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PRJEB1986: zebrafish developmental stages transcriptome

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Results for hoxc9a

Z-value: 1.22

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Transcription factors associated with hoxc9a

Gene Symbol Gene ID Gene Info
hoxc9a
ENSDARG00000092809 homeobox C9a

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
hoxc9adr11_v1_chr23_+_36095260_36095260-0.436.9e-02Click!

Activity profile of hoxc9a motif

Sorted Z-values of hoxc9a motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr3_-_61205711 7.29 ENSDART00000055062
pvalb1
parvalbumin 1
chr8_+_47633438 5.87 ENSDART00000139096
si:ch211-251b21.1
si:ch211-251b21.1
chr8_+_6954984 5.21 ENSDART00000145610
si:ch211-255g12.6
si:ch211-255g12.6
chr6_-_46875310 4.64 ENSDART00000154442
igfn1.3
immunoglobulin-like and fibronectin type III domain containing 1, tandem duplicate 3
chr8_+_16004154 3.47 ENSDART00000134787
ENSDART00000172510
ENSDART00000141173
elavl4
ELAV like neuron-specific RNA binding protein 4
chr8_+_22931427 3.38 ENSDART00000063096
sypa
synaptophysin a
chr2_+_2223837 3.29 ENSDART00000101038
ENSDART00000129354
tmie
transmembrane inner ear
chr12_+_16440708 3.25 ENSDART00000113810
ankrd1b
ankyrin repeat domain 1b (cardiac muscle)
chr15_-_14375452 3.02 ENSDART00000160675
ENSDART00000164028
ENSDART00000171642
dpf1
D4, zinc and double PHD fingers family 1
chr5_+_36932718 2.96 ENSDART00000037879
crx
cone-rod homeobox
chr10_-_11385155 2.86 ENSDART00000064214
plac8.1
placenta-specific 8, tandem duplicate 1
chr21_-_131236 2.48 ENSDART00000160005
si:ch1073-398f15.1
si:ch1073-398f15.1
chr13_-_43599898 2.38 ENSDART00000084416
ENSDART00000145705
ablim1a
actin binding LIM protein 1a
chr11_-_6188413 2.37 ENSDART00000109972
ccl44
chemokine (C-C motif) ligand 44
chr5_-_51619262 2.31 ENSDART00000134606
ENSDART00000081249
otpb
orthopedia homeobox b
chr12_-_20362041 2.27 ENSDART00000184145
ENSDART00000105952
aqp8a.2
aquaporin 8a, tandem duplicate 2
chr15_+_8043751 2.24 ENSDART00000193701
cadm2b
cell adhesion molecule 2b
chr3_+_34821327 2.12 ENSDART00000055262
cdk5r1a
cyclin-dependent kinase 5, regulatory subunit 1a (p35)
chr10_+_26571174 2.07 ENSDART00000148617
ENSDART00000112956
slc9a6b
solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6b
chr12_+_27213733 1.93 ENSDART00000133048
nbr1a
neighbor of brca1 gene 1a
chr5_-_51619742 1.78 ENSDART00000188537
otpb
orthopedia homeobox b
chr21_+_11969603 1.69 ENSDART00000142247
ENSDART00000140652
mlnl
motilin-like
chr17_+_36627099 1.56 ENSDART00000154104
impg1b
interphotoreceptor matrix proteoglycan 1b
chr16_-_27749172 1.53 ENSDART00000145198
steap4
STEAP family member 4
chr9_+_44722205 1.52 ENSDART00000086176
ENSDART00000145271
ENSDART00000132696
nckap1
NCK-associated protein 1
chr7_+_31879986 1.52 ENSDART00000138491
mybpc3
myosin binding protein C, cardiac
chr1_-_23157583 1.49 ENSDART00000144208
adgrl3.1
adhesion G protein-coupled receptor L3.1
chr17_+_18117029 1.48 ENSDART00000154646
ENSDART00000179739
bcl11ba
B cell CLL/lymphoma 11Ba
chr14_+_21783400 1.47 ENSDART00000164023
ankrd13d
ankyrin repeat domain 13 family, member D
chr25_-_7999756 1.46 ENSDART00000159908
camk1db
calcium/calmodulin-dependent protein kinase 1Db
chr4_+_11439511 1.42 ENSDART00000150485
pcloa
piccolo presynaptic cytomatrix protein a
chr5_+_9408901 1.41 ENSDART00000193364
FP236810.1

