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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Smad4

Z-value: 1.00

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Transcription factors associated with Smad4

Gene Symbol Gene ID Gene Info
ENSRNOG00000051965 SMAD family member 4

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Smad4rn6_v1_chr18_-_69657301_696573010.465.7e-18Click!

Activity profile of Smad4 motif

Sorted Z-values of Smad4 motif

Promoter Log-likelihood Transcript Gene Gene Info
chr3_+_56862691 39.59 ENSRNOT00000087712
glutamate decarboxylase 1
chr16_-_39476384 28.64 ENSRNOT00000092968
glycoprotein m6a
chr13_-_91872954 27.80 ENSRNOT00000004613
ENSRNOT00000079263
cell adhesion molecule 3
chr10_-_45297385 26.55 ENSRNOT00000041187
histone cluster 3 H2B family member b
chr10_-_107539658 25.72 ENSRNOT00000089346
RNA binding protein, fox-1 homolog 3
chr1_+_196996581 25.64 ENSRNOT00000021690
interleukin 21 receptor
chr2_+_209839299 25.56 ENSRNOT00000092450
potassium voltage-gated channel subfamily A member 2
chr2_+_209838869 25.51 ENSRNOT00000092365
potassium voltage-gated channel subfamily A member 2
chr16_-_39476025 25.16 ENSRNOT00000014312
glycoprotein m6a
chr10_-_107539465 25.11 ENSRNOT00000004524
RNA binding protein, fox-1 homolog 3
chr17_-_43770561 22.62 ENSRNOT00000088408
histone H4 variant H4-v.1
chr8_+_58347736 21.49 ENSRNOT00000080227
ENSRNOT00000066222
solute carrier family 35, member F2
chr1_+_100299626 21.27 ENSRNOT00000092327
ENSRNOT00000044257
SH3 and multiple ankyrin repeat domains 1
chr8_-_98738446 21.25 ENSRNOT00000019860
Zic family member 1
chr4_+_153774486 20.63 ENSRNOT00000074096
tubulin, alpha 8
chr1_+_78800754 20.55 ENSRNOT00000084601
dishevelled-binding antagonist of beta-catenin 3
chr17_-_44744902 17.41 ENSRNOT00000085381
histone H4 variant H4-v.1
chr10_-_94352880 17.28 ENSRNOT00000035973
LIM domain containing 2
chr9_+_117583610 17.06 ENSRNOT00000088647
ENSRNOT00000049426
erythrocyte membrane protein band 4.1-like 3
chr7_-_120403523 16.69 ENSRNOT00000015283
SRY box 10
chr17_+_44520537 16.30 ENSRNOT00000077985
histone cluster 1, H2ai-like2
chr7_-_70842405 16.20 ENSRNOT00000047449
neurexophilin 4
chr9_+_2190915 15.81 ENSRNOT00000077417
SATB homeobox 1
chr18_+_52215682 14.55 ENSRNOT00000037901
multiple EGF-like domains 10
chr8_-_50228369 14.39 ENSRNOT00000024030
transgelin
chr13_-_70625842 13.87 ENSRNOT00000092499
laminin subunit gamma 2
chr5_-_152473868 12.98 ENSRNOT00000022130
family with sequence similarity 110, member D
chr17_-_43821536 12.50 ENSRNOT00000072286
histone H4 variant H4-v.1
chr13_-_70626252 12.47 ENSRNOT00000036947
laminin subunit gamma 2
chr17_-_44520240 12.31 ENSRNOT00000086538
histone cluster 1 H2B family member h
chr1_-_72727112 11.38 ENSRNOT00000031172
BR serine/threonine kinase 1
chr1_+_99486253 11.32 ENSRNOT00000074820
uncharacterized LOC102546648
chr7_+_119647375 11.07 ENSRNOT00000046563
potassium channel tetramerization domain containing 17
chr7_+_123168811 10.20 ENSRNOT00000007091
cold shock domain containing C2
chr12_+_21767606 10.07 ENSRNOT00000059602
neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter 1-like
chr14_-_34561696 9.79 ENSRNOT00000059763
steroid 5 alpha-reductase 3
chr13_+_57131395 9.66 ENSRNOT00000017884
potassium sodium-activated channel subfamily T member 2
chr16_+_61758917 8.82 ENSRNOT00000084858
leptin receptor overlapping transcript-like 1
chrX_+_106823491 8.77 ENSRNOT00000045997
brain expressed X-linked 3
chr15_+_4240203 8.59 ENSRNOT00000010178
MSS51 mitochondrial translational activator
chr13_+_48287873 8.51 ENSRNOT00000068223
family with sequence similarity 72, member A
chr4_+_102351036 8.48 ENSRNOT00000079277

