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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Hoxc9

Z-value: 1.09

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Transcription factors associated with Hoxc9

Gene Symbol Gene ID Gene Info
Hoxc9
ENSRNOG00000016199 homeobox C9

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Hoxc9rn6_v1_chr7_+_144595960_1445959600.434.2e-16Click!

Activity profile of Hoxc9 motif

Sorted Z-values of Hoxc9 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr20_+_26999795 53.50 ENSRNOT00000057872
Mypn
myopalladin
chr7_-_29171783 50.68 ENSRNOT00000079235
Mybpc1
myosin binding protein C, slow type
chr19_+_50848736 45.04 ENSRNOT00000077053
Cdh13
cadherin 13
chr10_-_8498422 43.99 ENSRNOT00000082332
Rbfox1
RNA binding protein, fox-1 homolog 1
chr17_-_78735324 37.71 ENSRNOT00000036299
Cdnf
cerebral dopamine neurotrophic factor
chr1_-_215838209 37.68 ENSRNOT00000050760
Igf2
insulin-like growth factor 2
chr1_+_167870452 34.32 ENSRNOT00000025027
Olr63
olfactory receptor 63
chr8_+_64481172 34.11 ENSRNOT00000015332
Pkm
pyruvate kinase, muscle
chr13_+_106463368 32.37 ENSRNOT00000003489
Esrrg
estrogen-related receptor gamma
chr7_-_130120579 31.89 ENSRNOT00000044376
Mapk12
mitogen-activated protein kinase 12
chrX_-_142248369 27.93 ENSRNOT00000091330
Fgf13
fibroblast growth factor 13
chr8_+_119228612 27.40 ENSRNOT00000078439
ENSRNOT00000043737
Lrrc2
leucine rich repeat containing 2
chr3_-_23020441 25.73 ENSRNOT00000017651
Nr5a1
nuclear receptor subfamily 5, group A, member 1
chr12_+_27155587 22.06 ENSRNOT00000044800
AABR07035916.1

