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GSE58827: Dynamics of the Mouse Liver

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Results for Rara

Z-value: 0.87

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Transcription factors associated with Rara

Gene Symbol Gene ID Gene Info
Rara
ENSMUSG00000037992.10 retinoic acid receptor, alpha

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Raramm10_v2_chr11_+_98937669_98937735-0.124.9e-01Click!

Activity profile of Rara motif

Sorted Z-values of Rara motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr19_+_37697792 12.02 ENSMUST00000025946.5
Cyp26a1
cytochrome P450, family 26, subfamily a, polypeptide 1
chr8_-_72212837 8.58 ENSMUST00000098630.3
Cib3
calcium and integrin binding family member 3
chr4_-_46991842 7.52 ENSMUST00000107749.2
Gabbr2
gamma-aminobutyric acid (GABA) B receptor, 2
chr11_-_5915124 7.16 ENSMUST00000109823.2
ENSMUST00000109822.1
Gck
glucokinase
chr19_-_8405060 7.05 ENSMUST00000064507.5
ENSMUST00000120540.1
ENSMUST00000096269.4
Slc22a30
solute carrier family 22, member 30
chr19_-_7802578 4.75 ENSMUST00000120522.1
ENSMUST00000065634.7
Slc22a26
solute carrier family 22 (organic cation transporter), member 26
chr7_-_141010759 4.05 ENSMUST00000026565.6
Ifitm3
interferon induced transmembrane protein 3
chr11_+_98960412 3.93 ENSMUST00000107473.2
Rara
retinoic acid receptor, alpha
chrX_-_75874536 3.23 ENSMUST00000033547.7
Pls3
plastin 3 (T-isoform)
chr10_+_4611971 2.75 ENSMUST00000105590.1
ENSMUST00000067086.7
Esr1
estrogen receptor 1 (alpha)
chr7_-_44670820 2.73 ENSMUST00000048102.7
Myh14
myosin, heavy polypeptide 14
chr3_+_89229046 2.70 ENSMUST00000041142.3
Muc1
mucin 1, transmembrane
chr5_-_105239533 2.30 ENSMUST00000065588.6
Gbp10
guanylate-binding protein 10
chr6_-_124542281 2.28 ENSMUST00000159463.1
ENSMUST00000162844.1
ENSMUST00000160505.1
ENSMUST00000162443.1
C1s
complement component 1, s subcomponent
chr2_+_169633517 2.06 ENSMUST00000109157.1
Tshz2
teashirt zinc finger family member 2
chr2_+_120977017 1.86 ENSMUST00000067582.7
Tmem62
transmembrane protein 62
chr11_-_5261558 1.82 ENSMUST00000020662.8
Kremen1
kringle containing transmembrane protein 1
chr4_+_150853919 1.77 ENSMUST00000073600.2
Errfi1
ERBB receptor feedback inhibitor 1
chr14_-_30353468 1.74 ENSMUST00000112249.1
Cacna1d
calcium channel, voltage-dependent, L type, alpha 1D subunit
chr5_+_138255608 1.73 ENSMUST00000062067.6
Lamtor4
late endosomal/lysosomal adaptor, MAPK and MTOR activator 4
chr1_+_157458554 1.72 ENSMUST00000046743.4
ENSMUST00000119891.1
BC026585
cDNA sequence BC026585
chr7_+_17150210 1.68 ENSMUST00000108491.1
ENSMUST00000065540.5
Ceacam3
carcinoembryonic antigen-related cell adhesion molecule 3
chr2_-_5012716 1.51 ENSMUST00000027980.7
Mcm10
minichromosome maintenance deficient 10 (S. cerevisiae)
chr12_-_54862783 1.45 ENSMUST00000078124.7
Cfl2
cofilin 2, muscle
chr6_+_91157373 1.38 ENSMUST00000155007.1
Hdac11
histone deacetylase 11
chr5_+_114853660 1.31 ENSMUST00000031547.5
4930519G04Rik
RIKEN cDNA 4930519G04 gene
chr5_+_87925624 1.16 ENSMUST00000113271.2
Csn3
casein kappa
chr8_+_106150359 1.15 ENSMUST00000034377.6
Pla2g15
phospholipase A2, group XV
chr3_+_79345361 1.12 ENSMUST00000164216.1
Gm17359
predicted gene, 17359
chr9_+_75410145 1.10 ENSMUST00000180533.1
ENSMUST00000180574.1
4933433G15Rik
RIKEN cDNA 4933433G15 gene
chr14_-_70207637 1.02 ENSMUST00000022682.5
Sorbs3
sorbin and SH3 domain containing 3
chr12_+_87026564 0.93 ENSMUST00000110187.1
ENSMUST00000156162.1
Tmem63c
transmembrane protein 63c
chr3_-_36475688 0.91 ENSMUST00000029266.8
Anxa5
annexin A5
chr3_-_88058446 0.90 ENSMUST00000029708.6
Apoa1bp
apolipoprotein A-I binding protein
chr5_+_53267103 0.85 ENSMUST00000121042.1
Smim20
small integral membrane protein 20
chr2_-_91070283 0.84 ENSMUST00000111436.2
ENSMUST00000073575.5
Slc39a13
solute carrier family 39 (metal ion transporter), member 13
chr12_-_108893197 0.81 ENSMUST00000161154.1
ENSMUST00000161410.1
Wars
tryptophanyl-tRNA synthetase
chr5_-_114273702 0.79 ENSMUST00000144050.1
ENSMUST00000044790.5
Foxn4
forkhead box N4
chr7_+_120635176 0.73 ENSMUST00000033176.5
Uqcrc2
ubiquinol cytochrome c reductase core protein 2
