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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Clock

Z-value: 0.42

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Transcription factors associated with Clock

Gene Symbol Gene ID Gene Info
ENSRNOG00000002175 clock circadian regulator

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Clockrn6_v1_chr14_+_34455934_34455934-0.091.1e-01Click!

Activity profile of Clock motif

Sorted Z-values of Clock motif

Promoter Log-likelihood Transcript Gene Gene Info
chr10_-_83898527 12.72 ENSRNOT00000009815
ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9)
chr9_-_82419288 11.28 ENSRNOT00000004797
tubulin, alpha 4A
chr2_-_233743866 11.28 ENSRNOT00000087062
glutamyl aminopeptidase
chr5_+_140979435 8.11 ENSRNOT00000056592
poly(A) binding protein, cytoplasmic 4
chr13_-_70783515 7.46 ENSRNOT00000003605
laminin subunit gamma 1
chr2_-_30246010 7.27 ENSRNOT00000023900
methylcrotonoyl-CoA carboxylase 2
chr15_+_4064706 7.10 ENSRNOT00000011956
synaptopodin 2-like
chr10_-_32471454 6.78 ENSRNOT00000003224
sarcoglycan, delta
chr12_-_3924415 6.50 ENSRNOT00000067752

chr14_+_33580541 6.24 ENSRNOT00000002905
phosphoribosyl pyrophosphate amidotransferase
chr8_-_115140080 5.69 ENSRNOT00000015851
aminoacylase 1
chr6_-_55001464 5.56 ENSRNOT00000006618
aryl hydrocarbon receptor
chr3_+_11424099 5.55 ENSRNOT00000019184
prostaglandin E synthase 2
chrX_+_16946207 5.19 ENSRNOT00000003981
similar to cysteine-rich protein 2
chr3_+_113415774 5.08 ENSRNOT00000056151
small EDRK-rich factor 2
chr3_-_163935617 4.90 ENSRNOT00000074023
potassium voltage-gated channel subfamily B member 1
chr5_+_167141875 4.80 ENSRNOT00000089314
solute carrier family 2 member 5
chr10_+_83476107 4.69 ENSRNOT00000075733
prohibitin
chr1_+_219759183 4.59 ENSRNOT00000026316
pyruvate carboxylase
chr1_-_163328591 4.06 ENSRNOT00000034843
tsukushi, small leucine rich proteoglycan
chr6_+_99282850 4.04 ENSRNOT00000008374
methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1
chr9_-_20621051 4.03 ENSRNOT00000015918
TNF receptor superfamily member 21
chr10_-_11760620 3.81 ENSRNOT00000009283
deoxyribonuclease 1
chr10_-_62698541 3.79 ENSRNOT00000019759
coronin 6
chr6_+_80220547 3.51 ENSRNOT00000086221
ENSRNOT00000077435
ENSRNOT00000059318
ENSRNOT00000089010
melanoma inhibitory activity 2
chr7_+_123043503 3.51 ENSRNOT00000026258
ENSRNOT00000086355
TEF, PAR bZIP transcription factor
chr2_-_2683116 3.44 ENSRNOT00000016838
Rho-related BTB domain containing 3
chr14_-_33580566 3.41 ENSRNOT00000063942
phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthase
chr10_-_57618527 3.20 ENSRNOT00000037517
complement C1q binding protein
chr7_+_77966722 3.01 ENSRNOT00000006142
collagen triple helix repeat containing 1
chr2_-_204032023 2.74 ENSRNOT00000040430
ATPase Na+/K+ transporting subunit alpha 1
chr10_-_37455022 2.70 ENSRNOT00000016742
ubiquitin-conjugating enzyme E2 B
chr11_-_80826505 2.58 ENSRNOT00000032383
receptor (chemosensory) transporter protein 1
chr16_-_75855745 2.54 ENSRNOT00000031291
1-acylglycerol-3-phosphate O-acyltransferase 5
chr4_+_78981987 2.50 ENSRNOT00000012490
coiled-coil domain containing 126
chr4_-_77489535 2.45 ENSRNOT00000008728
protein disulfide isomerase family A, member 4
chr19_+_53055745 2.34 ENSRNOT00000074430
forkhead box L1
chr6_+_43829945 2.19 ENSRNOT00000086548
Kruppel-like factor 11
chr11_-_83985385 1.93 ENSRNOT00000002334
endothelin-converting enzyme 2-like
chrX_-_64702441 1.91 ENSRNOT00000051132
APC membrane recruitment protein 1
chr5_+_165405168 1.88 ENSRNOT00000014934
spermidine synthase
chr9_+_17817721 1.81 ENSRNOT00000086986
ENSRNOT00000026920
heat shock protein 90 alpha family class B member 1
chr7_-_27240528 1.74 ENSRNOT00000029435
ENSRNOT00000079731
heat shock protein 90 beta family member 1
chr3_+_61685619 1.73 ENSRNOT00000002140
homeo box D1
chr11_+_47090245 1.72 ENSRNOT00000060645