chr20_-_25826658 21.08 ENSRNOT00000057950
ENSRNOT00000084660
Ctnna3
catenin alpha 3
chr1_+_201055644 20.98 ENSRNOT00000054937
ENSRNOT00000047161
Tacc2
transforming, acidic coiled-coil containing protein 2
chr16_+_8207223 18.74 ENSRNOT00000026751
Oxnad1
oxidoreductase NAD-binding domain containing 1
chr16_+_22361998 18.70 ENSRNOT00000016193
Slc18a1
solute carrier family 18 member A1
chrX_+_119390013 18.59 ENSRNOT00000074269
Agtr2
angiotensin II receptor, type 2
chr13_-_36290531 18.44 ENSRNOT00000071388
Steap3
STEAP3 metalloreductase
chrX_+_136460215 17.02 ENSRNOT00000093538
Arhgap36
Rho GTPase activating protein 36
chr8_+_130350510 16.45 ENSRNOT00000073376
Ss18l2
SS18 like 2
chr19_-_37427989 15.32 ENSRNOT00000022863
Tppp3
tubulin polymerization-promoting protein family member 3
chr1_-_56683731 15.14 ENSRNOT00000014552
Thbs2
thrombospondin 2
chr18_+_61261418 14.71 ENSRNOT00000064250
Zfp532
zinc finger protein 532
chr10_-_85974644 13.88 ENSRNOT00000006098
ENSRNOT00000082974
Cacnb1
calcium voltage-gated channel auxiliary subunit beta 1
chr2_+_233602732 13.10 ENSRNOT00000044232
Pitx2
paired-like homeodomain 2
chr2_-_96032722 12.95 ENSRNOT00000015746
LOC100360846
proteasome subunit beta type 6-like
chr7_+_123578878 12.20 ENSRNOT00000011316
Smdt1
single-pass membrane protein with aspartate-rich tail 1
chr8_+_36625733 11.11 ENSRNOT00000016248
Cdon
cell adhesion associated, oncogene regulated
chr1_+_201620642 10.88 ENSRNOT00000093674
Dmbt1
deleted in malignant brain tumors 1
chr9_-_52238564 8.76 ENSRNOT00000005073
Col5a2
collagen type V alpha 2 chain
chr3_+_14889510 8.68 ENSRNOT00000080760
Dab2ip
DAB2 interacting protein
chr11_-_60679555 8.46 ENSRNOT00000059735
Ccdc80
coiled-coil domain containing 80
chr15_+_34234755 7.59 ENSRNOT00000059987
Dcaf11
DDB1 and CUL4 associated factor 11
chr15_+_34234193 7.28 ENSRNOT00000077584
Dcaf11
DDB1 and CUL4 associated factor 11
chr1_+_41323194 6.68 ENSRNOT00000026350
Esr1
estrogen receptor 1
chr6_-_25507073 6.06 ENSRNOT00000061176
Plb1
phospholipase B1
chr1_-_7480825 5.02 ENSRNOT00000048754
Phactr2
phosphatase and actin regulator 2
chr6_-_123577695 4.79 ENSRNOT00000006604
Foxn3
forkhead box N3
chr1_+_79754587 4.63 ENSRNOT00000083211
Micb
MHC class I polypeptide-related sequence B
chr3_-_103128243 4.26 ENSRNOT00000046310
Olr779
olfactory receptor 779
chr3_-_103400272 4.05 ENSRNOT00000046527
Olr790
olfactory receptor 790
chr5_+_154489590 4.02 ENSRNOT00000035788
Id3
inhibitor of DNA binding 3, HLH protein
chr10_+_103874383 3.96 ENSRNOT00000038935
Otop2
otopetrin 2
chr18_-_24823837 3.38 ENSRNOT00000021405
ENSRNOT00000090390
Myo7b
myosin VIIb
chr1_-_140860882 3.25 ENSRNOT00000067889
ENSRNOT00000024253
ENSRNOT00000079100
Mfge8
milk fat globule-EGF factor 8 protein
chr3_-_103447716 3.09 ENSRNOT00000074196
Olr791
olfactory receptor 791
chr5_-_128839433 3.04 ENSRNOT00000065280
Osbpl9
oxysterol binding protein-like 9
chr3_-_103152122 3.02 ENSRNOT00000045743
Olr781
olfactory receptor 781
chr2_+_23257915 2.96 ENSRNOT00000080942
AABR07007675.1

chrX_+_15113878 2.94 ENSRNOT00000007464
Wdr13
WD repeat domain 13
chr15_-_36321572 2.89 ENSRNOT00000073934
AABR07018016.1

chr13_-_61306939 2.88 ENSRNOT00000086610
Rgs21
regulator of G-protein signaling 21
chr3_-_103485806 2.71 ENSRNOT00000072524
Olr789
olfactory receptor 789
chr2_-_236149971 2.33 ENSRNOT00000089472
AABR07013412.1

chr4_-_119399130 2.27 ENSRNOT00000042796
Vom1r101
vomeronasal 1 receptor 101
chr8_-_63291966 2.15 ENSRNOT00000077762
AABR07070278.1

chr6_-_33691301 2.00 ENSRNOT00000008008
Rhob
ras homolog family member B
chr1_-_200548317 2.00 ENSRNOT00000088610
AABR07005806.1

chr1_-_155955173 1.82 ENSRNOT00000079345
AABR07004776.1

chr7_+_42304534 1.58 ENSRNOT00000085097
Kitlg
KIT ligand
chr20_-_27083410 1.58 ENSRNOT00000000432
Atoh7
atonal bHLH transcription factor 7
chr17_+_41798783 1.36 ENSRNOT00000023519
Nrsn1
neurensin 1
chr4_+_133540540 0.92 ENSRNOT00000073232
AABR07061556.1