chr10_+_21993890 0.70 ENSMUST00000092673.4
Sgk1
serum/glucocorticoid regulated kinase 1
chr7_+_45873127 0.68 ENSMUST00000107718.1
Kdelr1
KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1
chr2_-_91070180 0.68 ENSMUST00000153367.1
ENSMUST00000079976.3
Slc39a13
solute carrier family 39 (metal ion transporter), member 13
chr14_-_16575456 0.67 ENSMUST00000063750.6
Rarb
retinoic acid receptor, beta
chr10_+_19951055 0.65 ENSMUST00000152533.1
Map3k5
mitogen-activated protein kinase kinase kinase 5
chr8_-_119778380 0.64 ENSMUST00000049156.5
Tldc1
TBC/LysM associated domain containing 1
chr14_+_64588112 0.63 ENSMUST00000181808.1
A930011O12Rik
RIKEN cDNA A930011O12 gene
chr6_+_115601907 0.61 ENSMUST00000000449.7
Mkrn2
makorin, ring finger protein, 2
chr2_+_181365384 0.59 ENSMUST00000108807.2
Zgpat
zinc finger, CCCH-type with G patch domain
chr17_-_67632707 0.55 ENSMUST00000097290.2
Lrrc30
leucine rich repeat containing 30
chr7_+_45872772 0.53 ENSMUST00000002855.5
ENSMUST00000107719.1
Kdelr1
KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1
chr7_-_141429433 0.52 ENSMUST00000124444.1
Cend1
cell cycle exit and neuronal differentiation 1
chr6_-_54972603 0.51 ENSMUST00000060655.8
Nod1
nucleotide-binding oligomerization domain containing 1
chr3_+_93468751 0.49 ENSMUST00000029516.2
Tchhl1
trichohyalin-like 1
chr14_-_74947865 0.47 ENSMUST00000088970.5
Lrch1
leucine-rich repeats and calponin homology (CH) domain containing 1
chr7_+_15750377 0.45 ENSMUST00000098802.3
ENSMUST00000173053.1
Obox5
oocyte specific homeobox 5
chrX_+_106187100 0.43 ENSMUST00000081593.6
Pgk1
phosphoglycerate kinase 1
chr7_-_141429351 0.43 ENSMUST00000164387.1
ENSMUST00000137488.1
ENSMUST00000084436.3
Cend1
cell cycle exit and neuronal differentiation 1
chr2_-_181365306 0.42 ENSMUST00000108808.1
ENSMUST00000170190.1
ENSMUST00000127988.1
Arfrp1
ADP-ribosylation factor related protein 1
chr7_-_131146306 0.39 ENSMUST00000070980.3
4933402N03Rik
RIKEN cDNA 4933402N03 gene
chr4_-_152318458 0.38 ENSMUST00000170820.1
ENSMUST00000076183.5
Rnf207
ring finger protein 207
chr10_+_82812123 0.37 ENSMUST00000178540.1
ENSMUST00000076984.6
1700028I16Rik
RIKEN cDNA 1700028I16 gene
chr4_+_141444654 0.36 ENSMUST00000006377.6
Zbtb17
zinc finger and BTB domain containing 17
chr6_-_6217023 0.34 ENSMUST00000015256.8
Slc25a13
solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 13
chr4_+_42969945 0.33 ENSMUST00000030163.5
1700022I11Rik
RIKEN cDNA 1700022I11 gene
chr4_+_41348996 0.33 ENSMUST00000072866.5
ENSMUST00000108060.3
Ubap1
ubiquitin-associated protein 1
chr6_-_39810881 0.33 ENSMUST00000114797.1
ENSMUST00000031978.8
Mrps33
mitochondrial ribosomal protein S33
chr3_-_75556759 0.32 ENSMUST00000162138.1
ENSMUST00000029424.5
ENSMUST00000161137.1
Pdcd10
programmed cell death 10
chr4_+_48045144 0.28 ENSMUST00000030025.3
Nr4a3
nuclear receptor subfamily 4, group A, member 3
chr4_-_128609981 0.21 ENSMUST00000141040.1
ENSMUST00000147876.1
ENSMUST00000097877.2
Zscan20
zinc finger and SCAN domains 20
chr10_-_89257790 0.21 ENSMUST00000045601.7
Ano4
anoctamin 4
chr3_+_79884931 0.20 ENSMUST00000135021.1
Fam198b
family with sequence similarity 198, member B
chr17_-_56133817 0.20 ENSMUST00000167545.1
Sema6b
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B
chr1_-_163403627 0.17 ENSMUST00000045138.4
Gorab
golgin, RAB6-interacting
chr7_+_17713233 0.17 ENSMUST00000081907.6
Ceacam5
carcinoembryonic antigen-related cell adhesion molecule 5
chr11_+_94629741 0.15 ENSMUST00000021239.6
Lrrc59
leucine rich repeat containing 59
chr3_-_95015214 0.15 ENSMUST00000128438.1
ENSMUST00000149747.1
ENSMUST00000019482.1
Zfp687
zinc finger protein 687
chr9_-_43105718 0.13 ENSMUST00000165665.1
Arhgef12
Rho guanine nucleotide exchange factor (GEF) 12
chr13_+_111255010 0.09 ENSMUST00000054716.3
Actbl2
actin, beta-like 2
chr13_+_94875600 0.08 ENSMUST00000022195.10
Otp
orthopedia homolog (Drosophila)
chr9_-_109074049 0.04 ENSMUST00000161521.1
ENSMUST00000045011.2
Atrip
ATR interacting protein
chr1_+_131750485 0.03 ENSMUST00000147800.1
Slc26a9
solute carrier family 26, member 9
chr7_-_104279732 0.03 ENSMUST00000051795.9
Trim5
tripartite motif-containing 5