chr8_+_44990014 1.63 ENSRNOT00000044608
heat shock protein family A (Hsp70) member 8
chr10_+_46783979 1.45 ENSRNOT00000005237
GID complex subunit 4
chr4_-_78879294 1.44 ENSRNOT00000084543
insulin-like growth factor 2 mRNA binding protein 3
chr5_-_58124681 1.34 ENSRNOT00000019795
sigma non-opioid intracellular receptor 1
chr10_-_40375605 1.33 ENSRNOT00000014464
annexin A6
chr6_-_51257625 1.24 ENSRNOT00000012004
HMG-box transcription factor 1
chr19_+_58565576 1.19 ENSRNOT00000026965
nucleoside-triphosphatase, cancer-related
chr3_+_14588870 1.19 ENSRNOT00000071712
spermidine synthase-like
chr14_+_36216002 1.18 ENSRNOT00000038506
sec1 family domain containing 2
chr10_-_107324355 1.09 ENSRNOT00000064450
ubiquitin specific peptidase 36
chr3_+_148635775 1.03 ENSRNOT00000067261
transmembrane 9 superfamily member 4
chr2_-_148891900 0.99 ENSRNOT00000018488
siah E3 ubiquitin protein ligase 2
chr10_-_37209881 0.95 ENSRNOT00000090475
SEC24 homolog A, COPII coat complex component
chr5_+_74649765 0.94 ENSRNOT00000075952
paralemmin 2
chrX_+_43881246 0.92 ENSRNOT00000005153
hypothetical LOC317456
chr2_-_187160215 0.91 ENSRNOT00000092780
neurotrophic receptor tyrosine kinase 1
chr16_+_49462889 0.90 ENSRNOT00000039909
ankyrin repeat domain 37
chr15_+_4554603 0.86 ENSRNOT00000075153
potassium two pore domain channel subfamily K member 5
chr10_+_88764732 0.84 ENSRNOT00000026662
signal transducer and activator of transcription 5A
chr7_-_83701447 0.82 ENSRNOT00000088893

chr13_-_90814119 0.80 ENSRNOT00000011208
transgelin 2
chr4_+_113948514 0.75 ENSRNOT00000011521
mannosyl-oligosaccharide glucosidase
chr1_-_198120061 0.70 ENSRNOT00000026231
SLX1 structure-specific endonuclease subunit homolog B (S. cerevisiae)
chr6_+_33786627 0.69 ENSRNOT00000008359
pumilio RNA-binding family member 2
chr5_+_116421894 0.66 ENSRNOT00000080577
ENSRNOT00000086628
ENSRNOT00000004017
nuclear factor I/A
chr13_+_35554964 0.51 ENSRNOT00000072632
transmembrane protein 185B
chr1_+_198120099 0.45 ENSRNOT00000073652
bolA family member 2
chr16_+_7103998 0.29 ENSRNOT00000016581
polybromo 1
chr9_-_61690956 0.15 ENSRNOT00000066589
heat shock protein family D member 1
chr3_+_122803772 0.12 ENSRNOT00000009564
NOP56 ribonucleoprotein
chr13_+_100129761 0.03 ENSRNOT00000038340
eukaryotic translation initiation factor 3, subunit E-like 1
chr10_+_59000397 0.02 ENSRNOT00000021134
MYB binding protein 1a
chr3_+_107142762 0.01 ENSRNOT00000006177
similar to CDNA sequence BC052040

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
2.4 7.3 GO:0006552 leucine catabolic process(GO:0006552)
2.3 11.3 GO:0002003 angiotensin maturation(GO:0002003)
2.1 6.2 GO:0006543 glutamine catabolic process(GO:0006543)
1.4 5.6 GO:0040009 regulation of growth rate(GO:0040009)
1.3 4.0 GO:0000105 histidine biosynthetic process(GO:0000105)
1.2 4.7 GO:0045917 positive regulation of complement activation(GO:0045917) positive regulation of protein activation cascade(GO:2000259)
1.1 4.6 GO:0019072 viral genome packaging(GO:0019072) viral RNA genome packaging(GO:0019074)
1.1 3.2 GO:1901165 positive regulation of trophoblast cell migration(GO:1901165)
1.0 4.1 GO:1903334 positive regulation of protein folding(GO:1903334)
1.0 4.0 GO:0032696 negative regulation of interleukin-13 production(GO:0032696)
1.0 4.8 GO:0015755 fructose transport(GO:0015755)
0.8 4.9 GO:0010701 positive regulation of norepinephrine secretion(GO:0010701)
0.8 4.1 GO:0061073 ciliary body morphogenesis(GO:0061073)
0.8 2.3 GO:0061146 Peyer's patch morphogenesis(GO:0061146)
0.8 3.0 GO:0043932 ossification involved in bone remodeling(GO:0043932)
0.7 3.4 GO:0006189 'de novo' IMP biosynthetic process(GO:0006189)
0.6 3.1 GO:0008295 spermidine biosynthetic process(GO:0008295)
0.6 1.8 GO:0034486 vacuolar transmembrane transport(GO:0034486) chaperone-mediated protein transport involved in chaperone-mediated autophagy(GO:0061741) negative regulation of complement-dependent cytotoxicity(GO:1903660)
0.6 3.5 GO:0070973 protein localization to endoplasmic reticulum exit site(GO:0070973)
0.5 2.7 GO:0031947 negative regulation of glucocorticoid metabolic process(GO:0031944) negative regulation of glucocorticoid biosynthetic process(GO:0031947) potassium ion import across plasma membrane(GO:1990573)
0.4 12.7 GO:0015985 energy coupled proton transport, down electrochemical gradient(GO:0015985) ATP synthesis coupled proton transport(GO:0015986)
0.4 7.5 GO:0031581 hemidesmosome assembly(GO:0031581)
0.2 1.9 GO:0072161 mesenchymal cell differentiation involved in kidney development(GO:0072161) mesenchymal cell differentiation involved in renal system development(GO:2001012)
0.2 0.8 GO:0060375 development of secondary male sexual characteristics(GO:0046544) regulation of mast cell differentiation(GO:0060375)
0.2 0.7 GO:1904431 positive regulation of t-circle formation(GO:1904431)
0.2 1.7 GO:0071318 cellular response to ATP(GO:0071318)
0.1 1.3 GO:0038003 opioid receptor signaling pathway(GO:0038003)
0.1 2.2 GO:0000083 regulation of transcription involved in G1/S transition of mitotic cell cycle(GO:0000083)
0.1 3.8 GO:0006308 DNA catabolic process(GO:0006308)
0.1 2.6 GO:0051205 protein insertion into membrane(GO:0051205)
0.1 1.0 GO:0070072 vacuolar proton-transporting V-type ATPase complex assembly(GO:0070072)
0.1 8.1 GO:0061515 myeloid cell development(GO:0061515)
0.1 0.9 GO:2000189 regulation of low-density lipoprotein particle receptor biosynthetic process(GO:0045714) positive regulation of cholesterol homeostasis(GO:2000189)
0.1 7.1 GO:0032233 positive regulation of actin filament bundle assembly(GO:0032233)
0.1 0.5 GO:0044571 [2Fe-2S] cluster assembly(GO:0044571)
0.1 5.5 GO:0045454 cell redox homeostasis(GO:0045454)
0.1 0.7 GO:1900246 positive regulation of RIG-I signaling pathway(GO:1900246)
0.1 1.3 GO:0051560 mitochondrial calcium ion homeostasis(GO:0051560)
0.1 0.7 GO:0072189 ureter development(GO:0072189)
0.1 1.2 GO:0032369 negative regulation of lipid transport(GO:0032369)
0.0 0.1 GO:0002840 T cell mediated immune response to tumor cell(GO:0002424) regulation of T cell mediated immune response to tumor cell(GO:0002840) protein import into mitochondrial intermembrane space(GO:0045041)
