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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for six4a+six4b

Z-value: 0.73

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Transcription factors associated with six4a+six4b

Gene Symbol Gene ID Gene Info
ENSDARG00000004695 SIX homeobox 4a
ENSDARG00000031983 SIX homeobox 4b

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
six4bdr11_v1_chr20_+_20484827_20484827-0.857.5e-06Click!
six4adr11_v1_chr13_-_31647323_31647323-0.711.1e-03Click!

Activity profile of six4a+six4b motif

Sorted Z-values of six4a+six4b motif

Promoter Log-likelihood Transcript Gene Gene Info
chr22_+_25236657 2.33 ENSDART00000138012
zgc:172218
chr2_+_68789 2.31 ENSDART00000058569
claudin 1
chr22_+_25242322 2.14 ENSDART00000134628
si:ch211-226h8.8
chr22_+_25236888 1.99 ENSDART00000037286
zgc:172218
chr3_-_54607166 1.64 ENSDART00000021977
DNA (cytosine-5-)-methyltransferase 1
chr9_+_2041535 1.62 ENSDART00000093187
limb and neural patterns a
chr5_+_13472234 1.58 ENSDART00000114069
ENSDART00000132406
cyclin and CBS domain divalent metal cation transport mediator 4b
chr9_+_8396755 1.31 ENSDART00000043067
zgc:171776
chr15_-_35126332 1.29 ENSDART00000007636
zgc:55413
chr18_+_27511976 1.17 ENSDART00000132017
ENSDART00000140781
tumor protein p53 inducible protein 11b
chr1_-_6085750 1.12 ENSDART00000138891
si:ch1073-345a8.1
chr19_-_11031145 1.09 ENSDART00000151375
ENSDART00000027598
ENSDART00000137865
ENSDART00000188025
tropomyosin 3
chr19_-_6983002 1.02 ENSDART00000104891
zinc finger protein 384 like
chr16_-_17347727 1.01 ENSDART00000144392
zyxin
chr12_+_1592146 1.01 ENSDART00000184575
ENSDART00000192902
solute carrier family 39 member 11
chr7_-_60351537 1.00 ENSDART00000159875
phospholipase C, beta 3 (phosphatidylinositol-specific)
chr20_+_26943072 0.93 ENSDART00000153215
cell division cycle associated 4
chr16_+_35905031 0.87 ENSDART00000162411
SH3 domain containing 21
chr7_+_48297842 0.81 ENSDART00000052123
solute carrier family 25, member 44 b
chr20_-_51831657 0.80 ENSDART00000165076
melanoma inhibitory activity family, member 3
chr6_-_3978919 0.75 ENSDART00000167753
solute carrier family 25 (aspartate/glutamate carrier), member 12
chr9_+_27750490 0.75 ENSDART00000125303
ENSDART00000189279
ENSDART00000021065
ENSDART00000148060
RAB5B, member RAS oncogene family
chr22_+_2751887 0.75 ENSDART00000133652
si:dkey-20i20.11
chr12_-_4475890 0.72 ENSDART00000092492
si:ch211-173d10.1
chr7_-_58130703 0.72 ENSDART00000172082
ankyrin 2b, neuronal
chr24_-_23839647 0.72 ENSDART00000125190
RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)
chr10_+_39283985 0.71 ENSDART00000016464
decapping enzyme, scavenger
chr19_-_6083761 0.70 ENSDART00000151185
ENSDART00000143941
glycogen synthase kinase 3 alpha a
chr2_-_43739559 0.68 ENSDART00000138947
kinesin family member 5B, a
chr3_+_52953489 0.67 ENSDART00000125136
DSN1 homolog, MIS12 kinetochore complex component
chr17_-_13072334 0.66 ENSDART00000159598