Network of associatons between targets according to the STRING database.

First level regulatory network of Rara

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
3.0 12.0 GO:0034653 diterpenoid catabolic process(GO:0016103) retinoic acid catabolic process(GO:0034653)
1.4 7.2 GO:0009730 detection of carbohydrate stimulus(GO:0009730) detection of hexose stimulus(GO:0009732) detection of monosaccharide stimulus(GO:0034287) detection of glucose(GO:0051594)
1.3 3.9 GO:0060010 Sertoli cell fate commitment(GO:0060010)
0.8 11.8 GO:0015747 urate transport(GO:0015747)
0.5 2.8 GO:0060011 Sertoli cell proliferation(GO:0060011) prostate epithelial cord elongation(GO:0060523)
0.4 1.7 GO:0086046 membrane depolarization during SA node cell action potential(GO:0086046)
0.4 1.5 GO:0030043 actin filament fragmentation(GO:0030043)
0.4 1.8 GO:0042536 negative regulation of tumor necrosis factor biosynthetic process(GO:0042536)
0.3 0.9 GO:0021933 radial glia guided migration of cerebellar granule cell(GO:0021933)
0.3 0.8 GO:0006436 tryptophanyl-tRNA aminoacylation(GO:0006436)
0.2 7.5 GO:0007214 gamma-aminobutyric acid signaling pathway(GO:0007214)
0.2 1.2 GO:0006621 protein retention in ER lumen(GO:0006621)
0.2 4.1 GO:0046597 negative regulation of viral entry into host cell(GO:0046597)
0.2 1.1 GO:0034638 phosphatidylcholine catabolic process(GO:0034638)
0.2 0.9 GO:0070459 prolactin secretion(GO:0070459)
0.1 0.4 GO:1903116 positive regulation of actin filament-based movement(GO:1903116)
0.1 3.2 GO:0051639 actin filament network formation(GO:0051639)
0.1 0.3 GO:1903588 negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis(GO:1903588)
0.1 0.7 GO:0006627 protein processing involved in protein targeting to mitochondrion(GO:0006627)
0.1 0.3 GO:0032765 positive regulation of mast cell cytokine production(GO:0032765)
0.1 0.3 GO:0043490 malate-aspartate shuttle(GO:0043490)
0.1 2.7 GO:0071625 vocalization behavior(GO:0071625)
0.1 0.7 GO:0003406 retinal pigment epithelium development(GO:0003406)
0.1 1.5 GO:0071577 zinc II ion transmembrane transport(GO:0071577)
0.1 0.5 GO:0002606 positive regulation of dendritic cell antigen processing and presentation(GO:0002606)
0.1 1.7 GO:0061462 protein localization to lysosome(GO:0061462)
0.1 2.2 GO:0042832 defense response to protozoan(GO:0042832)
0.1 0.8 GO:0097034 mitochondrial respiratory chain complex IV assembly(GO:0033617) mitochondrial respiratory chain complex IV biogenesis(GO:0097034)
0.0 0.7 GO:0043402 glucocorticoid mediated signaling pathway(GO:0043402)
0.0 0.8 GO:0035881 amacrine cell differentiation(GO:0035881)
0.0 0.2 GO:0061589 calcium activated phosphatidylserine scrambling(GO:0061589)
0.0 1.5 GO:0006270 DNA replication initiation(GO:0006270)
0.0 0.7 GO:1902170 cellular response to reactive nitrogen species(GO:1902170)
0.0 0.6 GO:0007175 negative regulation of epidermal growth factor-activated receptor activity(GO:0007175)
0.0 1.4 GO:0014003 oligodendrocyte development(GO:0014003)
0.0 0.3 GO:0043162 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway(GO:0043162)
0.0 0.6 GO:1903204 negative regulation of oxidative stress-induced neuron death(GO:1903204)