chr17_-_51262430 1.41 ENSDART00000163222
trappc12
trafficking protein particle complex 12
chr10_+_439692 1.40 ENSDART00000147740
zdhhc8a
zinc finger, DHHC-type containing 8a
chr6_+_55032439 1.38 ENSDART00000164232
ENSDART00000158845
ENSDART00000157584
ENSDART00000026359
ENSDART00000122794
ENSDART00000183742
mybphb
myosin binding protein Hb
chr2_-_18830722 1.32 ENSDART00000165330
ENSDART00000165698
pbx1a
pre-B-cell leukemia homeobox 1a
chr7_+_31879649 1.29 ENSDART00000099789
mybpc3
myosin binding protein C, cardiac
chr25_-_13842618 1.27 ENSDART00000160258
mapk8ip1a
mitogen-activated protein kinase 8 interacting protein 1a
chr4_+_10017049 1.25 ENSDART00000144175
ccdc136b
coiled-coil domain containing 136b
chr21_-_27338639 1.22 ENSDART00000130632
hif1al2
hypoxia-inducible factor 1, alpha subunit, like 2
chr5_-_11573490 1.19 ENSDART00000109577
FO704871.1

chr15_-_5467477 1.10 ENSDART00000123839
arrb1
arrestin, beta 1
chr20_-_34754617 1.09 ENSDART00000148066
znf395b
zinc finger protein 395b
chr7_-_41964877 1.04 ENSDART00000092351
ENSDART00000193395
ENSDART00000187947
neto2b
neuropilin (NRP) and tolloid (TLL)-like 2b
chr4_-_20235904 1.01 ENSDART00000146621
ENSDART00000193655
stk38l
serine/threonine kinase 38 like
chr25_+_14109626 1.00 ENSDART00000109883
actc1c
actin, alpha, cardiac muscle 1c
chr19_-_36234185 0.93 ENSDART00000186003
csmd2
CUB and Sushi multiple domains 2
chr1_-_681116 0.90 ENSDART00000165894
adamts1
ADAM metallopeptidase with thrombospondin type 1 motif, 1
chr18_-_39288894 0.90 ENSDART00000186216
mapk6
mitogen-activated protein kinase 6
chr1_-_39909985 0.89 ENSDART00000181673
stox2a
storkhead box 2a
chr3_+_40809011 0.87 ENSDART00000033713
arpc1b
actin related protein 2/3 complex, subunit 1B
chr14_+_11762991 0.84 ENSDART00000110004
frmpd3
FERM and PDZ domain containing 3
chr19_-_10425140 0.84 ENSDART00000145319
si:ch211-171h4.3
si:ch211-171h4.3
chr14_-_4044545 0.80 ENSDART00000169527
snx25
sorting nexin 25
chr14_-_31715373 0.77 ENSDART00000127303
ENSDART00000173274
ENSDART00000173435
ENSDART00000172876
ENSDART00000173036
map7d3
MAP7 domain containing 3
chr14_+_35024521 0.76 ENSDART00000158634
ENSDART00000170631
ebf3a
early B cell factor 3a
chr17_+_45454943 0.72 ENSDART00000074838
kcnk3b
potassium channel, subfamily K, member 3b
chr7_-_41693004 0.67 ENSDART00000121509
malrd1
MAM and LDL receptor class A domain containing 1
chr13_+_15004398 0.64 ENSDART00000057810
emx1
empty spiracles homeobox 1
chr10_-_19801821 0.62 ENSDART00000148013
gfra2b
GDNF family receptor alpha 2b
chr15_+_22722684 0.60 ENSDART00000156760
grik4
glutamate receptor, ionotropic, kainate 4
chr1_-_59422880 0.56 ENSDART00000167244
si:ch211-188p14.2
si:ch211-188p14.2
chr3_-_8388344 0.55 ENSDART00000146856
rbfox3b
RNA binding fox-1 homolog 3b
chr19_+_4916233 0.55 ENSDART00000159512
ppp1r1b
protein phosphatase 1, regulatory (inhibitor) subunit 1B
chr1_-_39943596 0.52 ENSDART00000149730
stox2a
storkhead box 2a
chr23_+_20669149 0.51 ENSDART00000138936
arhgef3l
Rho guanine nucleotide exchange factor (GEF) 3, like
chr20_-_36107422 0.49 ENSDART00000146055
ptchd4
patched domain containing 4
chr18_-_26510545 0.48 ENSDART00000135133
FRMD5
si:ch211-69m14.1
chr17_-_20849879 0.47 ENSDART00000088100
ENSDART00000149630
ank3b
ankyrin 3b
chr13_+_40501455 0.47 ENSDART00000114985
hpse2
heparanase 2
chr12_-_6905375 0.46 ENSDART00000152322
pcdh15b
protocadherin-related 15b
chr14_+_36231126 0.45 ENSDART00000141766
elovl6
ELOVL fatty acid elongase 6
chr7_-_31938938 0.45 ENSDART00000132353
bdnf
brain-derived neurotrophic factor
chr25_-_5963535 0.44 ENSDART00000155751
nuak1b
NUAK family, SNF1-like kinase, 1b
chr17_+_26208630 0.43 ENSDART00000087084
grid1a
glutamate receptor, ionotropic, delta 1a
chr1_-_6085750 0.43 ENSDART00000138891
si:ch1073-345a8.1
si:ch1073-345a8.1
chr2_-_41723487 0.43 ENSDART00000170171
zgc:110158
zgc:110158
chr21_-_38853737 0.42 ENSDART00000184100
tlr22
toll-like receptor 22
chr8_-_23701880 0.42 ENSDART00000139897
si:ch73-237c6.1
si:ch73-237c6.1
chr23_+_3721042 0.40 ENSDART00000143323
smim29
small integral membrane protein 29
chr17_+_19626479 0.38 ENSDART00000044993
ENSDART00000131863
rgs7a
regulator of G protein signaling 7a
chr25_+_15997957 0.36 ENSDART00000140047
ppfibp2b
PTPRF interacting protein, binding protein 2b (liprin beta 2)
chr14_-_30141162 0.36 ENSDART00000053916
mtnr1ab
melatonin receptor 1A b
chr6_+_52804267 0.35 ENSDART00000065681
matn4
matrilin 4
chr18_-_2433011 0.34 ENSDART00000181922
ENSDART00000193276
CR769778.1