chr4_-_170145262 8.39 ENSRNOT00000074526
histone cluster 1, H4b
chr2_+_241909832 7.82 ENSRNOT00000047975
protein phosphatase 3 catalytic subunit alpha
chrX_+_96991658 7.80 ENSRNOT00000049969

chr2_-_187822997 7.78 ENSRNOT00000092932
semaphorin 4A
chr10_-_90240509 7.61 ENSRNOT00000028407
ataxin 7-like 3
chr17_-_9695292 7.28 ENSRNOT00000036162
proline rich 7 (synaptic)
chr7_-_14418950 7.01 ENSRNOT00000066722
RAS protein activator like 3
chr1_+_79989019 6.85 ENSRNOT00000020428
dystrophia myotonica-protein kinase
chr8_-_115358046 6.81 ENSRNOT00000017607
glutamate metabotropic receptor 2
chr4_-_103369224 6.75 ENSRNOT00000075709

chr10_+_47765432 6.63 ENSRNOT00000078231
microfibril-associated glycoprotein 4-like
chrX_+_107370431 5.47 ENSRNOT00000044372
transcription elongation factor A like 1
chr13_-_94355219 5.29 ENSRNOT00000005332
phospholipase D family, member 5
chr15_+_23792931 5.24 ENSRNOT00000092091
sterile alpha motif domain containing 4A
chr1_-_101514547 4.99 ENSRNOT00000079633
protein phosphatase 1, regulatory subunit 15A
chr15_-_29852665 4.99 ENSRNOT00000040046

chr2_+_198360998 4.92 ENSRNOT00000046129
histone cluster 2, H2be
chr10_+_68588789 4.89 ENSRNOT00000049614

chr17_+_78739389 4.79 ENSRNOT00000020384
uncharacterized LOC102547897
chr2_+_203768729 4.78 ENSRNOT00000018895
immunoglobulin superfamily, member 3
chr4_-_82209933 4.54 ENSRNOT00000091106
homeobox protein Hox-A10-like
chr4_-_82295470 4.48 ENSRNOT00000091073
homeobox A10
chr4_+_84194347 4.38 ENSRNOT00000084256
chimerin 2
chr14_-_35149608 3.85 ENSRNOT00000003050
ENSRNOT00000090654
KIT proto-oncogene receptor tyrosine kinase
chr2_-_5577369 3.71 ENSRNOT00000093420
nuclear receptor subfamily 2, group F, member 1
chr10_-_88670430 3.58 ENSRNOT00000025547
hypocretin neuropeptide precursor
chr6_+_108745895 3.26 ENSRNOT00000061786
eukaryotic translation initiation factor 3 subunit H
chr12_+_37668369 3.15 ENSRNOT00000001419
cyclin-dependent kinase 2 associated protein 1
chr17_+_23135985 2.12 ENSRNOT00000090794
neural precursor cell expressed, developmentally down-regulated 9
chr5_-_152464850 2.05 ENSRNOT00000021937
zinc finger protein 593
chr15_-_29865536 2.01 ENSRNOT00000085893