0.0 0.4 GO:0034067 protein localization to Golgi apparatus(GO:0034067)
0.0 0.4 GO:0007398 ectoderm development(GO:0007398)
0.0 1.0 GO:0051496 positive regulation of stress fiber assembly(GO:0051496)
0.0 0.4 GO:0031639 plasminogen activation(GO:0031639)
0.0 0.9 GO:0007595 lactation(GO:0007595)
0.0 0.2 GO:1901620 regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning(GO:1901620)
0.0 1.8 GO:0090090 negative regulation of canonical Wnt signaling pathway(GO:0090090)
0.0 0.5 GO:0000027 ribosomal large subunit assembly(GO:0000027)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
1.5 7.5 GO:0038039 G-protein coupled receptor heterodimeric complex(GO:0038039)
0.5 2.7 GO:0097513 myosin II filament(GO:0097513)
0.4 7.2 GO:0045180 basal cortex(GO:0045180)
0.4 2.8 GO:0097550 transcriptional preinitiation complex(GO:0097550)
0.3 1.7 GO:0071986 Ragulator complex(GO:0071986)
0.2 1.5 GO:0031298 replication fork protection complex(GO:0031298)
0.2 1.7 GO:1990454 L-type voltage-gated calcium channel complex(GO:1990454)
0.1 0.7 GO:1990604 IRE1-TRAF2-ASK1 complex(GO:1990604)
0.1 0.7 GO:0005750 mitochondrial respiratory chain complex III(GO:0005750)
0.0 3.2 GO:0032420 stereocilium(GO:0032420)
0.0 0.3 GO:0000813 ESCRT I complex(GO:0000813)
0.0 1.2 GO:0005801 cis-Golgi network(GO:0005801)
0.0 0.5 GO:0030687 preribosome, large subunit precursor(GO:0030687)
0.0 1.4 GO:0000118 histone deacetylase complex(GO:0000118)
0.0 2.4 GO:0030018 Z disc(GO:0030018)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
4.0 12.0 GO:0008401 retinoic acid 4-hydroxylase activity(GO:0008401)
1.3 7.5 GO:0004965 G-protein coupled GABA receptor activity(GO:0004965)
0.9 2.8 GO:0038052 type 1 metabotropic glutamate receptor binding(GO:0031798) RNA polymerase II transcription factor activity, estrogen-activated sequence-specific DNA binding(GO:0038052)
0.8 11.8 GO:1901702 urate transmembrane transporter activity(GO:0015143) salt transmembrane transporter activity(GO:1901702)
0.7 7.2 GO:0004396 glucokinase activity(GO:0004340) hexokinase activity(GO:0004396)
0.3 1.2 GO:0046923 ER retention sequence binding(GO:0046923)
0.3 3.9 GO:0035014 phosphatidylinositol 3-kinase regulator activity(GO:0035014)
0.3 0.8 GO:0004830 tryptophan-tRNA ligase activity(GO:0004830)
0.2 1.7 GO:0086007 voltage-gated calcium channel activity involved in cardiac muscle cell action potential(GO:0086007)
0.1 2.7 GO:0030898 actin-dependent ATPase activity(GO:0030898)
0.1 1.1 GO:0047499 calcium-independent phospholipase A2 activity(GO:0047499)
0.1 0.4 GO:0016774 phosphotransferase activity, carboxyl group as acceptor(GO:0016774)
0.1 1.5 GO:0003688 DNA replication origin binding(GO:0003688)
0.1 0.7 GO:0043423 3-phosphoinositide-dependent protein kinase binding(GO:0043423)
0.1 0.3 GO:0015183 L-aspartate transmembrane transporter activity(GO:0015183)
0.1 1.4 GO:0032041 histone deacetylase activity (H3-K14 specific)(GO:0031078) NAD-dependent histone deacetylase activity (H3-K14 specific)(GO:0032041)
0.1 1.0 GO:0017166 vinculin binding(GO:0017166)
0.0 1.5 GO:0005385 zinc ion transmembrane transporter activity(GO:0005385)