chr11_-_3334248 0.32 ENSDART00000154314
ENSDART00000121861
prph
peripherin
chr19_+_41006975 0.30 ENSDART00000138555
ENSDART00000049842
casd1
CAS1 domain containing 1
chr10_+_37173029 0.25 ENSDART00000136510
ksr1a
kinase suppressor of ras 1a
chr2_+_10127762 0.25 ENSDART00000100726
insl5b
insulin-like 5b
chr2_-_41723165 0.23 ENSDART00000155577
zgc:110158
zgc:110158
chr10_+_20128267 0.19 ENSDART00000064615
dmtn
dematin actin binding protein
chr17_+_15788100 0.19 ENSDART00000027667
rragd
ras-related GTP binding D
chr7_-_26408472 0.19 ENSDART00000111494
gal3st4
galactose-3-O-sulfotransferase 4
chr23_-_3721444 0.18 ENSDART00000141682
nudt3a
nudix (nucleoside diphosphate linked moiety X)-type motif 3a
chr3_-_37699992 0.18 ENSDART00000151193
gpatch8
G patch domain containing 8
chr17_+_51262556 0.17 ENSDART00000186748
ENSDART00000181606
ENSDART00000063738
ENSDART00000189066
eipr1
EARP complex and GARP complex interacting protein 1
chr14_-_17072736 0.15 ENSDART00000106333
phox2bb
paired-like homeobox 2bb
chr25_-_1720736 0.13 ENSDART00000097256
SLC6A13
solute carrier family 6 member 13
chr11_-_40457325 0.10 ENSDART00000128442
tnfrsf1b
tumor necrosis factor receptor superfamily, member 1B
chr22_+_31330485 0.09 ENSDART00000192585
grip2b
glutamate receptor interacting protein 2b
chr11_+_19159083 0.09 ENSDART00000138964
adamts9
ADAM metallopeptidase with thrombospondin type 1 motif, 9
chr25_+_3058924 0.06 ENSDART00000029580
fth1b
ferritin, heavy polypeptide 1b
chr3_+_25825043 0.03 ENSDART00000153749
pik3r6b
phosphoinositide-3-kinase, regulatory subunit 6b
chr7_+_31051603 0.02 ENSDART00000108721
tjp1a
tight junction protein 1a
chr3_-_51109286 0.02 ENSDART00000172010
si:ch211-148f13.1
si:ch211-148f13.1

Network of associatons between targets according to the STRING database.