chr2_+_66940057 0.64 ENSRNOT00000043050
Cdh9
cadherin 9
chr11_-_37253776 0.53 ENSRNOT00000002215
Dscam
DS cell adhesion molecule
chr4_-_18396035 0.48 ENSRNOT00000034692
Sema3a
semaphorin 3A
chr10_-_88107232 0.44 ENSRNOT00000019330
ENSRNOT00000076770
Krt9
keratin 9
chr2_-_140334912 0.24 ENSRNOT00000015067
Elf2
E74-like factor 2
chr2_-_173087648 0.22 ENSRNOT00000091079
Iqcj
IQ motif containing J
chr15_-_27001826 0.20 ENSRNOT00000016693
Olr1608
olfactory receptor 1608
chr4_-_85329362 0.18 ENSRNOT00000014925
Crhr2
corticotropin releasing hormone receptor 2

Network of associatons between targets according to the STRING database.

First level regulatory network of Hoxc9

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
6.4 25.7 GO:2000195 negative regulation of female gonad development(GO:2000195)
6.2 18.6 GO:0007199 G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger(GO:0007199) regulation of metanephros size(GO:0035566)
6.1 18.4 GO:1902167 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator(GO:1902167)
5.6 45.0 GO:0055095 lipoprotein particle mediated signaling(GO:0055095) low-density lipoprotein particle mediated signaling(GO:0055096)
5.4 37.7 GO:0038028 insulin receptor signaling pathway via phosphatidylinositol 3-kinase(GO:0038028)
5.1 50.7 GO:0071688 striated muscle myosin thick filament assembly(GO:0071688)
4.9 53.5 GO:0048739 cardiac muscle fiber development(GO:0048739)
4.4 13.1 GO:0021539 subthalamus development(GO:0021539) deltoid tuberosity development(GO:0035993) pulmonary vein morphogenesis(GO:0060577)
4.0 27.9 GO:0045200 establishment or maintenance of neuroblast polarity(GO:0045196) establishment of neuroblast polarity(GO:0045200)
3.7 18.7 GO:0051581 negative regulation of neurotransmitter uptake(GO:0051581) regulation of serotonin uptake(GO:0051611) negative regulation of serotonin uptake(GO:0051612)
3.4 34.1 GO:0042866 pyruvate biosynthetic process(GO:0042866)
2.6 21.1 GO:0086073 cardiac muscle cell-cardiac muscle cell adhesion(GO:0086042) bundle of His cell-Purkinje myocyte adhesion involved in cell communication(GO:0086073)
2.2 11.1 GO:0014816 skeletal muscle satellite cell differentiation(GO:0014816)
2.2 8.8 GO:1903225 negative regulation of endodermal cell differentiation(GO:1903225)
2.2 8.7 GO:0036324 vascular endothelial growth factor receptor-2 signaling pathway(GO:0036324)
1.8 44.0 GO:2001014 regulation of skeletal muscle cell differentiation(GO:2001014)
1.7 6.7 GO:1990375 baculum development(GO:1990375)
1.6 21.0 GO:0022027 interkinetic nuclear migration(GO:0022027)
1.2 12.2 GO:0036444 calcium ion transmembrane import into mitochondrion(GO:0036444)
0.8 37.7 GO:0071542 dopaminergic neuron differentiation(GO:0071542)
0.8 32.4 GO:0048384 retinoic acid receptor signaling pathway(GO:0048384)
0.7 3.4 GO:1904970 brush border assembly(GO:1904970)
0.6 6.1 GO:2000344 positive regulation of acrosome reaction(GO:2000344)
0.5 10.9 GO:0001833 inner cell mass cell proliferation(GO:0001833)
0.4 3.2 GO:2000427 positive regulation of apoptotic cell clearance(GO:2000427)