chr2_-_40135942 0.64 ENSDART00000176951
ENSDART00000098632
ENSDART00000148563
ENSDART00000149895
eph receptor A4a
chr16_+_50755133 0.64 ENSDART00000029283
zgc:110372
chr1_+_37752171 0.61 ENSDART00000183247
ENSDART00000189756
ENSDART00000139448
si:ch211-15e22.3
chr18_-_39188664 0.60 ENSDART00000162983
mitogen-activated protein kinase 6
chr3_+_18579806 0.60 ENSDART00000180967
ENSDART00000089765
Rho GTPase activating protein 17b
chr7_-_54217547 0.58 ENSDART00000162777
ENSDART00000188268
ENSDART00000165875
casein kinase 1, gamma 1
chr20_+_37866686 0.58 ENSDART00000036546
vasohibin 2
chr10_-_39283883 0.58 ENSDART00000023831
cryptochrome circadian clock 5
chr8_+_35964482 0.57 ENSDART00000129357
ENSDART00000154953
glycosyltransferase 1 domain containing 1
chr2_-_30770736 0.56 ENSDART00000131230
regulator of G protein signaling 20
chr23_+_27779452 0.55 ENSDART00000134785
lysine (K)-specific methyltransferase 2D
chr21_+_34167178 0.49 ENSDART00000158308
transient receptor potential cation channel, subfamily C, member 5b
chr12_+_23991276 0.48 ENSDART00000153136
proteasome activator subunit 4b
chr20_-_6184167 0.48 ENSDART00000147451
UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6
chr25_+_5604512 0.48 ENSDART00000042781
plexin b2b
chr11_+_24851671 0.45 ENSDART00000167659
importin 9
chr7_+_38770167 0.45 ENSDART00000190827
Rho GTPase activating protein 1
chr24_-_25166416 0.45 ENSDART00000111552
ENSDART00000169495
pleckstrin homology-like domain, family B, member 2b
chr6_-_40657653 0.42 ENSDART00000154359
peptidylprolyl isomerase (cyclophilin)-like 1
chr2_-_20666920 0.39 ENSDART00000143437
ENSDART00000114546
ENSDART00000136113
ENSDART00000179247
dual specificity phosphatase 12
chr4_+_288633 0.39 ENSDART00000183304

chr9_-_34882516 0.38 ENSDART00000011163
acetylserotonin O-methyltransferase-like
chr5_+_12908781 0.38 ENSDART00000051663
peptidylprolyl isomerase (cyclophilin)-like 2
chr5_+_66044128 0.38 ENSDART00000165573
Janus kinase 2b
chr12_-_20658285 0.37 ENSDART00000080888
SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)
chr11_+_1602916 0.35 ENSDART00000184434
ENSDART00000112597
ENSDART00000192165
si:dkey-40c23.2
si:dkey-40c23.3
chr21_+_34686764 0.33 ENSDART00000005479
choroideremia (Rab escort protein 1)
chr20_+_22067337 0.33 ENSDART00000152636
clock circadian regulator a
chr3_+_15773991 0.32 ENSDART00000089923
zinc finger protein 652
chr10_-_32610776 0.32 ENSDART00000017436
monoacylglycerol O-acyltransferase 2
chr2_-_30784198 0.31 ENSDART00000182523
ENSDART00000147355
regulator of G protein signaling 20
chr13_+_4883377 0.31 ENSDART00000181530
ENSDART00000092521
mitochondrial calcium uptake 1
chr5_+_55221593 0.30 ENSDART00000073638
transmembrane channel-like 2a
chr23_+_45785563 0.30 ENSDART00000186027

chr19_-_10330778 0.29 ENSDART00000081465
ENSDART00000136653
ENSDART00000171232
coiled-coil domain containing 106b
chr11_-_10850936 0.29 ENSDART00000091901
proteasome 26S subunit, non-ATPase 14
chr18_-_12416019 0.29 ENSDART00000144799
si:ch211-1e14.1
chr1_+_55140970 0.28 ENSDART00000039807
myoglobin
chr7_+_53498152 0.27 ENSDART00000184497
zinc finger protein 609b
chr20_-_20248408 0.26 ENSDART00000183234
protein phosphatase 2, regulatory subunit B', epsilon isoform a
chr13_-_14269626 0.25 ENSDART00000079176
GDNF family receptor alpha 4a
chr9_-_40873934 0.24 ENSDART00000066424
protein O-fucosyltransferase 2
chr14_-_4043818 0.24 ENSDART00000179870
sorting nexin 25
chr19_+_37135700 0.21 ENSDART00000103159
small integral membrane protein 12
chr8_+_7801060 0.21 ENSDART00000161618
transcription factor binding to IGHM enhancer 3a
chr6_-_35310224 0.20 ENSDART00000148997
nitric oxide synthase 1 (neuronal) adaptor protein a
chr7_+_39360797 0.20 ENSDART00000173481
acid phosphatase 2, lysosomal
chr1_+_1941031 0.20 ENSDART00000110331
si:ch211-132g1.7
chr18_+_19419120 0.19 ENSDART00000025107
mitogen-activated protein kinase kinase 1
chr5_-_57723929 0.19 ENSDART00000144237
grass carp reovirus (GCRV)-induced gene 2p
chr16_-_46567136 0.18 ENSDART00000159180
si:dkey-152b24.7
chr18_+_5308392 0.17 ENSDART00000179072
deoxyuridine triphosphatase
chr12_-_31484677 0.16 ENSDART00000066578
tectorin beta
chr14_-_31856819 0.15 ENSDART00000003345
Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6
chr8_+_23485079 0.15 ENSDART00000026316
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Gb
chr2_+_29491314 0.09 ENSDART00000181774
discs, large (Drosophila) homolog-associated protein 1a
chr12_+_31422557 0.09 ENSDART00000153179
zinc finger, DHHC-type containing 6
chr1_-_45889820 0.09 ENSDART00000144735
patatin-like phospholipase domain containing 6
chr22_+_21317597 0.08 ENSDART00000132605
SHC (Src homology 2 domain containing) transforming protein 2
chr11_+_36683859 0.08 ENSDART00000170102
si:ch211-11c3.12
chr17_-_1407593 0.06 ENSDART00000157622
ENSDART00000159458
zinc finger and BTB domain containing 42
chr23_-_33944597 0.06 ENSDART00000133223
si:dkey-190g6.2
chr14_-_2209742 0.05 ENSDART00000054889
protocadherin 2 alpha b 5
chr2_+_25198648 0.05 ENSDART00000110922
protein phosphatase 2, regulatory subunit B'', alpha
chr22_-_36774057 0.04 ENSDART00000125048
aminoacylase 1
chr3_+_12718100 0.04 ENSDART00000162343
ENSDART00000192425
cytochrome P450, family 2, subfamily k, polypeptide 20
chr2_-_5404466 0.04 ENSDART00000152907
si:ch1073-184j22.2
chr2_+_43469241 0.03 ENSDART00000142078
ENSDART00000098265
neuropilin 1b
chr21_+_21679086 0.03 ENSDART00000146225
odorant receptor, family E, subfamily 125, member 5
chr18_+_7264961 0.03 ENSDART00000188461