First level regulatory network of hoxc9a

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
0.7 4.1 GO:0021767 mammillary body development(GO:0021767)
0.6 2.8 GO:0003210 cardiac atrium formation(GO:0003210)
0.4 1.5 GO:0015677 copper ion import(GO:0015677)
0.3 1.1 GO:1900120 microglial cell activation(GO:0001774) regulation of cytokine activity(GO:0060300) regulation of receptor binding(GO:1900120) regulation of chemokine activity(GO:1900136)
0.2 1.3 GO:0048795 swim bladder morphogenesis(GO:0048795)
0.2 2.1 GO:1990118 sodium ion import(GO:0097369) sodium ion import across plasma membrane(GO:0098719) sodium ion import into cell(GO:1990118)
0.2 3.3 GO:0060088 auditory receptor cell stereocilium organization(GO:0060088)
0.2 1.4 GO:0007084 mitotic nuclear envelope reassembly(GO:0007084)
0.1 1.0 GO:2000312 regulation of kainate selective glutamate receptor activity(GO:2000312)
0.1 1.4 GO:1904071 presynaptic active zone assembly(GO:1904071)
0.1 2.6 GO:0030032 lamellipodium assembly(GO:0030032)
0.1 1.3 GO:2000054 negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification(GO:2000054)
0.1 0.6 GO:0035777 pronephric distal tubule development(GO:0035777)
0.1 2.1 GO:0035622 intrahepatic bile duct development(GO:0035622)
0.1 6.9 GO:0035249 synaptic transmission, glutamatergic(GO:0035249)
0.1 0.5 GO:0050962 detection of light stimulus involved in visual perception(GO:0050908) detection of light stimulus involved in sensory perception(GO:0050962)
0.1 2.4 GO:0048247 lymphocyte chemotaxis(GO:0048247)
0.1 3.0 GO:0042462 eye photoreceptor cell development(GO:0042462)
0.1 0.1 GO:0032292 peripheral nervous system axon ensheathment(GO:0032292)
0.0 1.2 GO:0071456 cellular response to hypoxia(GO:0071456)
0.0 0.9 GO:0002574 thrombocyte differentiation(GO:0002574)
0.0 0.1 GO:0061549 sympathetic ganglion development(GO:0061549)
0.0 0.4 GO:0048672 positive regulation of collateral sprouting(GO:0048672)
0.0 0.2 GO:1901911 diphosphoinositol polyphosphate metabolic process(GO:0071543) diadenosine pentaphosphate metabolic process(GO:1901906) diadenosine pentaphosphate catabolic process(GO:1901907) diadenosine hexaphosphate metabolic process(GO:1901908) diadenosine hexaphosphate catabolic process(GO:1901909) adenosine 5'-(hexahydrogen pentaphosphate) metabolic process(GO:1901910) adenosine 5'-(hexahydrogen pentaphosphate) catabolic process(GO:1901911)
0.0 0.8 GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway(GO:0030512) negative regulation of cellular response to transforming growth factor beta stimulus(GO:1903845)
0.0 1.5 GO:0071391 cellular response to estrogen stimulus(GO:0071391)
0.0 0.8 GO:0000187 activation of MAPK activity(GO:0000187)
0.0 0.7 GO:0030322 stabilization of membrane potential(GO:0030322)
0.0 1.5 GO:0030866 cortical actin cytoskeleton organization(GO:0030866)
0.0 0.4 GO:0034626 fatty acid elongation, saturated fatty acid(GO:0019367) fatty acid elongation, unsaturated fatty acid(GO:0019368) fatty acid elongation, monounsaturated fatty acid(GO:0034625) fatty acid elongation, polyunsaturated fatty acid(GO:0034626)
0.0 1.3 GO:0046328 regulation of JNK cascade(GO:0046328)
0.0 1.7 GO:0019722 calcium-mediated signaling(GO:0019722)
0.0 2.2 GO:0021782 glial cell development(GO:0021782)
0.0 0.5 GO:0035025 positive regulation of Rho protein signal transduction(GO:0035025)
0.0 1.9 GO:0016236 macroautophagy(GO:0016236)
0.0 6.6 GO:0045944 positive regulation of transcription from RNA polymerase II promoter(GO:0045944)
0.0 0.4 GO:0042149 cellular response to glucose starvation(GO:0042149)
0.0 0.2 GO:0071230 cellular response to amino acid stimulus(GO:0071230)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.6 6.5 GO:0032983 kainate selective glutamate receptor complex(GO:0032983)
0.4 2.1 GO:0016533 cyclin-dependent protein kinase 5 holoenzyme complex(GO:0016533)
0.3 1.5 GO:0031258 lamellipodium membrane(GO:0031258)
0.2 1.6 GO:0033165 interphotoreceptor matrix(GO:0033165)