chr1_-_168587241 1.83 ENSRNOT00000021254
olfactory receptor 104
chr8_+_36766977 1.55 ENSRNOT00000017648
pseudouridylate synthase 3
chr10_+_46940965 1.51 ENSRNOT00000005366
LLGL1, scribble cell polarity complex component
chr7_-_143217535 1.39 ENSRNOT00000088316
type II keratin Kb15
chr12_-_41671437 1.29 ENSRNOT00000001883
LIM homeobox 5
chr3_+_102683148 0.77 ENSRNOT00000046220
similar to olfactory receptor Olfr1289
chr6_+_29012207 0.68 ENSRNOT00000079077
ATPase family, AAA domain containing 2B
chr10_+_56453877 0.63 ENSRNOT00000031640
phospholipid scramblase 3
chr12_+_4546287 0.50 ENSRNOT00000001416
HIG1 hypoxia inducible domain family, member 2A-like 1
chr15_+_32188736 0.39 ENSRNOT00000081436

chr8_+_117280705 0.27 ENSRNOT00000085038
ubiquitin specific peptidase 19
chr11_+_9642365 0.16 ENSRNOT00000087080
ENSRNOT00000042384
roundabout guidance receptor 1
chr3_+_172155496 0.03 ENSRNOT00000066279
syntaxin 16

Network of associatons between targets according to the STRING database.

