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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Msx3

Z-value: 0.42

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Transcription factors associated with Msx3

Gene Symbol Gene ID Gene Info
Msx3
ENSRNOG00000046776 msh homeobox 3

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Msx3rn6_v1_chr1_-_212517151_212517151-0.257.4e-06Click!

Activity profile of Msx3 motif

Sorted Z-values of Msx3 motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr17_-_69404323 12.03 ENSRNOT00000051342
ENSRNOT00000066282
Akr1c2
aldo-keto reductase family 1, member C2
chr5_+_28485619 11.73 ENSRNOT00000093341
ENSRNOT00000093129
LOC100912373
uncharacterized LOC100912373
chr8_+_48718329 10.93 ENSRNOT00000089763
Slc37a4
solute carrier family 37 member 4
chr1_+_185863043 10.14 ENSRNOT00000079072
Sox6
SRY box 6
chr10_+_84135116 8.83 ENSRNOT00000031035
Hoxb7
homeo box B7
chr9_-_18371856 8.69 ENSRNOT00000027293
Supt3h
SPT3 homolog, SAGA and STAGA complex component
chr6_-_42002819 8.51 ENSRNOT00000032417
Greb1
growth regulation by estrogen in breast cancer 1
chr8_-_119012671 8.38 ENSRNOT00000028435
Pth1r
parathyroid hormone 1 receptor
chr16_-_24951612 8.02 ENSRNOT00000018987
Tktl2
transketolase-like 2
chr3_-_165700489 7.74 ENSRNOT00000017008
Zfp93
zinc finger protein 93
chr13_-_111972603 7.62 ENSRNOT00000007870
Hsd11b1
hydroxysteroid 11-beta dehydrogenase 1
chr3_-_165537940 7.42 ENSRNOT00000071119
ENSRNOT00000070964
Sall4
spalt-like transcription factor 4
chr18_-_13183263 7.02 ENSRNOT00000050933
Ccdc178
coiled-coil domain containing 178
chrX_-_98095663 6.77 ENSRNOT00000004491
Rbm31y
RNA binding motif 31, Y-linked
chr8_+_128027958 6.40 ENSRNOT00000045049
Acaa1b
acetyl-Coenzyme A acyltransferase 1B
chr18_+_45023932 6.07 ENSRNOT00000039379
Fam170a
family with sequence similarity 170, member A
chr1_+_101603222 5.50 ENSRNOT00000033278
Izumo1
izumo sperm-egg fusion 1
chr1_-_14117021 5.24 ENSRNOT00000004344
RGD1560303
similar to hypothetical protein 4933423E17
chr4_-_178168690 5.13 ENSRNOT00000020729
Sox5
SRY box 5
chr4_+_147832136 4.99 ENSRNOT00000064603
Rho
rhodopsin
chr6_-_86223052 4.84 ENSRNOT00000046828
Fscb
fibrous sheath CABYR binding protein
chr7_-_143167772 4.44 ENSRNOT00000011374
Krt85
keratin 85
chr9_+_60900213 4.38 ENSRNOT00000017859
Ccdc150
coiled-coil domain containing 150
chr20_+_32717564 4.22 ENSRNOT00000030642
Rfx6
regulatory factor X, 6
chr18_+_12056113 3.80 ENSRNOT00000038450
Dsg4
desmoglein 4
chr14_+_23405717 3.69 ENSRNOT00000029805
Tmprss11c
transmembrane protease, serine 11C
chr4_-_176606382 3.49 ENSRNOT00000065576
Recql
RecQ like helicase
chr7_+_143122269 3.43 ENSRNOT00000082542
ENSRNOT00000045495
ENSRNOT00000081386
ENSRNOT00000067422
Krt86
keratin 86
chr16_+_2634603 3.07 ENSRNOT00000019113
Hesx1
HESX homeobox 1
chr3_+_112346627 2.93 ENSRNOT00000074392
Snap23
synaptosomal-associated protein 23
chr2_+_220432037 2.89 ENSRNOT00000021988
Frrs1
ferric-chelate reductase 1
chr15_+_39779648 2.86 ENSRNOT00000084505
Cab39l
calcium binding protein 39-like
chrX_+_110789269 2.85 ENSRNOT00000086014
Rnf128
ring finger protein 128, E3 ubiquitin protein ligase
chr20_+_44680449 2.82 ENSRNOT00000000728
Traf3ip2
Traf3 interacting protein 2
chr6_+_8886591 2.69 ENSRNOT00000091510
ENSRNOT00000089174
Six3
SIX homeobox 3
chr12_-_45801842 2.36 ENSRNOT00000078837
AABR07036513.1