0.0 3.4 GO:0042147 retrograde transport, endosome to Golgi(GO:0042147)
0.0 6.6 GO:0055001 muscle cell development(GO:0055001)
0.0 2.5 GO:0006487 protein N-linked glycosylation(GO:0006487)
0.0 0.8 GO:0009311 oligosaccharide metabolic process(GO:0009311)
0.0 1.2 GO:0006904 vesicle docking involved in exocytosis(GO:0006904)
0.0 1.1 GO:1903146 regulation of mitophagy(GO:1903146)
0.0 2.5 GO:0006639 acylglycerol metabolic process(GO:0006639)
0.0 4.2 GO:0006520 cellular amino acid metabolic process(GO:0006520)
0.0 1.0 GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process(GO:0043154)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.9 7.5 GO:0043259 laminin-1 complex(GO:0005606) laminin-10 complex(GO:0043259)
1.5 7.4 GO:0034751 aryl hydrocarbon receptor complex(GO:0034751)
1.1 6.8 GO:0016012 sarcoglycan complex(GO:0016012)
1.0 12.7 GO:0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)(GO:0000276)
0.9 4.7 GO:0031315 extrinsic component of mitochondrial outer membrane(GO:0031315)
0.8 11.3 GO:0031983 vesicle lumen(GO:0031983)
0.5 1.6 GO:1990836 lysosomal matrix(GO:1990836)
0.4 4.2 GO:0034663 endoplasmic reticulum chaperone complex(GO:0034663)
0.2 0.7 GO:0033557 Slx1-Slx4 complex(GO:0033557)
0.2 2.7 GO:0005890 sodium:potassium-exchanging ATPase complex(GO:0005890)
0.2 3.5 GO:0070971 endoplasmic reticulum exit site(GO:0070971)
0.2 8.8 GO:0010494 cytoplasmic stress granule(GO:0010494)
0.1 4.9 GO:0032809 neuronal cell body membrane(GO:0032809)
0.1 0.9 GO:0030127 COPII vesicle coat(GO:0030127)
0.1 1.3 GO:0005640 nuclear outer membrane(GO:0005640)
0.0 7.1 GO:0030018 Z disc(GO:0030018)
0.0 6.1 GO:0042383 sarcolemma(GO:0042383)
0.0 3.0 GO:0005581 collagen trimer(GO:0005581)
0.0 12.3 GO:0005759 mitochondrial matrix(GO:0005759)
0.0 0.3 GO:0090544 BAF-type complex(GO:0090544)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
1.9 5.7 GO:0004046 aminoacylase activity(GO:0004046)
1.9 5.6 GO:0004874 aryl hydrocarbon receptor activity(GO:0004874)
1.8 5.5 GO:0050220 prostaglandin-E synthase activity(GO:0050220)
1.6 4.7 GO:0031871 proteinase activated receptor binding(GO:0031871)
1.5 4.6 GO:0004736 pyruvate carboxylase activity(GO:0004736)
1.0 4.0 GO:0004487 methylenetetrahydrofolate dehydrogenase (NAD+) activity(GO:0004487)
0.9 7.3 GO:0016421 CoA carboxylase activity(GO:0016421)
0.8 7.5 GO:0043208 glycosphingolipid binding(GO:0043208)
0.8 3.2 GO:0030984 kininogen binding(GO:0030984)
0.6 12.7 GO:0046933 proton-transporting ATP synthase activity, rotational mechanism(GO:0046933)
0.6 2.5 GO:0030144 alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity(GO:0030144)
0.6 1.8 GO:0017098 UTP binding(GO:0002134) sulfonylurea receptor binding(GO:0017098) pyrimidine ribonucleoside binding(GO:0032551)
0.6 3.5 GO:0042954 lipoprotein transporter activity(GO:0042954)
0.5 4.8 GO:0070061 fructose binding(GO:0070061)
0.5 2.6 GO:0031849 olfactory receptor binding(GO:0031849)
0.5 11.3 GO:0070006 metalloaminopeptidase activity(GO:0070006)
0.4 4.5 GO:0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters(GO:0016888)
0.4 1.6 GO:0031686 A1 adenosine receptor binding(GO:0031686)
0.3 2.7 GO:1990239 steroid hormone binding(GO:1990239)
0.2 4.9 GO:0015271 outward rectifier potassium channel activity(GO:0015271)
0.2 3.7 GO:0008143 poly(A) binding(GO:0008143)
0.2 1.3 GO:0004985 opioid receptor activity(GO:0004985)
0.2 2.5 GO:0003841 1-acylglycerol-3-phosphate O-acyltransferase activity(GO:0003841)
0.2 1.2 GO:0098519 nucleotide phosphatase activity, acting on free nucleotides(GO:0098519)
0.2 1.7 GO:0046790 virion binding(GO:0046790)
