity(GO:0017020)
0.3 1.4 GO:0004666 prostaglandin-endoperoxide synthase activity(GO:0004666)
0.3 3.5 GO:0004568 chitinase activity(GO:0004568)
0.3 0.8 GO:0047389 glycerophosphocholine phosphodiesterase activity(GO:0047389)
0.2 1.5 GO:0055056 D-glucose transmembrane transporter activity(GO:0055056)
0.2 8.9 GO:0008020 G-protein coupled photoreceptor activity(GO:0008020)
0.1 0.7 GO:0002058 uracil binding(GO:0002058) pyrimidine nucleobase binding(GO:0002061) dihydropyrimidine dehydrogenase (NADP+) activity(GO:0017113)
0.1 0.5 GO:0005521 lamin binding(GO:0005521)
0.1 1.2 GO:0035381 extracellular ATP-gated cation channel activity(GO:0004931) ATP-gated ion channel activity(GO:0035381)
0.1 0.6 GO:0070888 E-box binding(GO:0070888)
0.1 1.6 GO:0005452 inorganic anion exchanger activity(GO:0005452)
0.1 0.2 GO:0008061 chitin binding(GO:0008061)
0.1 0.4 GO:0004839 ubiquitin activating enzyme activity(GO:0004839)
0.0 0.4 GO:0015386 monovalent cation:proton antiporter activity(GO:0005451) sodium:proton antiporter activity(GO:0015385) potassium:proton antiporter activity(GO:0015386)
0.0 0.5 GO:0015129 lactate transmembrane transporter activity(GO:0015129)
0.0 2.1 GO:0015020 glucuronosyltransferase activity(GO:0015020)
0.0 2.8 GO:0005245 voltage-gated calcium channel activity(GO:0005245)
0.0 0.4 GO:1905030 voltage-gated sodium channel activity(GO:0005248) voltage-gated ion channel activity involved in regulation of postsynaptic membrane potential(GO:1905030)
0.0 0.1 GO:0043734 oxidative DNA demethylase activity(GO:0035516) DNA-N1-methyladenine dioxygenase activity(GO:0043734) RNA N6-methyladenosine dioxygenase activity(GO:1990931)
0.0 1.3 GO:0071949 FAD binding(GO:0071949)
0.0 1.1 GO:0019706 protein-cysteine S-palmitoyltransferase activity(GO:0019706) protein-cysteine S-acyltransferase activity(GO:0019707)
0.0 0.1 GO:0031419 cobalamin binding(GO:0031419)
0.0 0.4 GO:0016411 acylglycerol O-acyltransferase activity(GO:0016411)
0.0 0.9 GO:0030215 semaphorin receptor binding(GO:0030215)
0.0 2.1 GO:0005126 cytokine receptor binding(GO:0005126)
0.0 0.8 GO:0032934 sterol binding(GO:0032934)
0.0 0.9 GO:0005212 structural constituent of eye lens(GO:0005212)
0.0 2.3 GO:0019901 protein kinase binding(GO:0019901)
0.0 0.1 GO:0008821 crossover junction endodeoxyribonuclease activity(GO:0008821)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.0 0.8 SA CASPASE CASCADE Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade.
0.0 4.2 NABA ECM GLYCOPROTEINS Genes encoding structural ECM glycoproteins
0.0 2.1 NABA SECRETED FACTORS Genes encoding secreted soluble factors

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 1.4 REACTOME OPSINS Genes involved in Opsins
0.1 2.8 REACTOME O LINKED GLYCOSYLATION OF MUCINS Genes involved in O-linked glycosylation of mucins
0.0 1.5 REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides
0.0 0.4 REACTOME NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING Genes involved in Negative regulators of RIG-I/MDA5 signaling