0.3 1.6 GO:0070668 negative regulation of mast cell apoptotic process(GO:0033026) mast cell proliferation(GO:0070662) regulation of mast cell proliferation(GO:0070666) positive regulation of mast cell proliferation(GO:0070668)
0.3 13.9 GO:1901385 regulation of voltage-gated calcium channel activity(GO:1901385)
0.2 2.9 GO:0061469 regulation of type B pancreatic cell proliferation(GO:0061469)
0.2 4.8 GO:0097094 craniofacial suture morphogenesis(GO:0097094)
0.2 15.3 GO:0046785 microtubule polymerization(GO:0046785)
0.2 0.5 GO:0060060 post-embryonic retina morphogenesis in camera-type eye(GO:0060060)
0.2 4.0 GO:0030903 notochord development(GO:0030903)
0.2 15.1 GO:0051965 positive regulation of synapse assembly(GO:0051965)
0.1 2.3 GO:0019236 response to pheromone(GO:0019236)
0.1 13.2 GO:0045445 myoblast differentiation(GO:0045445)
0.1 1.6 GO:0021554 optic nerve development(GO:0021554)
0.1 0.5 GO:0021886 cerebral cortex tangential migration using cell-axon interactions(GO:0021824) gonadotrophin-releasing hormone neuronal migration to the hypothalamus(GO:0021828) hypothalamic tangential migration using cell-axon interactions(GO:0021856) hypothalamus gonadotrophin-releasing hormone neuron differentiation(GO:0021886) hypothalamus gonadotrophin-releasing hormone neuron development(GO:0021888) cranial ganglion development(GO:0061550) trigeminal ganglion development(GO:0061551) facioacoustic ganglion development(GO:1903375)
0.1 2.0 GO:0061154 endothelial tube morphogenesis(GO:0061154)
0.1 8.5 GO:0010811 positive regulation of cell-substrate adhesion(GO:0010811)
0.0 0.2 GO:2000293 regulation of defecation(GO:2000292) negative regulation of defecation(GO:2000293)
0.0 51.1 GO:0050911 detection of chemical stimulus involved in sensory perception of smell(GO:0050911)
0.0 4.6 GO:0019882 antigen processing and presentation(GO:0019882)
0.0 0.4 GO:0045109 intermediate filament organization(GO:0045109)
0.0 13.0 GO:0051603 proteolysis involved in cellular protein catabolic process(GO:0051603)
0.0 18.7 GO:0055114 oxidation-reduction process(GO:0055114)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
4.2 50.7 GO:0005859 muscle myosin complex(GO:0005859)
2.9 8.7 GO:1990032 parallel fiber(GO:1990032)
2.2 8.8 GO:0005588 collagen type V trimer(GO:0005588)
2.0 12.2 GO:1990246 uniplex complex(GO:1990246)
1.1 21.1 GO:0005916 fascia adherens(GO:0005916)
0.7 6.7 GO:0097550 transcriptional preinitiation complex(GO:0097550)
0.6 15.1 GO:0031091 platelet alpha granule(GO:0031091)
0.6 10.9 GO:0042589 zymogen granule membrane(GO:0042589)
0.5 13.0 GO:0005839 proteasome core complex(GO:0005839)
0.5 14.9 GO:0080008 Cul4-RING E3 ubiquitin ligase complex(GO:0080008)
0.5 18.4 GO:0005771 multivesicular body(GO:0005771)
0.5 8.5 GO:0005614 interstitial matrix(GO:0005614)
0.5 27.9 GO:0016328 lateral plasma membrane(GO:0016328)
0.4 44.0 GO:0005901 caveola(GO:0005901)
0.4 13.9 GO:0005891 voltage-gated calcium channel complex(GO:0005891)
0.4 53.5 GO:0030018 Z disc(GO:0030018)
0.3 4.6 GO:0031362 anchored component of external side of plasma membrane(GO:0031362)
0.2 25.7 GO:0090575 RNA polymerase II transcription factor complex(GO:0090575)
0.2 30.8 GO:0005802 trans-Golgi network(GO:0005802)
