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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Msx2_Hoxd4

Z-value: 0.35

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Transcription factors associated with Msx2_Hoxd4

Gene Symbol Gene ID Gene Info
Msx2
ENSRNOG00000018355 msh homeobox 2
Hoxd4
ENSRNOG00000001578 homeo box D4

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Msx2rn6_v1_chr17_+_11683862_116838620.486.5e-20Click!

Activity profile of Msx2_Hoxd4 motif

Sorted Z-values of Msx2_Hoxd4 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr8_-_47094352 11.65 ENSRNOT00000048347
Grik4
glutamate ionotropic receptor kainate type subunit 4
chr20_-_25826658 7.78 ENSRNOT00000057950
ENSRNOT00000084660
Ctnna3
catenin alpha 3
chr6_+_64789940 7.67 ENSRNOT00000085979
ENSRNOT00000059739
ENSRNOT00000051908
ENSRNOT00000082793
ENSRNOT00000078583
ENSRNOT00000091677
ENSRNOT00000093241
Nrcam
neuronal cell adhesion molecule
chr15_-_71779033 6.14 ENSRNOT00000017765
Pcdh20
protocadherin 20
chr7_+_44009069 5.94 ENSRNOT00000005523
Mgat4c
MGAT4 family, member C
chr4_-_64330996 5.82 ENSRNOT00000016088
Ptn
pleiotrophin
chrX_+_84064427 5.51 ENSRNOT00000046364
Zfp711
zinc finger protein 711
chr11_+_61605937 4.85 ENSRNOT00000093455
ENSRNOT00000093242
Gramd1c
GRAM domain containing 1C
chr5_-_168734296 4.59 ENSRNOT00000066120
Camta1
calmodulin binding transcription activator 1
chr2_-_35104963 4.56 ENSRNOT00000018058
Rgs7bp
regulator of G-protein signaling 7-binding protein
chr9_+_73418607 4.42 ENSRNOT00000092547
Map2
microtubule-associated protein 2
chr9_-_30844199 4.35 ENSRNOT00000017169
Col19a1
collagen type XIX alpha 1 chain
chr7_-_69982592 3.90 ENSRNOT00000040010
RGD1564306
similar to developmental pluripotency associated 5
chr3_+_61613774 3.59 ENSRNOT00000002148
Hoxd10
homeo box D10
chr1_+_47032113 3.41 ENSRNOT00000024412
Tulp4
tubby like protein 4
chr3_-_52447622 3.20 ENSRNOT00000083552
Scn1a
sodium voltage-gated channel alpha subunit 1
chr12_+_39423596 3.01 ENSRNOT00000066952
Ift81
intraflagellar transport 81
chrX_+_908044 2.96 ENSRNOT00000072087
Zfp300
zinc finger protein 300
chr3_-_25212049 2.91 ENSRNOT00000040023
Lrp1b
LDL receptor related protein 1B
chr18_+_54108493 2.80 ENSRNOT00000029239
RGD1312005
similar to DD1
chr13_-_76049363 2.70 ENSRNOT00000075865
ENSRNOT00000007455
Brinp2
BMP/retinoic acid inducible neural specific 2
chr5_+_104698040 2.61 ENSRNOT00000009127
Adamtsl1
ADAMTS-like 1
chr11_-_782954 2.59 ENSRNOT00000040065
Epha3
Eph receptor A3
chr2_+_127489771 2.49 ENSRNOT00000093581
Intu
inturned planar cell polarity protein
chr20_+_25990656 2.39 ENSRNOT00000081254
Lrrtm3
leucine rich repeat transmembrane neuronal 3
chr6_-_76552559 2.38 ENSRNOT00000065230
Ralgapa1
Ral GTPase activating protein catalytic alpha subunit 1
chr2_-_210766501 2.38 ENSRNOT00000025800
Gstm3
glutathione S-transferase mu 3
chr13_-_86671515 2.31 ENSRNOT00000082869
AABR07021704.1