chr12_-_22138382 2.33 ENSRNOT00000001899
Lrch4
leucine rich repeats and calponin homology domain containing 4
chr16_-_75241303 2.31 ENSRNOT00000058056
Defb2
defensin beta 2
chr2_-_158156444 2.30 ENSRNOT00000088559
Veph1
ventricular zone expressed PH domain-containing 1
chr2_+_248398917 2.30 ENSRNOT00000045855
Gbp1
guanylate binding protein 1
chr1_+_217459215 2.27 ENSRNOT00000092386
ENSRNOT00000092357
Shank2
SH3 and multiple ankyrin repeat domains 2
chr10_-_87286387 2.24 ENSRNOT00000044206
Krt28
keratin 28
chrM_+_9870 2.15 ENSRNOT00000044582
Mt-nd4l
mitochondrially encoded NADH 4L dehydrogenase
chr3_+_161160920 2.15 ENSRNOT00000019849
Spint4
serine protease inhibitor, Kunitz type 4
chr7_-_73130740 2.13 ENSRNOT00000075584
9430069I07Rik
RIKEN cDNA 9430069I07 gene
chr7_-_15706893 2.11 ENSRNOT00000042742
Olr1092
olfactory receptor 1092
chr5_-_115387377 2.09 ENSRNOT00000036030
ENSRNOT00000077492
RGD1560146
similar to hypothetical protein MGC34837
chr5_+_6373583 2.09 ENSRNOT00000084749
AABR07046778.1

chr7_-_143967484 1.72 ENSRNOT00000081758
Sp7
Sp7 transcription factor
chr1_-_172076138 1.71 ENSRNOT00000051241
Olr239
olfactory receptor 239
chrM_+_9451 1.70 ENSRNOT00000041241
Mt-nd3
mitochondrially encoded NADH dehydrogenase 3
chr3_-_10196626 1.66 ENSRNOT00000012234
Prdm12
PR/SET domain 12
chr6_-_36876805 1.60 ENSRNOT00000006482
Msgn1
mesogenin 1
chr10_-_87195075 1.58 ENSRNOT00000014851
Krt24
keratin 24
chr3_-_77800137 1.52 ENSRNOT00000071319
AABR07052831.1

chr6_-_50618694 1.51 ENSRNOT00000008980
Dld
dihydrolipoamide dehydrogenase
chr15_-_36798814 1.49 ENSRNOT00000065764
Cenpj
centromere protein J
chr10_-_88000423 1.40 ENSRNOT00000076787
ENSRNOT00000046751
ENSRNOT00000091394
Krt32
keratin 32
chr1_-_8885967 1.35 ENSRNOT00000016102
Gje1
gap junction protein, epsilon 1
chr2_-_192812008 1.29 ENSRNOT00000080554
Lce6a
late cornified envelope 6A
chr9_-_24467892 1.29 ENSRNOT00000060803
Defb18
defensin beta 18
chr6_-_111417813 1.10 ENSRNOT00000016324
ENSRNOT00000085458
Sptlc2
serine palmitoyltransferase, long chain base subunit 2
chr5_-_56567320 1.08 ENSRNOT00000066081
Topors
TOP1 binding arginine/serine rich protein
chr8_+_115546893 1.02 ENSRNOT00000018932
Dcaf1
DDB1 and CUL4 associated factor 1
chr13_-_101667147 0.90 ENSRNOT00000080475
AABR07021987.1

chr10_+_82032656 0.86 ENSRNOT00000067751
Ankrd40
ankyrin repeat domain 40
chrX_-_70835089 0.76 ENSRNOT00000076351
Tex11
testis expressed 11
chr1_-_167971151 0.75 ENSRNOT00000043023
Olr53
olfactory receptor 53
chr8_+_79638696 0.74 ENSRNOT00000085959
Dyx1c1
dyslexia susceptibility 1 candidate 1
chr2_+_195996521 0.71 ENSRNOT00000082849
Pogz
pogo transposable element with ZNF domain
chr11_-_28979169 0.65 ENSRNOT00000061601
AABR07033580.1

chr12_+_18679789 0.64 ENSRNOT00000001863
Cyp3a9
cytochrome P450, family 3, subfamily a, polypeptide 9
chr16_-_16762240 0.61 ENSRNOT00000080746
AABR07024790.1