0.1 34.1 GO:0061695 transferase complex, transferring phosphorus-containing groups(GO:0061695)
0.1 6.1 GO:0031526 brush border membrane(GO:0031526)
0.1 3.4 GO:0016459 myosin complex(GO:0016459)
0.1 18.7 GO:0030659 cytoplasmic vesicle membrane(GO:0030659)
0.1 13.1 GO:0005667 transcription factor complex(GO:0005667)
0.0 2.0 GO:0097610 cleavage furrow(GO:0032154) cell surface furrow(GO:0097610)
0.0 13.7 GO:0005874 microtubule(GO:0005874)
0.0 1.4 GO:0030426 growth cone(GO:0030426)
0.0 43.7 GO:0005615 extracellular space(GO:0005615)
0.0 47.0 GO:0005739 mitochondrion(GO:0005739)
0.0 0.2 GO:0070852 cell body fiber(GO:0070852)
0.0 75.5 GO:0005886 plasma membrane(GO:0005886)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
11.3 45.0 GO:0055100 adiponectin binding(GO:0055100)
8.5 34.1 GO:0004743 pyruvate kinase activity(GO:0004743)
8.1 32.4 GO:0050682 AF-2 domain binding(GO:0050682)
6.5 104.2 GO:0051371 muscle alpha-actinin binding(GO:0051371)
6.2 18.7 GO:0015222 serotonin transmembrane transporter activity(GO:0015222)
4.6 18.4 GO:0000293 ferric-chelate reductase activity(GO:0000293)
3.7 18.6 GO:0004945 angiotensin type II receptor activity(GO:0004945)
2.3 21.1 GO:0086080 protein binding involved in heterotypic cell-cell adhesion(GO:0086080)
2.0 6.1 GO:0050253 retinyl-palmitate esterase activity(GO:0050253)
1.6 10.9 GO:0035375 zymogen binding(GO:0035375)
1.4 8.7 GO:0035662 Toll-like receptor 4 binding(GO:0035662)
1.4 31.7 GO:0005159 insulin-like growth factor receptor binding(GO:0005159)
1.3 6.7 GO:0031798 type 1 metabotropic glutamate receptor binding(GO:0031798)
1.1 31.9 GO:0004707 MAP kinase activity(GO:0004707)
0.7 13.9 GO:0008331 high voltage-gated calcium channel activity(GO:0008331)
0.6 27.9 GO:0048487 beta-tubulin binding(GO:0048487)
0.5 13.0 GO:0070003 threonine-type endopeptidase activity(GO:0004298) threonine-type peptidase activity(GO:0070003)
0.4 25.7 GO:0004879 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding(GO:0004879) transcription factor activity, direct ligand regulated sequence-specific DNA binding(GO:0098531)
0.3 3.2 GO:0008429 phosphatidylethanolamine binding(GO:0008429)
0.3 13.1 GO:0001102 RNA polymerase II activating transcription factor binding(GO:0001102)
0.2 8.5 GO:0001968 fibronectin binding(GO:0001968)
0.2 1.6 GO:0005173 stem cell factor receptor binding(GO:0005173)
0.2 31.4 GO:0008083 growth factor activity(GO:0008083)
0.2 4.0 GO:0043425 bHLH transcription factor binding(GO:0043425)
0.2 5.0 GO:0004864 protein phosphatase inhibitor activity(GO:0004864)
0.2 21.0 GO:0035257 nuclear hormone receptor binding(GO:0035257)
0.2 41.9 GO:0008022 protein C-terminus binding(GO:0008022)
0.2 8.8 GO:0005201 extracellular matrix structural constituent(GO:0005201)
0.1 2.9 GO:1990841 promoter-specific chromatin binding(GO:1990841)
0.1 16.5 GO:0003713 transcription coactivator activity(GO:0003713)
0.1 4.6 GO:0003823 antigen binding(GO:0003823)
0.0 0.2 GO:0015056 corticotrophin-releasing factor receptor activity(GO:0015056) corticotropin-releasing hormone receptor activity(GO:0043404)
0.0 0.5 GO:0045499 chemorepellent activity(GO:0045499)
0.0 3.4 GO:0003774 motor activity(GO:0003774)