chr22_+_15310103 0.03 ENSDART00000145849

chr2_+_30465102 0.03 ENSDART00000188404
neuropilin (NRP) and tolloid (TLL)-like 1
chr25_-_13201458 0.03 ENSDART00000192451
si:ch211-194m7.4
chr19_+_10331325 0.02 ENSDART00000143930
transmembrane protein 238a
chr21_-_36396334 0.02 ENSDART00000183627
mitochondrial ribosomal protein L22
chr23_+_16469530 0.02 ENSDART00000132898
neurotensin receptor 1 (high affinity)
chr3_+_1096831 0.02 ENSDART00000132817
si:ch1073-322p19.1
chr15_-_37834433 0.02 ENSDART00000189748
si:dkey-238d18.3
chr14_+_24042760 0.02 ENSDART00000106096
dopamine receptor D1a
chr6_+_39085969 0.01 ENSDART00000004240
protease, serine, 60.1
chr19_-_15434813 0.00 ENSDART00000019843
finTRIM family, member 55
chr9_+_11034314 0.00 ENSDART00000032695
acid-sensing (proton-gated) ion channel family member 4a
chr18_+_32444636 0.00 ENSDART00000164223
vomeronasal 2 receptor, a1
chr6_+_40591149 0.00 ENSDART00000189060
ENSDART00000188298
fibroblast growth factor receptor substrate 3

Network of associatons between targets according to the STRING database.