0.2 4.0 GO:0005031 tumor necrosis factor-activated receptor activity(GO:0005031) death receptor activity(GO:0005035)
0.2 2.4 GO:0015037 peptide disulfide oxidoreductase activity(GO:0015037)
0.2 6.2 GO:0051539 4 iron, 4 sulfur cluster binding(GO:0051539)
0.2 3.4 GO:0016881 acid-amino acid ligase activity(GO:0016881)
0.1 3.0 GO:0017147 Wnt-protein binding(GO:0017147)
0.1 11.3 GO:0005200 structural constituent of cytoskeleton(GO:0005200)
0.1 1.4 GO:0048027 mRNA 5'-UTR binding(GO:0048027)
0.0 0.8 GO:0015926 glucosidase activity(GO:0015926)
0.0 3.1 GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups(GO:0016765)
0.0 1.3 GO:0015485 cholesterol binding(GO:0015485)
0.0 0.1 GO:0034186 apolipoprotein A-I binding(GO:0034186)
0.0 1.9 GO:0005546 phosphatidylinositol-4,5-bisphosphate binding(GO:0005546)
0.0 10.9 GO:0003779 actin binding(GO:0003779)
0.0 1.0 GO:0031624 ubiquitin conjugating enzyme binding(GO:0031624)
0.0 3.4 GO:0017137 Rab GTPase binding(GO:0017137)
0.0 0.1 GO:1990226 histone methyltransferase binding(GO:1990226)
0.0 0.7 GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding(GO:0000979)
0.0 1.1 GO:0004843 thiol-dependent ubiquitin-specific protease activity(GO:0004843)
0.0 3.4 GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001077)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 7.5 PID INTEGRIN4 PATHWAY Alpha6 beta4 integrin-ligand interactions
0.1 5.5 PID IFNG PATHWAY IFN-gamma pathway
0.1 3.0 PID WNT SIGNALING PATHWAY Wnt signaling network
0.1 0.8 PID IL5 PATHWAY IL5-mediated signaling events
0.0 1.2 PID MYC PATHWAY C-MYC pathway
0.0 1.7 PID IL6 7 PATHWAY IL6-mediated signaling events
0.0 1.8 PID VEGFR1 2 PATHWAY Signaling events mediated by VEGFR1 and VEGFR2
0.0 1.6 PID CMYB PATHWAY C-MYB transcription factor network
0.0 0.7 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
0.8 9.7 REACTOME PURINE RIBONUCLEOSIDE MONOPHOSPHATE BIOSYNTHESIS Genes involved in Purine ribonucleoside monophosphate biosynthesis
0.8 12.7 REACTOME FORMATION OF ATP BY CHEMIOSMOTIC COUPLING Genes involved in Formation of ATP by chemiosmotic coupling
0.6 11.3 REACTOME POST CHAPERONIN TUBULIN FOLDING PATHWAY Genes involved in Post-chaperonin tubulin folding pathway
0.4 7.3 REACTOME BRANCHED CHAIN AMINO ACID CATABOLISM Genes involved in Branched-chain amino acid catabolism
0.3 4.8 REACTOME FACILITATIVE NA INDEPENDENT GLUCOSE TRANSPORTERS Genes involved in Facilitative Na+-independent glucose transporters
0.2 1.7 REACTOME ACTIVATION OF CHAPERONE GENES BY ATF6 ALPHA Genes involved in Activation of Chaperone Genes by ATF6-alpha
0.2 3.2 REACTOME INTRINSIC PATHWAY Genes involved in Intrinsic Pathway
0.2 1.8 REACTOME THE NLRP3 INFLAMMASOME Genes involved in The NLRP3 inflammasome
0.1 4.6 REACTOME GLUCONEOGENESIS Genes involved in Gluconeogenesis
0.1 4.9 REACTOME REGULATION OF INSULIN SECRETION BY GLUCAGON LIKE PEPTIDE1 Genes involved in Regulation of Insulin Secretion by Glucagon-like Peptide-1
0.1 2.5 REACTOME SYNTHESIS OF PA Genes involved in Synthesis of PA
0.1 4.0 REACTOME METABOLISM OF VITAMINS AND COFACTORS Genes involved in Metabolism of vitamins and cofactors
0.1 1.6 REACTOME LYSOSOME VESICLE BIOGENESIS Genes involved in Lysosome Vesicle Biogenesis
0.1 7.5 REACTOME L1CAM INTERACTIONS Genes involved in L1CAM interactions
0.1 2.7 REACTOME ION TRANSPORT BY P TYPE ATPASES Genes involved in Ion transport by P-type ATPases
0.1 0.8 REACTOME IL 7 SIGNALING Genes involved in Interleukin-7 signaling
0.0 0.3 REACTOME METABOLISM OF POLYAMINES Genes involved in Metabolism of polyamines
0.0 1.4 REACTOME PPARA ACTIVATES GENE EXPRESSION Genes involved in PPARA Activates Gene Expression
0.0 1.4 REACTOME DIABETES PATHWAYS Genes involved in Diabetes pathways