chr18_-_26656879 2.06 ENSRNOT00000086729
Epb41l4a
erythrocyte membrane protein band 4.1 like 4A
chr13_-_27192592 1.95 ENSRNOT00000040021
Serpinb3
serpin family B member 3
chr4_+_24222500 1.80 ENSRNOT00000045346
Zfp804b
zinc finger protein 804B
chr9_-_63641400 1.75 ENSRNOT00000087684
Satb2
SATB homeobox 2
chr2_-_181531978 1.64 ENSRNOT00000072029
Npy2r
neuropeptide Y receptor Y2
chr10_+_65733991 1.62 ENSRNOT00000013698
Slc46a1
solute carrier family 46 member 1
chr15_+_32894938 1.48 ENSRNOT00000012837
Abhd4
abhydrolase domain containing 4
chr12_-_35979193 1.46 ENSRNOT00000071104
Tmem132b
transmembrane protein 132B
chr13_+_46169963 1.34 ENSRNOT00000005212
Thsd7b
thrombospondin type 1 domain containing 7B
chr15_+_56666012 1.32 ENSRNOT00000013408
Htr2a
5-hydroxytryptamine receptor 2A
chr4_+_31333970 1.29 ENSRNOT00000064866
LOC100911994
coiled-coil domain-containing protein 132-like
chr7_+_35773928 1.23 ENSRNOT00000034639
Cep83
centrosomal protein 83
chr5_-_128446725 1.20 ENSRNOT00000011272
Btf3l4
basic transcription factor 3-like 4
chr8_-_43192910 1.02 ENSRNOT00000060101
Olr1302
olfactory receptor 1302
chr9_+_10941613 1.01 ENSRNOT00000070794
Sema6b
semaphorin 6B
chr7_-_143392777 1.00 ENSRNOT00000086504
ENSRNOT00000038105
Krt72
keratin 72
chr8_+_56585396 0.95 ENSRNOT00000085316
ENSRNOT00000034924
Rdx
radixin
chr10_-_87232723 0.90 ENSRNOT00000015150
Krt25
keratin 25
chr6_-_94834908 0.85 ENSRNOT00000006284
L3hypdh
trans-L-3-hydroxyproline dehydratase
chr2_+_196013799 0.85 ENSRNOT00000084023
Pogz
pogo transposable element with ZNF domain
chr2_+_72006099 0.84 ENSRNOT00000034044
Cdh12
cadherin 12
chr16_-_24951612 0.80 ENSRNOT00000018987
Tktl2
transketolase-like 2
chr4_-_157304653 0.77 ENSRNOT00000051613
Lrrc23
leucine rich repeat containing 23
chr19_-_22194740 0.76 ENSRNOT00000086187
Phkb
phosphorylase kinase regulatory subunit beta
chr2_-_185005572 0.69 ENSRNOT00000093291
Fam160a1
family with sequence similarity 160, member A1
chr2_+_154604832 0.64 ENSRNOT00000013777
Vom2r44
vomeronasal 2 receptor 44
chr8_+_43705216 0.62 ENSRNOT00000090425
AC115384.1

chr4_-_78879294 0.59 ENSRNOT00000084543
Igf2bp3
insulin-like growth factor 2 mRNA binding protein 3
chrX_-_106607352 0.58 ENSRNOT00000082858
AABR07040624.1

chr1_+_150310319 0.55 ENSRNOT00000042081
Olr34
olfactory receptor 34
chr6_+_101532518 0.47 ENSRNOT00000075054
Gphn
gephyrin
chr8_+_43747548 0.45 ENSRNOT00000092067
Olr1327
olfactory receptor 1327
chr19_+_25043680 0.44 ENSRNOT00000043971
Adgrl1
adhesion G protein-coupled receptor L1
chr19_+_43163129 0.44 ENSRNOT00000073721
Clec18a
C-type lectin domain family 18, member A
chr13_+_90533365 0.43 ENSRNOT00000082469
Dcaf8
DDB1 and CUL4 associated factor 8
chr1_+_279633671 0.35 ENSRNOT00000036012
ENSRNOT00000091669
Ccdc172
coiled-coil domain containing 172
chr13_-_32427177 0.35 ENSRNOT00000044628
Cdh19
cadherin 19
chr2_-_33025271 0.35 ENSRNOT00000074941
NEWGENE_1310139
microtubule associated serine/threonine kinase family member 4
chr6_-_99214251 0.34 ENSRNOT00000042682
Esr2
estrogen receptor 2
chr4_-_129619142 0.32 ENSRNOT00000047453
Lmod3
leiomodin 3
chr1_+_169115981 0.25 ENSRNOT00000067478
Olr135
olfactory receptor 135
chr7_+_122818975 0.22 ENSRNOT00000000206
Ep300
E1A binding protein p300
chr1_+_79474809 0.17 ENSRNOT00000044927
Ceacam12
carcinoembryonic antigen-related cell adhesion molecule 12
chr1_+_168390615 0.13 ENSRNOT00000039822
Olr87
olfactory receptor 87
chr17_+_45670284 0.13 ENSRNOT00000086536
Olr1660
olfactory receptor 1660
chr6_-_146902339 0.12 ENSRNOT00000050893
Abcb5
ATP binding cassette subfamily B member 5
chr3_-_74014795 0.11 ENSRNOT00000073426
Olr516
olfactory receptor 516
chr7_-_143408276 0.09 ENSRNOT00000013122
ENSRNOT00000091540
Krt73
keratin 73
chr19_+_32308236 0.09 ENSRNOT00000015508
Mmaa
methylmalonic aciduria (cobalamin deficiency) cblA type
chr4_+_8066737 0.07 ENSRNOT00000063994
Srpk2
SRSF protein kinase 2
chr1_-_56683731 0.01 ENSRNOT00000014552
Thbs2
thrombospondin 2

Network of associatons between targets according to the STRING database.