0.1 1.4 GO:0098982 GABA-ergic synapse(GO:0098982)
0.1 3.0 GO:0071565 nBAF complex(GO:0071565)
0.1 1.4 GO:0030008 TRAPP complex(GO:0030008)
0.1 3.5 GO:0043204 perikaryon(GO:0043204)
0.1 1.9 GO:0000407 pre-autophagosomal structure(GO:0000407)
0.0 3.7 GO:0048786 presynaptic active zone(GO:0048786)
0.0 0.9 GO:0005885 Arp2/3 protein complex(GO:0005885)
0.0 2.4 GO:0097517 stress fiber(GO:0001725) contractile actin filament bundle(GO:0097517)
0.0 0.2 GO:0034448 EGO complex(GO:0034448) Gtr1-Gtr2 GTPase complex(GO:1990131)
0.0 0.5 GO:0032420 stereocilium(GO:0032420)
0.0 2.1 GO:0055037 recycling endosome(GO:0055037)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.6 6.5 GO:0015277 kainate selective glutamate receptor activity(GO:0015277)
0.8 3.3 GO:0061629 RNA polymerase II sequence-specific DNA binding transcription factor binding(GO:0061629)
0.4 1.5 GO:0052851 cupric reductase activity(GO:0008823) ferric-chelate reductase (NADPH) activity(GO:0052851)
0.3 2.8 GO:0032036 myosin heavy chain binding(GO:0032036)
0.3 2.3 GO:0015250 water channel activity(GO:0015250)
0.2 0.7 GO:0005252 open rectifier potassium channel activity(GO:0005252)
0.2 2.1 GO:0005451 monovalent cation:proton antiporter activity(GO:0005451) sodium:proton antiporter activity(GO:0015385) potassium:proton antiporter activity(GO:0015386)
0.2 2.1 GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity(GO:0061575)
0.1 1.4 GO:0051721 protein phosphatase 2A binding(GO:0051721)
0.1 3.4 GO:0017075 syntaxin-1 binding(GO:0017075)
0.1 1.4 GO:0098882 structural constituent of presynaptic active zone(GO:0098882)
0.1 0.4 GO:0008502 melatonin receptor activity(GO:0008502)
0.1 2.4 GO:0048020 CCR chemokine receptor binding(GO:0048020)
0.0 0.8 GO:0004708 MAP kinase kinase activity(GO:0004708)
0.0 0.2 GO:0000298 endopolyphosphatase activity(GO:0000298) diphosphoinositol-polyphosphate diphosphatase activity(GO:0008486) bis(5'-adenosyl)-hexaphosphatase activity(GO:0034431) bis(5'-adenosyl)-pentaphosphatase activity(GO:0034432)
0.0 0.4 GO:0005163 nerve growth factor receptor binding(GO:0005163) neurotrophin receptor binding(GO:0005165)
0.0 1.5 GO:0004683 calmodulin-dependent protein kinase activity(GO:0004683)
0.0 0.9 GO:0004707 MAP kinase activity(GO:0004707)
0.0 0.3 GO:0016413 O-acetyltransferase activity(GO:0016413)
0.0 0.4 GO:0102336 fatty acid elongase activity(GO:0009922) 3-oxo-arachidoyl-CoA synthase activity(GO:0102336) 3-oxo-cerotoyl-CoA synthase activity(GO:0102337) 3-oxo-lignoceronyl-CoA synthase activity(GO:0102338)
0.0 0.2 GO:0001733 galactosylceramide sulfotransferase activity(GO:0001733) galactose 3-O-sulfotransferase activity(GO:0050694)
0.0 1.9 GO:0043130 ubiquitin binding(GO:0043130)
0.0 3.0 GO:0001664 G-protein coupled receptor binding(GO:0001664)
0.0 0.5 GO:0004864 protein phosphatase inhibitor activity(GO:0004864)
0.0 0.4 GO:1904315 neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential(GO:0099529) transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential(GO:1904315)
0.0 1.6 GO:0008201 heparin binding(GO:0008201)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 1.1 PID IL8 CXCR1 PATHWAY IL8- and CXCR1-mediated signaling events
0.0 2.4 PID RAC1 PATHWAY RAC1 signaling pathway
0.0 0.1 SA MMP CYTOKINE CONNECTION Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix.
0.0 0.4 PID AJDISS 2PATHWAY Posttranslational regulation of adherens junction stability and dissassembly

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 0.4 REACTOME SYNTHESIS OF VERY LONG CHAIN FATTY ACYL COAS Genes involved in Synthesis of very long-chain fatty acyl-CoAs
0.0 1.1 REACTOME ACTIVATED NOTCH1 TRANSMITS SIGNAL TO THE NUCLEUS Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus
0.0 0.6 REACTOME IONOTROPIC ACTIVITY OF KAINATE RECEPTORS Genes involved in Ionotropic activity of Kainate Receptors
0.0 0.5 REACTOME DARPP 32 EVENTS Genes involved in DARPP-32 events
0.0 0.5 REACTOME HS GAG DEGRADATION Genes involved in HS-GAG degradation