chr16_-_75028977 0.60 ENSRNOT00000058071
Defb13
defensin beta 13
chr1_-_168930776 0.59 ENSRNOT00000021468
LOC103694854
olfactory receptor 52Z1-like
chr18_-_43945273 0.50 ENSRNOT00000088900
Dtwd2
DTW domain containing 2
chrY_-_1305026 0.49 ENSRNOT00000092901
Usp9y
ubiquitin specific peptidase 9, Y-linked
chr1_+_229889771 0.44 ENSRNOT00000085941
Olr348
olfactory receptor 348
chr1_-_149529350 0.35 ENSRNOT00000052226
Vom2r43
vomeronasal 2 receptor, 43
chr11_-_71136673 0.34 ENSRNOT00000042240
Fyttd1
forty-two-three domain containing 1
chrX_-_120521871 0.33 ENSRNOT00000080863
LOC100362376
LRRGT00025-like
chr1_-_101095594 0.32 ENSRNOT00000027944
Fcgrt
Fc fragment of IgG receptor and transporter
chr10_+_53740841 0.29 ENSRNOT00000004295
Myh2
myosin heavy chain 2
chr8_-_39551700 0.25 ENSRNOT00000091894
ENSRNOT00000076025
Pknox2
PBX/knotted 1 homeobox 2
chr4_-_66955732 0.24 ENSRNOT00000084282
Kdm7a
lysine (K)-specific demethylase 7A
chr3_-_30930141 0.23 ENSRNOT00000037001
AABR07051982.1

chr4_+_88694583 0.18 ENSRNOT00000009202
Ppm1k
protein phosphatase, Mg2+/Mn2+ dependent, 1K
chr8_+_43722228 0.16 ENSRNOT00000084016
Olr1325
olfactory receptor 1325
chr1_-_57518458 0.01 ENSRNOT00000002040
Pdcd2
programmed cell death 2

Network of associatons between targets according to the STRING database.