First level regulatory network of Msx2_Hoxd4

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
1.5 5.8 GO:1904373 retinal rod cell differentiation(GO:0060221) response to kainic acid(GO:1904373) positive regulation of skeletal muscle acetylcholine-gated channel clustering(GO:1904395)
1.0 7.8 GO:0086073 bundle of His cell-Purkinje myocyte adhesion involved in cell communication(GO:0086073)
0.9 2.6 GO:0097156 fasciculation of motor neuron axon(GO:0097156)
0.9 7.7 GO:0045162 clustering of voltage-gated sodium channels(GO:0045162)
0.8 2.4 GO:0018916 nitrobenzene metabolic process(GO:0018916)
0.6 1.9 GO:0035425 autocrine signaling(GO:0035425)
0.4 1.3 GO:0007208 phospholipase C-activating serotonin receptor signaling pathway(GO:0007208)
0.4 1.6 GO:0051958 methotrexate transport(GO:0051958)
0.4 2.5 GO:0035735 intraciliary transport involved in cilium morphogenesis(GO:0035735)
0.3 3.2 GO:0019227 neuronal action potential propagation(GO:0019227) action potential propagation(GO:0098870)
0.3 11.6 GO:0035235 ionotropic glutamate receptor signaling pathway(GO:0035235)
0.3 3.6 GO:0048935 peripheral nervous system neuron differentiation(GO:0048934) peripheral nervous system neuron development(GO:0048935)
0.2 1.2 GO:0051660 establishment of centrosome localization(GO:0051660)
0.2 1.6 GO:0090394 negative regulation of excitatory postsynaptic potential(GO:0090394)
0.2 2.4 GO:1902993 positive regulation of beta-amyloid formation(GO:1902004) positive regulation of amyloid precursor protein catabolic process(GO:1902993)
0.2 1.0 GO:1902966 regulation of protein localization to early endosome(GO:1902965) positive regulation of protein localization to early endosome(GO:1902966)
0.2 1.7 GO:0021902 commitment of neuronal cell to specific neuron type in forebrain(GO:0021902)
0.1 2.1 GO:0010839 negative regulation of keratinocyte proliferation(GO:0010839)
0.1 0.5 GO:0098953 receptor diffusion trapping(GO:0098953) postsynaptic neurotransmitter receptor diffusion trapping(GO:0098970) neurotransmitter receptor diffusion trapping(GO:0099628) protein localization to postsynaptic specialization membrane(GO:0099633) neurotransmitter receptor localization to postsynaptic specialization membrane(GO:0099645)
0.1 4.4 GO:0007026 negative regulation of microtubule depolymerization(GO:0007026)
0.1 0.3 GO:0008628 hormone-mediated apoptotic signaling pathway(GO:0008628) cellular response to magnetism(GO:0071259)
0.1 3.4 GO:0061512 protein localization to cilium(GO:0061512)
0.1 0.2 GO:0018076 positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response(GO:0006990) N-terminal peptidyl-lysine acetylation(GO:0018076)
0.1 0.8 GO:0051382 kinetochore assembly(GO:0051382)
0.0 7.3 GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules(GO:0007156)
0.0 0.3 GO:0051694 pointed-end actin filament capping(GO:0051694)
0.0 0.1 GO:0048749 compound eye development(GO:0048749)
0.0 0.9 GO:0045109 intermediate filament organization(GO:0045109)
0.0 2.7 GO:0050885 neuromuscular process controlling balance(GO:0050885)
0.0 2.7 GO:0071300 cellular response to retinoic acid(GO:0071300)
0.0 0.4 GO:0090129 positive regulation of synapse maturation(GO:0090129)
0.0 2.4 GO:0090630 activation of GTPase activity(GO:0090630)
0.0 4.4 GO:0007519 skeletal muscle tissue development(GO:0007519)
0.0 0.1 GO:0035063 nuclear speck organization(GO:0035063)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.9 11.6 GO:0032983 kainate selective glutamate receptor complex(GO:0032983)
0.5 4.4 GO:0097442 CA3 pyramidal cell dendrite(GO:0097442)
0.4 7.8 GO:0005916 fascia adherens(GO:0005916)
0.4 10.9 GO:0043194 axon initial segment(GO:0043194)
0.1 3.0 GO:0030992 intraciliary transport particle B(GO:0030992)