First level regulatory network of Smad4

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
8.5 51.1 GO:0021633 optic nerve structural organization(GO:0021633)
7.9 39.6 GO:0009449 gamma-aminobutyric acid biosynthetic process(GO:0009449)
5.3 21.3 GO:0050893 sensory processing(GO:0050893)
3.6 60.9 GO:0045653 negative regulation of megakaryocyte differentiation(GO:0045653)
2.8 17.1 GO:0071205 protein localization to juxtaparanode region of axon(GO:0071205)
2.1 14.5 GO:0014719 skeletal muscle satellite cell activation(GO:0014719) skeletal muscle satellite cell differentiation(GO:0014816) recognition of apoptotic cell(GO:0043654)
2.0 9.8 GO:0016095 polyprenol catabolic process(GO:0016095)
2.0 7.8 GO:1903244 positive regulation of cardiac muscle adaptation(GO:0010615) positive regulation of cardiac muscle hypertrophy in response to stress(GO:1903244) regulation of connective tissue replacement(GO:1905203)
1.8 7.0 GO:0051140 regulation of NK T cell proliferation(GO:0051140) positive regulation of NK T cell proliferation(GO:0051142)
1.7 5.0 GO:1902310 regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation(GO:0060734) response to methyl methanesulfonate(GO:0072702) cellular response to methyl methanesulfonate(GO:0072703) response to environmental enrichment(GO:0090648) positive regulation of peptidyl-serine dephosphorylation(GO:1902310)
1.7 21.5 GO:0032808 lacrimal gland development(GO:0032808)
1.5 20.6 GO:0035414 negative regulation of catenin import into nucleus(GO:0035414)
1.4 6.9 GO:0014722 regulation of skeletal muscle contraction by calcium ion signaling(GO:0014722)
1.3 8.8 GO:0032511 late endosome to vacuole transport via multivesicular body sorting pathway(GO:0032511)
1.3 26.3 GO:0070831 basement membrane assembly(GO:0070831)
1.3 53.8 GO:0051491 positive regulation of filopodium assembly(GO:0051491)
1.1 15.8 GO:0043374 CD8-positive, alpha-beta T cell differentiation(GO:0043374)
1.1 8.5 GO:0031547 brain-derived neurotrophic factor receptor signaling pathway(GO:0031547)
1.0 50.8 GO:0000381 regulation of alternative mRNA splicing, via spliceosome(GO:0000381)
1.0 3.8 GO:1905065 Kit signaling pathway(GO:0038109) melanocyte migration(GO:0097324) positive regulation of vascular smooth muscle cell differentiation(GO:1905065)
0.6 6.8 GO:0007196 adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway(GO:0007196)
0.5 27.8 GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules(GO:0007157)
0.5 3.7 GO:0021796 cerebral cortex regionalization(GO:0021796)
0.4 3.6 GO:0051970 negative regulation of transmission of nerve impulse(GO:0051970)
0.4 21.3 GO:0007628 adult walking behavior(GO:0007628)
0.4 11.1 GO:0032469 endoplasmic reticulum calcium ion homeostasis(GO:0032469)
0.4 7.8 GO:0045063 T-helper 1 cell differentiation(GO:0045063)
0.4 1.6 GO:1990481 mRNA pseudouridine synthesis(GO:1990481)
0.4 34.5 GO:0006334 nucleosome assembly(GO:0006334)
0.4 7.6 GO:0016578 histone deubiquitination(GO:0016578)
0.4 4.9 GO:0002227 innate immune response in mucosa(GO:0002227)
0.3 4.4 GO:0001675 acrosome assembly(GO:0001675)
0.3 2.0 GO:0000055 ribosomal large subunit export from nucleus(GO:0000055)
0.2 5.2 GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening(GO:0000289)
0.2 16.6 GO:0006342 chromatin silencing(GO:0006342)
0.2 1.3 GO:0021937 cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation(GO:0021937)
0.2 3.3 GO:0001731 formation of translation preinitiation complex(GO:0001731)
0.2 11.4 GO:0051298 centrosome duplication(GO:0051298)
0.1 8.6 GO:0035176 social behavior(GO:0035176) intraspecies interaction between organisms(GO:0051703)
0.1 10.2 GO:0043488 regulation of mRNA stability(GO:0043488)
0.1 4.5 GO:0060065 uterus development(GO:0060065)
0.1 1.5 GO:0035090 maintenance of apical/basal cell polarity(GO:0035090)
0.1 8.8 GO:0008625 extrinsic apoptotic signaling pathway via death domain receptors(GO:0008625)
0.1 3.1 GO:0060325 face morphogenesis(GO:0060325)
0.1 1.4 GO:0031424 keratinization(GO:0031424)
0.1 25.8 GO:0019221 cytokine-mediated signaling pathway(GO:0019221)
0.0 9.7 GO:0071804 cellular potassium ion transport(GO:0071804) potassium ion transmembrane transport(GO:0071805)
0.0 0.6 GO:0017121 phospholipid scrambling(GO:0017121)
0.0 0.3 GO:0048642 negative regulation of skeletal muscle tissue development(GO:0048642)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
6.6 26.3 GO:0005607 laminin-2 complex(GO:0005607)
4.3 68.1 GO:0044224 juxtaparanode region of axon(GO:0044224)
3.3 16.7 GO:0031315 extrinsic component of mitochondrial outer membrane(GO:0031315)
2.2 60.9 GO:0000788 nuclear nucleosome(GO:0000788)
1.3 7.8 GO:0005955 calcineurin complex(GO:0005955)
1.2 53.8 GO:0044295 axonal growth cone(GO:0044295)
1.0 39.6 GO:0060077 inhibitory synapse(GO:0060077)
0.8 13.9 GO:0017146 NMDA selective glutamate receptor complex(GO:0017146)
0.8 55.6 GO:0000786 nucleosome(GO:0000786)
0.6 7.6 GO:0000124 SAGA complex(GO:0000124)
0.5 14.5 GO:0001891 phagocytic cup(GO:0001891)
0.4 7.0 GO:0031235 intrinsic component of the cytoplasmic side of the plasma membrane(GO:0031235)
0.4 3.3 GO:0016282 eukaryotic 43S preinitiation complex(GO:0016282) eukaryotic 48S preinitiation complex(GO:0033290)
0.4 5.0 GO:0000164 protein phosphatase type 1 complex(GO:0000164)
0.3 15.8 GO:0005720 nuclear heterochromatin(GO:0005720)
0.3 50.8 GO:0043204 perikaryon(GO:0043204)
0.2 6.9 GO:0031307 integral component of mitochondrial outer membrane(GO:0031307)
0.2 27.8 GO:0005913 cell-cell adherens junction(GO:0005913)
0.2 1.5 GO:0000137 Golgi cis cisterna(GO:0000137)
0.1 3.8 GO:0042629 mast cell granule(GO:0042629)
0.1 8.4 GO:0031463 Cul3-RING ubiquitin ligase complex(GO:0031463)
0.1 9.7 GO:0008076 voltage-gated potassium channel complex(GO:0008076)
0.1 6.8 GO:0042734 presynaptic membrane(GO:0042734)
0.1 2.0 GO:0030687 preribosome, large subunit precursor(GO:0030687)
0.1 11.4 GO:0008021 synaptic vesicle(GO:0008021)
0.0 5.2 GO:0000932 cytoplasmic mRNA processing body(GO:0000932)
0.0 7.3 GO:0045211 postsynaptic membrane(GO:0045211)
0.0 3.6 GO:0005791 rough endoplasmic reticulum(GO:0005791)
0.0 1.4 GO:0045095 keratin filament(GO:0045095)
0.0 2.1 GO:0000922 spindle pole(GO:0000922)
0.0 8.8 GO:0005768 endosome(GO:0005768)
0.0 8.7 GO:0005789 endoplasmic reticulum membrane(GO:0005789)
0.0 4.5 GO:0005667 transcription factor complex(GO:0005667)
0.0 0.2 GO:0030673 axolemma(GO:0030673)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
7.9 39.6 GO:0004351 glutamate decarboxylase activity(GO:0004351)
3.0 21.3 GO:0030160 GKAP/Homer scaffold activity(GO:0030160) ankyrin repeat binding(GO:0071532)
2.6 51.1 GO:0015271 outward rectifier potassium channel activity(GO:0015271)
2.4 9.8 GO:0003865 3-oxo-5-alpha-steroid 4-dehydrogenase activity(GO:0003865) cholestenone 5-alpha-reductase activity(GO:0047751)
2.3 6.8 GO:0001641 group II metabotropic glutamate receptor activity(GO:0001641)
2.2 8.8 GO:0005163 nerve growth factor receptor binding(GO:0005163)
2.1 14.5 GO:0001849 complement component C1q binding(GO:0001849)
2.0 7.8 GO:0033192 calcium-dependent protein serine/threonine phosphatase activity(GO:0004723) calmodulin-dependent protein phosphatase activity(GO:0033192)
1.6 20.6 GO:0070097 delta-catenin binding(GO:0070097)
1.5 4.4 GO:0001565 phorbol ester receptor activity(GO:0001565)
0.9 11.4 GO:0050321 tau-protein kinase activity(GO:0050321)
0.7 2.0 GO:0031177 phosphopantetheine binding(GO:0031177)
0.7 11.1 GO:0097602 cullin family protein binding(GO:0097602)
0.5 3.7 GO:0044323 retinoic acid-responsive element binding(GO:0044323)
0.4 3.8 GO:0004716 receptor signaling protein tyrosine kinase activity(GO:0004716)
0.4 53.8 GO:0005262 calcium channel activity(GO:0005262)
0.4 9.7 GO:0015269 calcium-activated potassium channel activity(GO:0015269)
0.3 37.7 GO:0005200 structural constituent of cytoskeleton(GO:0005200)
0.3 61.6 GO:0042393 histone binding(GO:0042393)
0.3 66.3 GO:0044822 mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.2 25.6 GO:0004896 cytokine receptor activity(GO:0004896)
0.2 16.7 GO:0001190 transcriptional activator activity, RNA polymerase II transcription factor binding(GO:0001190) transcriptional repressor activity, RNA polymerase II activating transcription factor binding(GO:0098811)
0.2 5.0 GO:0008157 protein phosphatase 1 binding(GO:0008157)
0.2 3.1 GO:0070182 DNA polymerase binding(GO:0070182)
0.1 26.3 GO:0008201 heparin binding(GO:0008201)
0.1 7.6 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity(GO:0030374)
0.1 14.4 GO:0030674 protein binding, bridging(GO:0030674)
0.1 3.6 GO:0005184 neuropeptide hormone activity(GO:0005184)
0.1 1.6 GO:0009982 pseudouridine synthase activity(GO:0009982)
0.1 6.9 GO:0019888 protein phosphatase regulator activity(GO:0019888)
0.1 55.1 GO:0046982 protein heterodimerization activity(GO:0046982)
0.1 20.9 GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001077)
0.1 15.8 GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding(GO:0001227)
0.1 3.3 GO:0003743 translation initiation factor activity(GO:0003743)
0.0 0.6 GO:0017128 phospholipid scramblase activity(GO:0017128)
0.0 17.9 GO:0050839 cell adhesion molecule binding(GO:0050839)
0.0 8.5 GO:0005096 GTPase activator activity(GO:0005096)
0.0 0.3 GO:1990380 Lys48-specific deubiquitinase activity(GO:1990380)
0.0 0.2 GO:0008046 axon guidance receptor activity(GO:0008046) LRR domain binding(GO:0030275)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.5 26.3 PID INTEGRIN4 PATHWAY Alpha6 beta4 integrin-ligand interactions
0.2 15.8 PID CASPASE PATHWAY Caspase cascade in apoptosis
0.2 7.8 PID IL12 STAT4 PATHWAY IL12 signaling mediated by STAT4
0.2 11.4 PID LKB1 PATHWAY LKB1 signaling events
0.2 4.5 PID HDAC CLASSIII PATHWAY Signaling events mediated by HDAC Class III
0.1 3.8 PID KIT PATHWAY Signaling events mediated by Stem cell factor receptor (c-Kit)
0.1 5.0 PID BMP PATHWAY BMP receptor signaling
0.1 4.4 PID RAC1 REG PATHWAY Regulation of RAC1 activity
0.1 14.4 PID PDGFRB PATHWAY PDGFR-beta signaling pathway
0.1 3.1 ST FAS SIGNALING PATHWAY Fas Signaling Pathway
0.1 7.8 NABA ECM AFFILIATED Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
2.0 52.1 REACTOME PACKAGING OF TELOMERE ENDS Genes involved in Packaging Of Telomere Ends
1.5 39.6 REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION Genes involved in GABA synthesis, release, reuptake and degradation
1.0 51.1 REACTOME VOLTAGE GATED POTASSIUM CHANNELS Genes involved in Voltage gated Potassium channels
0.8 9.8 REACTOME ANDROGEN BIOSYNTHESIS Genes involved in Androgen biosynthesis
0.4 7.8 REACTOME OTHER SEMAPHORIN INTERACTIONS Genes involved in Other semaphorin interactions
0.3 15.8 REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS Genes involved in Apoptotic cleavage of cellular proteins
0.3 6.8 REACTOME CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS Genes involved in Class C/3 (Metabotropic glutamate/pheromone receptors)
0.3 26.3 REACTOME CELL JUNCTION ORGANIZATION Genes involved in Cell junction organization
0.3 7.8 REACTOME DARPP 32 EVENTS Genes involved in DARPP-32 events
0.2 5.0 REACTOME DOWNREGULATION OF TGF BETA RECEPTOR SIGNALING Genes involved in Downregulation of TGF-beta receptor signaling
0.2 3.8 REACTOME REGULATION OF KIT SIGNALING Genes involved in Regulation of KIT signaling
0.0 4.4 REACTOME SIGNALING BY RHO GTPASES Genes involved in Signaling by Rho GTPases
0.0 2.0 REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY Genes involved in Nuclear Receptor transcription pathway
0.0 3.6 REACTOME PEPTIDE LIGAND BINDING RECEPTORS Genes involved in Peptide ligand-binding receptors