First level regulatory network of Msx3

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
4.0 12.0 GO:0009753 response to jasmonic acid(GO:0009753) cellular response to jasmonic acid stimulus(GO:0071395)
2.5 15.3 GO:2000741 positive regulation of mesenchymal stem cell differentiation(GO:2000741)
2.5 7.6 GO:0006713 glucocorticoid catabolic process(GO:0006713)
1.6 10.9 GO:0035166 post-embryonic hemopoiesis(GO:0035166)
0.9 2.7 GO:0014016 neuroblast differentiation(GO:0014016)
0.6 5.0 GO:0016056 rhodopsin mediated signaling pathway(GO:0016056)
0.6 8.4 GO:0060732 positive regulation of inositol phosphate biosynthetic process(GO:0060732)
0.6 11.7 GO:0045947 negative regulation of translational initiation(GO:0045947)
0.6 1.7 GO:1900111 positive regulation of histone H3-K9 dimethylation(GO:1900111)
0.5 3.1 GO:0030916 otic vesicle formation(GO:0030916)
0.5 1.0 GO:1990164 histone H2A phosphorylation(GO:1990164)
0.5 1.5 GO:0009106 lipoate metabolic process(GO:0009106)
0.4 5.5 GO:0007342 fusion of sperm to egg plasma membrane(GO:0007342)
0.4 4.2 GO:0003310 pancreatic A cell differentiation(GO:0003310)
0.4 2.9 GO:0098967 exocytic insertion of neurotransmitter receptor to plasma membrane(GO:0098881) exocytic insertion of neurotransmitter receptor to postsynaptic membrane(GO:0098967)
0.4 8.7 GO:0016578 histone deubiquitination(GO:0016578)
0.4 2.3 GO:1900041 negative regulation of interleukin-2 secretion(GO:1900041)
0.4 1.5 GO:0061511 centriole elongation(GO:0061511)
0.4 7.4 GO:0001833 inner cell mass cell proliferation(GO:0001833)
0.4 1.1 GO:0006667 sphinganine metabolic process(GO:0006667)
0.3 3.7 GO:0097264 self proteolysis(GO:0097264)
0.3 8.8 GO:0090190 positive regulation of branching involved in ureteric bud morphogenesis(GO:0090190)
0.3 3.5 GO:0000733 DNA strand renaturation(GO:0000733)
0.3 5.2 GO:0035404 histone-serine phosphorylation(GO:0035404)
0.2 2.3 GO:0045199 maintenance of epithelial cell apical/basal polarity(GO:0045199)
0.2 2.3 GO:0098880 maintenance of postsynaptic specialization structure(GO:0098880) maintenance of postsynaptic density structure(GO:0099562)
0.2 0.6 GO:0009822 lipid hydroxylation(GO:0002933) alkaloid catabolic process(GO:0009822)
0.2 0.8 GO:0006311 meiotic gene conversion(GO:0006311) gene conversion(GO:0035822)
0.1 2.8 GO:0002230 positive regulation of defense response to virus by host(GO:0002230)
0.1 1.6 GO:0007379 segment specification(GO:0007379)
0.1 2.9 GO:0042036 negative regulation of cytokine biosynthetic process(GO:0042036)
0.1 1.7 GO:0009642 response to light intensity(GO:0009642)
0.1 1.7 GO:0060218 hematopoietic stem cell differentiation(GO:0060218)
0.1 1.1 GO:0051457 maintenance of protein location in nucleus(GO:0051457)
0.1 0.7 GO:0051382 kinetochore assembly(GO:0051382)
0.0 0.2 GO:0071557 histone H3-K27 demethylation(GO:0071557)
0.0 2.1 GO:0042773 ATP synthesis coupled electron transport(GO:0042773)
0.0 1.6 GO:0045103 intermediate filament-based process(GO:0045103)
0.0 3.8 GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules(GO:0007156)
0.0 0.3 GO:0001778 plasma membrane repair(GO:0001778)
0.0 0.3 GO:0038094 Fc-gamma receptor signaling pathway(GO:0038094)
0.0 1.4 GO:0002088 lens development in camera-type eye(GO:0002088)
0.0 4.2 GO:0042742 defense response to bacterium(GO:0042742)
0.0 6.4 GO:0006631 fatty acid metabolic process(GO:0006631)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.7 8.7 GO:0030914 STAGA complex(GO:0030914)
0.6 2.3 GO:0020005 symbiont-containing vacuole membrane(GO:0020005)
0.3 5.0 GO:0042622 photoreceptor outer segment membrane(GO:0042622)
0.3 1.5 GO:0043159 acrosomal matrix(GO:0043159) oxoglutarate dehydrogenase complex(GO:0045252)
0.3 5.2 GO:0031588 nucleotide-activated protein kinase complex(GO:0031588)
0.3 4.8 GO:0035686 sperm fibrous sheath(GO:0035686)
0.2 5.5 GO:0002080 acrosomal membrane(GO:0002080)
0.2 2.9 GO:0042581 specific granule(GO:0042581)
0.2 3.8 GO:0030057 desmosome(GO:0030057)
0.2 2.3 GO:0005883 neurofilament(GO:0005883)
0.1 1.1 GO:0031211 serine C-palmitoyltransferase complex(GO:0017059) endoplasmic reticulum palmitoyltransferase complex(GO:0031211)
0.1 8.7 GO:0045095 keratin filament(GO:0045095)
0.1 8.4 GO:0031526 brush border membrane(GO:0031526)
0.1 10.9 GO:0030176 integral component of endoplasmic reticulum membrane(GO:0030176)
0.1 3.8 GO:0030964 mitochondrial respiratory chain complex I(GO:0005747) NADH dehydrogenase complex(GO:0030964) respiratory chain complex I(GO:0045271)
0.1 0.8 GO:0000801 central element(GO:0000801)
0.1 7.4 GO:0000792 heterochromatin(GO:0000792)
0.1 1.4 GO:0005922 connexon complex(GO:0005922)
0.1 3.6 GO:0005882 intermediate filament(GO:0005882)
0.1 1.1 GO:0000930 gamma-tubulin complex(GO:0000930)
0.0 6.4 GO:0042579 peroxisome(GO:0005777) microbody(GO:0042579)
0.0 0.3 GO:0005826 actomyosin contractile ring(GO:0005826)
0.0 1.0 GO:0008180 COP9 signalosome(GO:0008180)
0.0 7.6 GO:0031965 nuclear membrane(GO:0031965)
0.0 3.6 GO:0044798 nuclear transcription factor complex(GO:0044798)
0.0 3.7 GO:0043204 perikaryon(GO:0043204)
0.0 1.4 GO:0016605 PML body(GO:0016605)
0.0 1.5 GO:0036064 ciliary basal body(GO:0036064)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
3.0 12.0 GO:0047023 androsterone dehydrogenase activity(GO:0047023)
2.5 7.6 GO:0003845 11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity(GO:0003845)
1.6 10.9 GO:0015526 hexose phosphate transmembrane transporter activity(GO:0015119) organophosphate:inorganic phosphate antiporter activity(GO:0015315) hexose-phosphate:inorganic phosphate antiporter activity(GO:0015526) glucose 6-phosphate:inorganic phosphate antiporter activity(GO:0061513)
1.0 11.7 GO:0008190 eukaryotic initiation factor 4E binding(GO:0008190)
0.9 6.4 GO:0003988 acetyl-CoA C-acyltransferase activity(GO:0003988)
0.7 2.9 GO:0000293 ferric-chelate reductase activity(GO:0000293)
0.6 5.5 GO:0086080 protein binding involved in heterotypic cell-cell adhesion(GO:0086080)
0.6 3.5 GO:0009378 four-way junction helicase activity(GO:0009378)
0.6 2.3 GO:0019002 GMP binding(GO:0019002)
0.6 5.0 GO:0009881 photoreceptor activity(GO:0009881)
0.3 5.2 GO:0004679 AMP-activated protein kinase activity(GO:0004679)
0.2 1.7 GO:1990226 histone methyltransferase binding(GO:1990226)
0.2 1.1 GO:0016454 serine C-palmitoyltransferase activity(GO:0004758) C-palmitoyltransferase activity(GO:0016454)
0.2 1.1 GO:0044547 DNA topoisomerase binding(GO:0044547)
0.2 1.5 GO:0034604 pyruvate dehydrogenase activity(GO:0004738) pyruvate dehydrogenase [NAD(P)+] activity(GO:0034603) pyruvate dehydrogenase (NAD+) activity(GO:0034604)
0.2 2.3 GO:0098919 structural constituent of postsynaptic specialization(GO:0098879) structural constituent of postsynaptic density(GO:0098919)
0.1 3.8 GO:0050136 NADH dehydrogenase (ubiquinone) activity(GO:0008137) NADH dehydrogenase (quinone) activity(GO:0050136)
0.1 2.7 GO:0001222 transcription corepressor binding(GO:0001222)
0.1 8.4 GO:0017046 peptide hormone binding(GO:0017046)
0.1 1.7 GO:0017151 DEAD/H-box RNA helicase binding(GO:0017151)
0.1 1.0 GO:0035184 histone threonine kinase activity(GO:0035184)
0.1 6.2 GO:0004402 histone acetyltransferase activity(GO:0004402)
0.1 13.2 GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001078)
0.1 2.9 GO:0005484 SNAP receptor activity(GO:0005484)
0.1 0.3 GO:0019770 IgG receptor activity(GO:0019770)
0.1 0.2 GO:0071558 histone demethylase activity (H3-K27 specific)(GO:0071558)
0.0 14.7 GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding(GO:0000978)
0.0 0.6 GO:0008395 steroid hydroxylase activity(GO:0008395)
0.0 8.7 GO:0044212 transcription regulatory region DNA binding(GO:0044212)
0.0 3.7 GO:0004252 serine-type endopeptidase activity(GO:0004252)
0.0 12.3 GO:0005198 structural molecule activity(GO:0005198)
0.0 2.9 GO:0061630 ubiquitin protein ligase activity(GO:0061630)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.3 8.7 PID MYC PATHWAY C-MYC pathway
0.2 5.0 PID RHODOPSIN PATHWAY Visual signal transduction: Rods
0.1 7.4 PID BETA CATENIN NUC PATHWAY Regulation of nuclear beta catenin signaling and target gene transcription
0.1 5.7 PID ERA GENOMIC PATHWAY Validated nuclear estrogen receptor alpha network
0.0 2.9 PID NFAT TFPATHWAY Calcineurin-regulated NFAT-dependent transcription in lymphocytes
0.0 1.5 ST JNK MAPK PATHWAY JNK MAPK Pathway