0.1 0.8 GO:0005964 phosphorylase kinase complex(GO:0005964)
0.1 1.2 GO:0097539 ciliary transition fiber(GO:0097539)
0.1 1.3 GO:0070852 cell body fiber(GO:0070852)
0.1 1.0 GO:0051286 cell tip(GO:0051286)
0.1 5.8 GO:0031594 neuromuscular junction(GO:0031594)
0.0 3.6 GO:0000932 cytoplasmic mRNA processing body(GO:0000932)
0.0 1.7 GO:0000118 histone deacetylase complex(GO:0000118)
0.0 2.0 GO:0036064 ciliary basal body(GO:0036064)
0.0 0.4 GO:0080008 Cul4-RING E3 ubiquitin ligase complex(GO:0080008)
0.0 0.5 GO:0060077 inhibitory synapse(GO:0060077)
0.0 1.2 GO:0031526 brush border membrane(GO:0031526)
0.0 2.4 GO:0045211 postsynaptic membrane(GO:0045211)
0.0 0.4 GO:0042734 presynaptic membrane(GO:0042734)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.7 15.5 GO:0086080 protein binding involved in heterotypic cell-cell adhesion(GO:0086080)
1.7 11.6 GO:0015277 kainate selective glutamate receptor activity(GO:0015277)
1.5 5.8 GO:0035373 chondroitin sulfate proteoglycan binding(GO:0035373)
0.4 1.3 GO:0071886 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding(GO:0071886)
0.4 1.6 GO:0015350 methotrexate transporter activity(GO:0015350)
0.3 1.6 GO:0001601 peptide YY receptor activity(GO:0001601)
0.3 2.6 GO:0005004 GPI-linked ephrin receptor activity(GO:0005004)
0.2 4.4 GO:0002162 dystroglycan binding(GO:0002162)
0.1 2.4 GO:0043295 glutathione binding(GO:0043295)
0.1 0.5 GO:0008940 nitrate reductase activity(GO:0008940)
0.1 3.2 GO:0031402 sodium ion binding(GO:0031402)
0.1 1.9 GO:0001618 virus receptor activity(GO:0001618)
0.1 0.8 GO:0004689 phosphorylase kinase activity(GO:0004689)
0.1 0.3 GO:1903924 estradiol binding(GO:1903924)
0.1 1.0 GO:0030215 semaphorin receptor binding(GO:0030215)
0.0 0.8 GO:0016854 racemase and epimerase activity(GO:0016854)
0.0 0.2 GO:0004468 lysine N-acetyltransferase activity, acting on acetyl phosphate as donor(GO:0004468)
0.0 5.9 GO:0016758 transferase activity, transferring hexosyl groups(GO:0016758)
0.0 0.4 GO:0015643 toxic substance binding(GO:0015643)
0.0 0.3 GO:0005523 tropomyosin binding(GO:0005523)
0.0 0.4 GO:0001871 pattern binding(GO:0001871) polysaccharide binding(GO:0030247)
0.0 2.1 GO:0005200 structural constituent of cytoskeleton(GO:0005200)
0.0 6.3 GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001077)
0.0 0.1 GO:0015562 efflux transmembrane transporter activity(GO:0015562)
0.0 0.4 GO:0048027 mRNA 5'-UTR binding(GO:0048027)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.3 5.8 PID SYNDECAN 3 PATHWAY Syndecan-3-mediated signaling events
0.1 4.4 NABA COLLAGENS Genes encoding collagen proteins
0.1 2.6 PID EPHA FWDPATHWAY EPHA forward signaling
0.1 4.4 PID LKB1 PATHWAY LKB1 signaling events
0.0 1.0 ST GA13 PATHWAY G alpha 13 Pathway
0.0 0.3 PID ERB GENOMIC PATHWAY Validated nuclear estrogen receptor beta network
0.0 4.6 NABA ECM REGULATORS Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.7 11.6 REACTOME IONOTROPIC ACTIVITY OF KAINATE RECEPTORS Genes involved in Ionotropic activity of Kainate Receptors
0.3 5.9 REACTOME N GLYCAN ANTENNAE ELONGATION Genes involved in N-Glycan antennae elongation
0.2 7.7 REACTOME INTERACTION BETWEEN L1 AND ANKYRINS Genes involved in Interaction between L1 and Ankyrins
0.1 1.3 REACTOME SEROTONIN RECEPTORS Genes involved in Serotonin receptors
0.1 4.4 REACTOME COLLAGEN FORMATION Genes involved in Collagen formation
0.0 1.6 REACTOME IRON UPTAKE AND TRANSPORT Genes involved in Iron uptake and transport
0.0 1.0 REACTOME RECYCLING PATHWAY OF L1 Genes involved in Recycling pathway of L1
0.0 0.8 REACTOME ADHERENS JUNCTIONS INTERACTIONS Genes involved in Adherens junctions interactions
0.0 0.2 REACTOME TRAF3 DEPENDENT IRF ACTIVATION PATHWAY Genes involved in TRAF3-dependent IRF activation pathway