0.0 5.7 GO:0008201 heparin binding(GO:0008201)
0.0 51.1 GO:0004984 olfactory receptor activity(GO:0004984)
0.0 10.2 GO:0015631 tubulin binding(GO:0015631)
0.0 2.0 GO:0019003 GDP binding(GO:0019003)
0.0 18.7 GO:0016491 oxidoreductase activity(GO:0016491)
0.0 2.3 GO:0016503 pheromone receptor activity(GO:0016503)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
2.5 31.9 PID P38 GAMMA DELTA PATHWAY Signaling mediated by p38-gamma and p38-delta
0.5 36.7 PID AJDISS 2PATHWAY Posttranslational regulation of adherens junction stability and dissassembly
0.5 11.1 PID HEDGEHOG 2PATHWAY Signaling events mediated by the Hedgehog family
0.4 13.1 ST MYOCYTE AD PATHWAY Myocyte Adrenergic Pathway is a specific case of the generalized Adrenergic Pathway.
0.4 15.1 PID INTEGRIN A4B1 PATHWAY Alpha4 beta1 integrin signaling events
0.2 8.7 PID RAS PATHWAY Regulation of Ras family activation
0.2 6.7 PID ER NONGENOMIC PATHWAY Plasma membrane estrogen receptor signaling
0.1 8.8 PID INTEGRIN1 PATHWAY Beta1 integrin cell surface interactions
0.1 18.4 PID P53 DOWNSTREAM PATHWAY Direct p53 effectors
0.1 3.2 PID TAP63 PATHWAY Validated transcriptional targets of TAp63 isoforms
0.1 21.4 NABA SECRETED FACTORS Genes encoding secreted soluble factors
0.1 10.9 NABA ECM GLYCOPROTEINS Genes encoding structural ECM glycoproteins
0.0 2.0 PID P75 NTR PATHWAY p75(NTR)-mediated signaling
0.0 0.5 PID HNF3A PATHWAY FOXA1 transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
2.1 31.9 REACTOME P38MAPK EVENTS Genes involved in p38MAPK events
1.8 37.7 REACTOME REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS Genes involved in Regulation of Insulin-like Growth Factor (IGF) Activity by Insulin-like Growth Factor Binding Proteins (IGFBPs)
1.3 50.7 REACTOME STRIATED MUSCLE CONTRACTION Genes involved in Striated Muscle Contraction
1.3 36.1 REACTOME ADHERENS JUNCTIONS INTERACTIONS Genes involved in Adherens junctions interactions
0.9 64.8 REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY Genes involved in Nuclear Receptor transcription pathway
0.8 18.7 REACTOME NA CL DEPENDENT NEUROTRANSMITTER TRANSPORTERS Genes involved in Na+/Cl- dependent neurotransmitter transporters
0.6 18.4 REACTOME TRANSFERRIN ENDOCYTOSIS AND RECYCLING Genes involved in Transferrin endocytosis and recycling
0.4 11.1 REACTOME MYOGENESIS Genes involved in Myogenesis
0.4 16.3 REACTOME NCAM1 INTERACTIONS Genes involved in NCAM1 interactions
0.1 15.1 REACTOME SIGNALING BY PDGF Genes involved in Signaling by PDGF
0.1 21.5 REACTOME G ALPHA I SIGNALLING EVENTS Genes involved in G alpha (i) signalling events
0.1 2.0 REACTOME GPVI MEDIATED ACTIVATION CASCADE Genes involved in GPVI-mediated activation cascade
0.1 1.6 REACTOME REGULATION OF KIT SIGNALING Genes involved in Regulation of KIT signaling
0.1 11.2 REACTOME SIGNALING BY RHO GTPASES Genes involved in Signaling by Rho GTPases
0.1 3.2 REACTOME AMYLOIDS Genes involved in Amyloids
0.1 0.5 REACTOME DSCAM INTERACTIONS Genes involved in DSCAM interactions
0.0 0.5 REACTOME SEMA3A PLEXIN REPULSION SIGNALING BY INHIBITING INTEGRIN ADHESION Genes involved in SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion