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avrg: GSE58827: Dynamics of the Mouse Liver

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Results for Clock

Z-value: 0.97

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Transcription factors associated with Clock

Gene Symbol Gene ID Gene Info
ENSMUSG00000029238.8 circadian locomotor output cycles kaput

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Clockmm10_v2_chr5_-_76304474_763045480.502.1e-03Click!

Activity profile of Clock motif

Sorted Z-values of Clock motif

Network of associatons between targets according to the STRING database.

First level regulatory network of Clock

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
0.5 3.8 GO:0070494 regulation of thrombin receptor signaling pathway(GO:0070494) negative regulation of thrombin receptor signaling pathway(GO:0070495)
0.2 1.2 GO:0097167 circadian regulation of translation(GO:0097167)
0.2 1.2 GO:0006189 'de novo' IMP biosynthetic process(GO:0006189)
0.2 0.9 GO:0097477 lateral motor column neuron migration(GO:0097477)
0.2 1.1 GO:0006543 glutamine catabolic process(GO:0006543)
0.2 0.7 GO:2000795 negative regulation of epithelial cell proliferation involved in lung morphogenesis(GO:2000795)
0.2 0.5 GO:0045041 positive regulation of T cell mediated immune response to tumor cell(GO:0002842) protein import into mitochondrial intermembrane space(GO:0045041)
0.2 0.5 GO:1903334 positive regulation of protein folding(GO:1903334)
0.1 1.3 GO:0035887 aortic smooth muscle cell differentiation(GO:0035887)
0.1 0.6 GO:0046654 tetrahydrofolate biosynthetic process(GO:0046654)
0.1 0.5 GO:0021660 rhombomere formation(GO:0021594) rhombomere 3 formation(GO:0021660) rhombomere 5 morphogenesis(GO:0021664) rhombomere 5 formation(GO:0021666)
0.1 0.5 GO:0090126 protein complex assembly involved in synapse maturation(GO:0090126)
0.1 1.7 GO:0033572 transferrin transport(GO:0033572)
0.1 0.9 GO:1990504 dense core granule exocytosis(GO:1990504)
0.1 0.3 GO:1902256 endocardial cushion fusion(GO:0003274) apoptotic process involved in outflow tract morphogenesis(GO:0003275) positive regulation of catagen(GO:0051795) regulation of apoptotic process involved in outflow tract morphogenesis(GO:1902256)
0.1 0.4 GO:0050812 regulation of acetyl-CoA biosynthetic process from pyruvate(GO:0010510) regulation of acyl-CoA biosynthetic process(GO:0050812)
0.1 2.4 GO:0048642 negative regulation of skeletal muscle tissue development(GO:0048642)
0.1 0.4 GO:0060376 positive regulation of mast cell differentiation(GO:0060376)
0.1 0.3 GO:0035973 aggrephagy(GO:0035973)
0.1 1.0 GO:1903800 positive regulation of production of miRNAs involved in gene silencing by miRNA(GO:1903800)
0.1 0.5 GO:0006344 maintenance of chromatin silencing(GO:0006344)
0.1 0.3 GO:1903416 response to glycoside(GO:1903416)
0.1 0.5 GO:0000320 re-entry into mitotic cell cycle(GO:0000320)
0.1 0.2 GO:1902915 negative regulation of protein K63-linked ubiquitination(GO:1900045) negative regulation of protein polyubiquitination(GO:1902915)
0.1 0.4 GO:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation(GO:0006616)
0.1 0.6 GO:0070574 cadmium ion transport(GO:0015691) cadmium ion transmembrane transport(GO:0070574)
0.1 0.3 GO:0048254 snoRNA localization(GO:0048254)
0.0 0.5 GO:0010650 positive regulation of cell communication by electrical coupling(GO:0010650) positive regulation of membrane depolarization during cardiac muscle cell action potential(GO:1900827)
0.0 0.2 GO:0006564 L-serine biosynthetic process(GO:0006564)
0.0 0.1 GO:0021529 spinal cord oligodendrocyte cell differentiation(GO:0021529) spinal cord oligodendrocyte cell fate specification(GO:0021530)
0.0 1.3 GO:0014002 astrocyte development(GO:0014002)
0.0 0.3 GO:0061143 alveolar primary septum development(GO:0061143)
0.0 0.3 GO:0006265 DNA topological change(GO:0006265)
0.0 0.3 GO:1903691 positive regulation of wound healing, spreading of epidermal cells(GO:1903691)
0.0 1.5 GO:1902175 regulation of oxidative stress-induced intrinsic apoptotic signaling pathway(GO:1902175)
0.0 0.4 GO:0006610 ribosomal protein import into nucleus(GO:0006610)
0.0 0.5 GO:0030322 stabilization of membrane potential(GO:0030322)
0.0 0.3 GO:0006983 ER overload response(GO:0006983)
0.0 0.3 GO:2000189 positive regulation of cholesterol homeostasis(GO:2000189)
0.0 0.1 GO:0046900 tetrahydrofolylpolyglutamate metabolic process(GO:0046900)
0.0 0.3 GO:0051901 positive regulation of mitochondrial depolarization(GO:0051901)
0.0 0.3 GO:0045075 interleukin-12 biosynthetic process(GO:0042090) regulation of interleukin-12 biosynthetic process(GO:0045075)
0.0 0.3 GO:1900246 positive regulation of RIG-I signaling pathway(GO:1900246)
0.0 0.5 GO:0043153 entrainment of circadian clock by photoperiod(GO:0043153)
0.0 0.3 GO:0043653 mitochondrial fragmentation involved in apoptotic process(GO:0043653)
0.0 0.2 GO:0048069 sphingosine-1-phosphate signaling pathway(GO:0003376) eye pigmentation(GO:0048069)
0.0 0.6 GO:0015936 coenzyme A metabolic process(GO:0015936)
0.0 0.1 GO:1904431 positive regulation of t-circle formation(GO:1904431)
0.0 0.1 GO:0072553 terminal button organization(GO:0072553)
0.0 0.1 GO:0060535 trachea cartilage morphogenesis(GO:0060535)
0.0 0.1 GO:0002003 angiotensin maturation(GO:0002003)
0.0 0.2 GO:2000465 regulation of glycogen (starch) synthase activity(GO:2000465)
0.0 0.3 GO:0031581 hemidesmosome assembly(GO:0031581)
0.0 0.2 GO:0018231 peptidyl-L-cysteine S-palmitoylation(GO:0018230) peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine(GO:0018231)
0.0 0.7 GO:0014037 Schwann cell differentiation(GO:0014037)
0.0 4.0 GO:0008643 carbohydrate transport(GO:0008643)
0.0 0.7 GO:0060445 branching involved in salivary gland morphogenesis(GO:0060445)
0.0 0.3 GO:0090209 negative regulation of triglyceride metabolic process(GO:0090209)
0.0 0.1 GO:0072161 mesenchymal cell differentiation involved in kidney development(GO:0072161) mesenchymal cell differentiation involved in renal system development(GO:2001012)
0.0 0.3 GO:0009083 branched-chain amino acid catabolic process(GO:0009083)
0.0 0.4 GO:0006991 response to sterol depletion(GO:0006991) SREBP signaling pathway(GO:0032933) cellular response to sterol depletion(GO:0071501)
0.0 0.5 GO:0071353 cellular response to interleukin-4(GO:0071353)
0.0 0.0 GO:0018214 peptidyl-glutamic acid carboxylation(GO:0017187) protein carboxylation(GO:0018214)
0.0 0.0 GO:0006222 UMP biosynthetic process(GO:0006222) pyrimidine ribonucleoside monophosphate metabolic process(GO:0009173) pyrimidine ribonucleoside monophosphate biosynthetic process(GO:0009174) UMP metabolic process(GO:0046049)
0.0 0.2 GO:0070816 phosphorylation of RNA polymerase II C-terminal domain(GO:0070816)
0.0 0.1 GO:0072189 ureter development(GO:0072189)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
0.3 1.1 GO:0031084 BLOC-2 complex(GO:0031084)
0.2 1.7 GO:1990712 HFE-transferrin receptor complex(GO:1990712)
0.1 0.4 GO:0005967 mitochondrial pyruvate dehydrogenase complex(GO:0005967)
0.1 0.5 GO:0097433 dense body(GO:0097433)
0.1 2.0 GO:0071564 npBAF complex(GO:0071564)
0.1 0.3 GO:0034274 Atg12-Atg5-Atg16 complex(GO:0034274)
0.1 0.9 GO:0071141 SMAD protein complex(GO:0071141)
0.1 0.5 GO:0046696 lipopolysaccharide receptor complex(GO:0046696)
0.1 0.3 GO:0005947 mitochondrial alpha-ketoglutarate dehydrogenase complex(GO:0005947)
0.1 0.3 GO:0005606 laminin-1 complex(GO:0005606) laminin-10 complex(GO:0043259)
0.1 0.2 GO:0070552 BRISC complex(GO:0070552)
0.1 0.3 GO:0001651 dense fibrillar component(GO:0001651)
0.1 4.3 GO:0009925 basal plasma membrane(GO:0009925)
0.0 0.4 GO:0005786 signal recognition particle, endoplasmic reticulum targeting(GO:0005786)
0.0 0.2 GO:0031428 box C/D snoRNP complex(GO:0031428)
0.0 0.4 GO:0090571 RNA polymerase II transcription repressor complex(GO:0090571)
0.0 0.7 GO:0044300 cerebellar mossy fiber(GO:0044300)
0.0 0.3 GO:0005890 sodium:potassium-exchanging ATPase complex(GO:0005890)
0.0 0.5 GO:0036057 filtration diaphragm(GO:0036056) slit diaphragm(GO:0036057)
0.0 0.2 GO:0034388 Pwp2p-containing subcomplex of 90S preribosome(GO:0034388)
0.0 0.1 GO:0099522 region of cytosol(GO:0099522) postsynaptic cytosol(GO:0099524)
0.0 0.4 GO:0034663 endoplasmic reticulum chaperone complex(GO:0034663)
0.0 0.3 GO:0000153 cytoplasmic ubiquitin ligase complex(GO:0000153)
0.0 0.2 GO:0000439 core TFIIH complex(GO:0000439)
0.0 0.3 GO:0030127 COPII vesicle coat(GO:0030127)
0.0 0.3 GO:0043203 axon hillock(GO:0043203)
0.0 0.2 GO:0002178 palmitoyltransferase complex(GO:0002178)
0.0 1.6 GO:0005604 basement membrane(GO:0005604)
0.0 4.1 GO:0000139 Golgi membrane(GO:0000139)
0.0 0.1 GO:0031983 vesicle lumen(GO:0031983)
0.0 0.1 GO:0070761 pre-snoRNP complex(GO:0070761)
0.0 0.9 GO:0042734 presynaptic membrane(GO:0042734)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.0 3.8 GO:0005008 hepatocyte growth factor-activated receptor activity(GO:0005008)
0.6 1.7 GO:0004998 transferrin receptor activity(GO:0004998)
0.3 1.0 GO:0035500 MH2 domain binding(GO:0035500)
0.2 0.6 GO:0019776 Atg8 ligase activity(GO:0019776)
0.2 0.6 GO:0004487 methylenetetrahydrofolate dehydrogenase (NAD+) activity(GO:0004487)
0.2 4.0 GO:0005351 sugar:proton symporter activity(GO:0005351)
0.1 0.9 GO:0070326 very-low-density lipoprotein particle receptor binding(GO:0070326)
0.1 1.5 GO:0031545 peptidyl-proline 4-dioxygenase activity(GO:0031545)
0.1 0.4 GO:0004740 pyruvate dehydrogenase (acetyl-transferring) kinase activity(GO:0004740)
0.1 0.4 GO:0034739 histone deacetylase activity (H4-K16 specific)(GO:0034739) Krueppel-associated box domain binding(GO:0035851)
0.1 0.3 GO:0034714 type III transforming growth factor beta receptor binding(GO:0034714)
0.1 0.5 GO:0034186 apolipoprotein A-I binding(GO:0034186)
0.1 0.3 GO:0097100 supercoiled DNA binding(GO:0097100)
0.1 0.2 GO:0008732 threonine aldolase activity(GO:0004793) L-allo-threonine aldolase activity(GO:0008732)
0.1 0.2 GO:0005118 sevenless binding(GO:0005118)
0.1 0.6 GO:0016421 CoA carboxylase activity(GO:0016421)
0.1 0.4 GO:0008312 signal recognition particle binding(GO:0005047) 7S RNA binding(GO:0008312)
0.1 0.2 GO:2001069 glycogen binding(GO:2001069)
0.0 0.5 GO:0043426 MRF binding(GO:0043426)
0.0 2.4 GO:0030332 cyclin binding(GO:0030332)
0.0 0.2 GO:0046624 sphingolipid transporter activity(GO:0046624)
0.0 1.3 GO:0016881 acid-amino acid ligase activity(GO:0016881)
0.0 0.5 GO:0097109 neuroligin family protein binding(GO:0097109)
0.0 0.2 GO:0031849 olfactory receptor binding(GO:0031849)
0.0 0.3 GO:0001094 TFIID-class transcription factor binding(GO:0001094)
0.0 0.1 GO:0031686 A1 adenosine receptor binding(GO:0031686)
0.0 0.5 GO:0022841 potassium ion leak channel activity(GO:0022841)
0.0 0.3 GO:0043208 glycosphingolipid binding(GO:0043208)
0.0 0.5 GO:0008353 RNA polymerase II carboxy-terminal domain kinase activity(GO:0008353)
0.0 0.3 GO:1990239 sodium:potassium-exchanging ATPase activity(GO:0005391) steroid hormone binding(GO:1990239)
0.0 0.7 GO:0070064 proline-rich region binding(GO:0070064)
0.0 0.3 GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor(GO:0016624)
0.0 1.2 GO:0070888 E-box binding(GO:0070888)
0.0 0.5 GO:0005537 mannose binding(GO:0005537)
0.0 0.7 GO:0001106 RNA polymerase II transcription corepressor activity(GO:0001106)
0.0 1.2 GO:0001105 RNA polymerase II transcription coactivator activity(GO:0001105)
0.0 0.5 GO:0017075 syntaxin-1 binding(GO:0017075)
0.0 1.2 GO:0016763 transferase activity, transferring pentosyl groups(GO:0016763)
0.0 0.5 GO:0071837 HMG box domain binding(GO:0071837)
0.0 0.7 GO:0016922 ligand-dependent nuclear receptor binding(GO:0016922)
0.0 0.2 GO:0015037 peptide disulfide oxidoreductase activity(GO:0015037)
0.0 0.2 GO:0034450 ubiquitin-ubiquitin ligase activity(GO:0034450)
0.0 0.1 GO:0050220 prostaglandin-E synthase activity(GO:0050220)
0.0 0.1 GO:0017108 5'-flap endonuclease activity(GO:0017108)
0.0 0.4 GO:0008139 nuclear localization sequence binding(GO:0008139)
0.0 0.3 GO:0005184 neuropeptide hormone activity(GO:0005184)
0.0 0.5 GO:0031624 ubiquitin conjugating enzyme binding(GO:0031624)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 1.7 PID CIRCADIAN PATHWAY Circadian rhythm pathway
0.1 3.7 PID ARF6 PATHWAY Arf6 signaling events
0.0 1.5 NABA BASEMENT MEMBRANES Genes encoding structural components of basement membranes
0.0 0.5 SA REG CASCADE OF CYCLIN EXPR Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.
0.0 0.8 PID HNF3A PATHWAY FOXA1 transcription factor network
0.0 1.7 PID HNF3B PATHWAY FOXA2 and FOXA3 transcription factor networks
0.0 0.3 SA MMP CYTOKINE CONNECTION Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix.
0.0 1.9 PID ERA GENOMIC PATHWAY Validated nuclear estrogen receptor alpha network
0.0 0.5 PID TOLL ENDOGENOUS PATHWAY Endogenous TLR signaling
0.0 1.1 PID AR TF PATHWAY Regulation of Androgen receptor activity
0.0 0.4 SA CASPASE CASCADE Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade.
0.0 0.6 PID LIS1 PATHWAY Lissencephaly gene (LIS1) in neuronal migration and development

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.2 2.3 REACTOME PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS Genes involved in Purine ribonucleoside monophosphate biosynthesis
0.1 3.8 REACTOME SEMA4D IN SEMAPHORIN SIGNALING Genes involved in Sema4D in semaphorin signaling
0.0 1.7 REACTOME TRANSFERRIN ENDOCYTOSIS AND RECYCLING Genes involved in Transferrin endocytosis and recycling
0.0 0.9 REACTOME BRANCHED CHAIN AMINO ACID CATABOLISM Genes involved in Branched-chain amino acid catabolism
0.0 0.4 REACTOME REGULATION OF PYRUVATE DEHYDROGENASE PDH COMPLEX Genes involved in Regulation of pyruvate dehydrogenase (PDH) complex
0.0 1.7 REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION Genes involved in BMAL1:CLOCK/NPAS2 Activates Circadian Expression
0.0 0.6 REACTOME ZINC TRANSPORTERS Genes involved in Zinc transporters
0.0 0.7 REACTOME RNA POL III TRANSCRIPTION TERMINATION Genes involved in RNA Polymerase III Transcription Termination
0.0 0.4 REACTOME IL 7 SIGNALING Genes involved in Interleukin-7 signaling
0.0 0.5 REACTOME PRE NOTCH TRANSCRIPTION AND TRANSLATION Genes involved in Pre-NOTCH Transcription and Translation
0.0 0.5 REACTOME INTERACTION BETWEEN L1 AND ANKYRINS Genes involved in Interaction between L1 and Ankyrins
0.0 0.6 REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION Genes involved in NOTCH1 Intracellular Domain Regulates Transcription
0.0 0.5 REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES Genes involved in Cross-presentation of soluble exogenous antigens (endosomes)