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.6 5.0 REACTOME OPSINS Genes involved in Opsins
0.2 7.6 REACTOME STEROID HORMONES Genes involved in Steroid hormones
0.2 10.9 REACTOME GLUCOSE TRANSPORT Genes involved in Glucose transport
0.2 2.9 REACTOME REGULATION OF AMPK ACTIVITY VIA LKB1 Genes involved in Regulation of AMPK activity via LKB1
0.1 1.5 REACTOME REGULATION OF PYRUVATE DEHYDROGENASE PDH COMPLEX Genes involved in Regulation of pyruvate dehydrogenase (PDH) complex
0.1 8.4 REACTOME CLASS B 2 SECRETIN FAMILY RECEPTORS Genes involved in Class B/2 (Secretin family receptors)
0.0 2.9 REACTOME TRANS GOLGI NETWORK VESICLE BUDDING Genes involved in trans-Golgi Network Vesicle Budding
0.0 2.3 REACTOME INTERFERON GAMMA SIGNALING Genes involved in Interferon gamma signaling
0.0 1.1 REACTOME SPHINGOLIPID DE NOVO BIOSYNTHESIS Genes involved in Sphingolipid de novo biosynthesis
0.0 1.5 REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES Genes involved in Loss of Nlp from mitotic centrosomes