First level regulatory network of six4a+six4b

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
0.5 1.6 GO:1903373 regulation of endoplasmic reticulum tubular network organization(GO:1903371) positive regulation of endoplasmic reticulum tubular network organization(GO:1903373)
0.3 1.6 GO:0032776 DNA methylation on cytosine(GO:0032776)
0.1 0.7 GO:0036371 protein localization to T-tubule(GO:0036371)
0.1 1.6 GO:0010960 magnesium ion homeostasis(GO:0010960)
0.1 0.7 GO:0000447 endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)(GO:0000447)
0.1 0.7 GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA(GO:0000290)
0.1 0.7 GO:0098935 dendritic transport(GO:0098935) anterograde dendritic transport(GO:0098937) anterograde dendritic transport of neurotransmitter receptor complex(GO:0098971)
0.1 0.6 GO:0003404 optic vesicle morphogenesis(GO:0003404)
0.1 0.5 GO:0007289 spermatid nucleus differentiation(GO:0007289) sperm chromatin condensation(GO:0035092) spermatogenesis, exchange of chromosomal proteins(GO:0035093)
0.1 0.3 GO:0006651 diacylglycerol biosynthetic process(GO:0006651)
0.1 0.8 GO:0015813 acidic amino acid transport(GO:0015800) aspartate transport(GO:0015810) L-glutamate transport(GO:0015813) malate-aspartate shuttle(GO:0043490)
0.1 0.9 GO:0048096 chromatin-mediated maintenance of transcription(GO:0048096)
0.1 0.6 GO:0003428 growth plate cartilage morphogenesis(GO:0003422) chondrocyte intercalation involved in growth plate cartilage morphogenesis(GO:0003428)
0.1 1.0 GO:0090279 regulation of calcium ion import(GO:0090279)
0.1 0.3 GO:0051561 positive regulation of mitochondrial calcium ion concentration(GO:0051561)
0.0 0.3 GO:0018344 protein geranylgeranylation(GO:0018344)
0.0 2.3 GO:0070830 apical junction assembly(GO:0043297) bicellular tight junction assembly(GO:0070830)
0.0 0.8 GO:0035459 cargo loading into vesicle(GO:0035459)
0.0 0.4 GO:0043328 protein targeting to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway(GO:0043328)
0.0 0.6 GO:0035020 regulation of Rac protein signal transduction(GO:0035020)
0.0 0.2 GO:0006004 fucose metabolic process(GO:0006004)
0.0 0.3 GO:0060004 reflex(GO:0060004) vestibular reflex(GO:0060005)
0.0 1.1 GO:0014866 skeletal myofibril assembly(GO:0014866)
0.0 0.6 GO:0043153 entrainment of circadian clock by photoperiod(GO:0043153)
0.0 0.5 GO:1902285 semaphorin-plexin signaling pathway involved in neuron projection guidance(GO:1902285) semaphorin-plexin signaling pathway involved in axon guidance(GO:1902287)
0.0 0.8 GO:0000413 protein peptidyl-prolyl isomerization(GO:0000413)
0.0 0.3 GO:0009648 photoperiodism(GO:0009648)
0.0 0.6 GO:0097192 signal transduction in absence of ligand(GO:0038034) extrinsic apoptotic signaling pathway in absence of ligand(GO:0097192)
0.0 0.5 GO:0006688 glycosphingolipid biosynthetic process(GO:0006688)
0.0 0.5 GO:0006828 manganese ion transport(GO:0006828)
0.0 0.2 GO:0045670 regulation of osteoclast differentiation(GO:0045670)
0.0 0.3 GO:0014823 response to activity(GO:0014823)
0.0 1.3 GO:0071560 transforming growth factor beta receptor signaling pathway(GO:0007179) response to transforming growth factor beta(GO:0071559) cellular response to transforming growth factor beta stimulus(GO:0071560)
0.0 0.3 GO:0031952 regulation of protein autophosphorylation(GO:0031952)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.5 1.6 GO:0098826 endoplasmic reticulum tubular network membrane(GO:0098826)
0.2 0.7 GO:0000941 condensed nuclear chromosome inner kinetochore(GO:0000941)
0.1 0.5 GO:1990111 spermatoproteasome complex(GO:1990111)
0.1 0.3 GO:0005968 Rab-protein geranylgeranyltransferase complex(GO:0005968)
0.1 0.4 GO:0000814 ESCRT II complex(GO:0000814)
0.1 0.3 GO:1990513 CLOCK-BMAL transcription complex(GO:1990513)
0.0 0.7 GO:0030315 T-tubule(GO:0030315)
0.0 0.8 GO:0070971 endoplasmic reticulum exit site(GO:0070971)
0.0 0.6 GO:0044666 MLL3/4 complex(GO:0044666)
0.0 0.7 GO:0030687 preribosome, large subunit precursor(GO:0030687)
0.0 0.3 GO:0008541 proteasome regulatory particle, lid subcomplex(GO:0008541)
0.0 0.3 GO:1990246 uniplex complex(GO:1990246)
0.0 0.5 GO:0002116 semaphorin receptor complex(GO:0002116)
0.0 0.4 GO:0045180 basal cortex(GO:0045180)
0.0 1.0 GO:0001725 stress fiber(GO:0001725) contractile actin filament bundle(GO:0097517)
0.0 2.3 GO:0005923 bicellular tight junction(GO:0005923) occluding junction(GO:0070160)
0.0 1.1 GO:0005884 actin filament(GO:0005884)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 0.6 GO:0003913 DNA photolyase activity(GO:0003913)
0.2 0.5 GO:0008489 UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity(GO:0008489)
0.1 1.6 GO:0003886 DNA (cytosine-5-)-methyltransferase activity(GO:0003886)
0.1 0.7 GO:0050072 m7G(5')pppN diphosphatase activity(GO:0050072)
0.1 0.3 GO:0004663 Rab geranylgeranyltransferase activity(GO:0004663)
0.1 1.4 GO:0015095 magnesium ion transmembrane transporter activity(GO:0015095)
0.1 0.4 GO:0047429 nucleoside-triphosphate diphosphatase activity(GO:0047429)
0.1 0.8 GO:0015183 L-aspartate transmembrane transporter activity(GO:0015183)
0.1 0.8 GO:0070628 proteasome binding(GO:0070628)
0.1 0.4 GO:0034450 ubiquitin-ubiquitin ligase activity(GO:0034450)
0.0 0.3 GO:0070888 E-box binding(GO:0070888)
0.0 0.7 GO:0004190 aspartic-type endopeptidase activity(GO:0004190) aspartic-type peptidase activity(GO:0070001)
0.0 0.6 GO:0005005 transmembrane-ephrin receptor activity(GO:0005005)
0.0 0.2 GO:0050998 nitric-oxide synthase binding(GO:0050998)
0.0 0.7 GO:0050321 tau-protein kinase activity(GO:0050321)
0.0 1.0 GO:0004435 phosphatidylinositol phospholipase C activity(GO:0004435) phospholipase C activity(GO:0004629)
0.0 6.9 GO:0030246 carbohydrate binding(GO:0030246)
0.0 0.2 GO:0003993 acid phosphatase activity(GO:0003993)
0.0 0.6 GO:0042800 histone methyltransferase activity (H3-K4 specific)(GO:0042800)
0.0 0.5 GO:0015279 store-operated calcium channel activity(GO:0015279)
0.0 0.7 GO:0008574 ATP-dependent microtubule motor activity, plus-end-directed(GO:0008574)
0.0 0.8 GO:0005347 ATP transmembrane transporter activity(GO:0005347)
0.0 0.5 GO:0017154 semaphorin receptor activity(GO:0017154)
0.0 0.6 GO:0004707 MAP kinase activity(GO:0004707)
0.0 0.2 GO:0008417 fucosyltransferase activity(GO:0008417)
0.0 0.3 GO:0019825 oxygen transporter activity(GO:0005344) oxygen binding(GO:0019825)
0.0 0.3 GO:0072542 phosphatase activator activity(GO:0019211) protein phosphatase activator activity(GO:0072542)
0.0 0.3 GO:0016411 acylglycerol O-acyltransferase activity(GO:0016411)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 2.3 PID NECTIN PATHWAY Nectin adhesion pathway
0.1 1.0 PID ECADHERIN KERATINOCYTE PATHWAY E-cadherin signaling in keratinocytes
0.1 1.2 PID AR NONGENOMIC PATHWAY Nongenotropic Androgen signaling
0.0 0.6 PID WNT CANONICAL PATHWAY Canonical Wnt signaling pathway
0.0 0.9 ST G ALPHA I PATHWAY G alpha i Pathway
0.0 1.6 PID RB 1PATHWAY Regulation of retinoblastoma protein
0.0 0.6 PID CDC42 REG PATHWAY Regulation of CDC42 activity
0.0 0.1 PID VEGFR1 PATHWAY VEGFR1 specific signals