0.0 0.9 GO:0005388 calcium-transporting ATPase activity(GO:0005388)
0.0 0.5 GO:0050700 CARD domain binding(GO:0050700)
0.0 0.7 GO:0003708 retinoic acid receptor activity(GO:0003708)
0.0 0.7 GO:0004709 MAP kinase kinase kinase activity(GO:0004709)
0.0 0.9 GO:0005227 calcium activated cation channel activity(GO:0005227)
0.0 5.4 GO:0000287 magnesium ion binding(GO:0000287)
0.0 4.7 GO:0051015 actin filament binding(GO:0051015)
0.0 0.6 GO:0001223 transcription coactivator binding(GO:0001223)
0.0 1.7 GO:0032947 protein complex scaffold(GO:0032947)
0.0 0.2 GO:0005229 intracellular calcium activated chloride channel activity(GO:0005229)
0.0 2.7 GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding(GO:0001078)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.1 7.8 ST JNK MAPK PATHWAY JNK MAPK Pathway
0.1 4.6 PID RETINOIC ACID PATHWAY Retinoic acid receptors-mediated signaling
0.1 2.8 PID FOXM1 PATHWAY FOXM1 transcription factor network
0.1 1.8 PID WNT SIGNALING PATHWAY Wnt signaling network
0.0 1.2 PID ARF 3PATHWAY Arf1 pathway
0.0 1.5 SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES Genes related to regulation of the actin cytoskeleton
0.0 1.4 PID HDAC CLASSII PATHWAY Signaling events mediated by HDAC Class II
0.0 3.8 NABA ECM AFFILIATED Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins
0.0 0.7 PID FOXO PATHWAY FoxO family signaling
0.0 0.4 PID MYC PATHWAY C-MYC pathway
0.0 0.4 PID HIF2PATHWAY HIF-2-alpha transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 12.0 REACTOME CYTOCHROME P450 ARRANGED BY SUBSTRATE TYPE Genes involved in Cytochrome P450 - arranged by substrate type
0.4 7.5 REACTOME CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS Genes involved in Class C/3 (Metabotropic glutamate/pheromone receptors)
0.3 2.3 REACTOME CREATION OF C4 AND C2 ACTIVATORS Genes involved in Creation of C4 and C2 activators
0.2 7.2 REACTOME REGULATION OF GLUCOKINASE BY GLUCOKINASE REGULATORY PROTEIN Genes involved in Regulation of Glucokinase by Glucokinase Regulatory Protein
0.1 2.9 REACTOME SEMA4D INDUCED CELL MIGRATION AND GROWTH CONE COLLAPSE Genes involved in Sema4D induced cell migration and growth-cone collapse
0.1 7.0 REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY Genes involved in Nuclear Receptor transcription pathway
0.1 4.1 REACTOME INTERFERON ALPHA BETA SIGNALING Genes involved in Interferon alpha/beta signaling
0.0 1.5 REACTOME ACTIVATION OF THE PRE REPLICATIVE COMPLEX Genes involved in Activation of the pre-replicative complex
0.0 0.8 REACTOME CYTOSOLIC TRNA AMINOACYLATION Genes involved in Cytosolic tRNA aminoacylation
0.0 1.0 REACTOME SMOOTH MUSCLE CONTRACTION Genes involved in Smooth Muscle Contraction
0.0 0.5 REACTOME ACTIVATED TAK1 MEDIATES P38 MAPK ACTIVATION Genes involved in activated TAK1 mediates p38 MAPK activation
0.0 0.8 REACTOME GLUCONEOGENESIS Genes involved in Gluconeogenesis
0.0 0.9 REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION Genes involved in NOTCH1 Intracellular Domain Regulates Transcription
0.0 0.7 REACTOME RESPIRATORY ELECTRON TRANSPORT Genes involved in Respiratory electron transport