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.3 2.3 REACTOME TIGHT JUNCTION INTERACTIONS Genes involved in Tight junction interactions
0.1 1.0 REACTOME REGULATION OF INSULIN SECRETION BY ACETYLCHOLINE Genes involved in Regulation of Insulin Secretion by Acetylcholine
0.1 0.7 REACTOME MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE Genes involved in mRNA Decay by 3' to 5' Exoribonuclease
0.0 1.1 REACTOME SMOOTH MUSCLE CONTRACTION Genes involved in Smooth Muscle Contraction
0.0 0.2 REACTOME RAF MAP KINASE CASCADE Genes involved in RAF/MAP kinase cascade
0.0 0.8 REACTOME GLUCONEOGENESIS Genes involved in Gluconeogenesis
0.0 0.9 REACTOME G ALPHA Z SIGNALLING EVENTS Genes involved in G alpha (z) signalling events
0.0 0.5 REACTOME N GLYCAN ANTENNAE ELONGATION Genes involved in N-Glycan antennae elongation
0.0 0.6 REACTOME O LINKED GLYCOSYLATION OF MUCINS Genes involved in O-linked glycosylation of mucins
0.0 0.4 REACTOME BASIGIN INTERACTIONS Genes involved in Basigin interactions
0.0 0.4 REACTOME ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT ESCRT Genes involved in Endosomal Sorting Complex Required For Transport (ESCRT)
0.0 0.2 REACTOME CELL EXTRACELLULAR MATRIX INTERACTIONS Genes involved in Cell-extracellular matrix interactions