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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Rara

Z-value: 0.74

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Transcription factors associated with Rara

Gene Symbol Gene ID Gene Info
Rara
ENSRNOG00000009972 retinoic acid receptor, alpha

Activity-expression correlation:

GenePromoterPearson corr. coef.P-valuePlot
Rararn6_v1_chr10_+_86860685_868606850.323.3e-09Click!

Activity profile of Rara motif

Sorted Z-values of Rara motif

Top targets:  

Promoter Log-likelihood Transcript Gene Gene Info
chr3_+_149624712 26.91 ENSRNOT00000018581
Bpifa1
BPI fold containing family A, member 1
chr2_+_188543137 25.82 ENSRNOT00000027850
Muc1
mucin 1, cell surface associated
chrX_+_139780386 20.95 ENSRNOT00000081147
AABR07041779.2

chr4_-_17594598 20.91 ENSRNOT00000008936
Sema3e
semaphorin 3E
chr5_-_50193571 19.17 ENSRNOT00000051243
Cfap206
cilia and flagella associated protein 206
chr4_-_11610518 18.79 ENSRNOT00000066643
Magi2
membrane associated guanylate kinase, WW and PDZ domain containing 2
chr13_+_47454591 17.09 ENSRNOT00000005791
LOC498222
similar to specifically androgen-regulated protein
chr10_+_90348299 14.01 ENSRNOT00000089616
Rundc3a
RUN domain containing 3A
chr4_+_96562725 13.73 ENSRNOT00000009094
Ndnf
neuron-derived neurotrophic factor
chr10_-_82229140 12.52 ENSRNOT00000004400
Epn3
epsin 3
chr1_-_173682226 11.94 ENSRNOT00000020137
Ric3
RIC3 acetylcholine receptor chaperone
chr7_+_30699476 11.77 ENSRNOT00000059269
Anks1b
ankyrin repeat and sterile alpha motif domain containing 1B
chr10_-_14056169 11.62 ENSRNOT00000017833
Syngr3
synaptogyrin 3
chr8_-_107656861 10.96 ENSRNOT00000050374
Mras
muscle RAS oncogene homolog
chr13_-_52197205 9.99 ENSRNOT00000009712
Shisa4
shisa family member 4
chr1_-_64350338 9.95 ENSRNOT00000078444
Cacng8
calcium voltage-gated channel auxiliary subunit gamma 8
chr20_-_31956649 9.87 ENSRNOT00000072429
Hk1
hexokinase 1
chr1_-_213973163 8.98 ENSRNOT00000024867
LOC100911402
cell cycle exit and neuronal differentiation protein 1-like
chrX_+_105537602 8.66 ENSRNOT00000029833
Armcx1
armadillo repeat containing, X-linked 1
chr5_-_141242131 8.13 ENSRNOT00000081482
Macf1
microtubule-actin crosslinking factor 1
chr2_-_123193130 8.05 ENSRNOT00000019554
Anxa5
annexin A5
chr18_+_60639860 7.87 ENSRNOT00000083363
Nedd4l
neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase
chr5_-_152473868 7.54 ENSRNOT00000022130
Fam110d
family with sequence similarity 110, member D
chr19_+_10563423 7.51 ENSRNOT00000021037
Dok4
docking protein 4
chr16_+_21061237 7.38 ENSRNOT00000092136
Ncan
neurocan
chr18_+_48434652 7.07 ENSRNOT00000047755
Prdm6
PR/SET domain 6
chr12_-_40590361 6.74 ENSRNOT00000067503
Tmem116
transmembrane protein 116
chr1_+_100299626 6.43 ENSRNOT00000092327
ENSRNOT00000044257
Shank1
SH3 and multiple ankyrin repeat domains 1
chr8_-_65587658 6.38 ENSRNOT00000091982
Lrrc49
leucine rich repeat containing 49
chr6_+_111049559 6.24 ENSRNOT00000015571
Tmem63c
transmembrane protein 63c
chr16_+_20432899 6.11 ENSRNOT00000026271
Mpv17l2
MPV17 mitochondrial inner membrane protein like 2
chr7_+_130532435 5.06 ENSRNOT00000092672
ENSRNOT00000092535
Shank3
SH3 and multiple ankyrin repeat domains 3
chr15_-_56970365 5.04 ENSRNOT00000047192
Lrch1
leucine rich repeats and calponin homology domain containing 1
chr3_+_20641664 4.89 ENSRNOT00000044699
AABR07051741.1

chr10_+_57218087 4.59 ENSRNOT00000089853
Mink1
misshapen-like kinase 1
chr18_-_86878142 4.39 ENSRNOT00000058139
Dok6
docking protein 6
chr2_+_178679395 4.37 ENSRNOT00000088686
Fam198b
family with sequence similarity 198, member B
chr7_-_139223116 4.16 ENSRNOT00000086559
Endou
endonuclease, poly(U)-specific
chr8_-_47393503 4.09 ENSRNOT00000059868
Arhgef12
Rho guanine nucleotide exchange factor 12
chr1_+_221538104 3.88 ENSRNOT00000028527
Batf2
basic leucine zipper ATF-like transcription factor 2
chr8_-_127900463 3.69 ENSRNOT00000078303
Slc22a13
solute carrier family 22 member 13
chr15_-_4057104 3.65 ENSRNOT00000084350
ENSRNOT00000012270
Sec24c
SEC24 homolog C, COPII coat complex component
chr11_-_64968437 3.38 ENSRNOT00000059541
Cox17
COX17 cytochrome c oxidase copper chaperone
chr14_+_85230648 3.11 ENSRNOT00000089866
Ap1b1
adaptor-related protein complex 1, beta 1 subunit
chrX_+_96991658 2.90 ENSRNOT00000049969
AABR07040288.1

chr4_+_101882994 2.88 ENSRNOT00000087773
AABR07060963.1

chr2_+_178679041 2.85 ENSRNOT00000013524
Fam198b
family with sequence similarity 198, member B
chr8_-_50277797 2.60 ENSRNOT00000082508
Pafah1b2
platelet-activating factor acetylhydrolase 1b, catalytic subunit 2
chr3_-_20518105 2.53 ENSRNOT00000050435
AABR07051735.1

chr12_+_50270189 2.52 ENSRNOT00000086782
Asphd2
aspartate beta-hydroxylase domain containing 2
chr3_-_20419417 2.37 ENSRNOT00000077772
AABR07051733.3

chr20_+_42966140 2.05 ENSRNOT00000000707
Marcks
myristoylated alanine rich protein kinase C substrate
chr10_-_56444847 2.03 ENSRNOT00000056872
ENSRNOT00000092662
Nlgn2
neuroligin 2
chr2_+_62887267 2.02 ENSRNOT00000048026
Drosha
drosha ribonuclease III
chr1_-_227486976 1.77 ENSRNOT00000035812
Ms4a14
membrane spanning 4-domains A14
chr10_+_68232094 1.68 ENSRNOT00000009172
Spaca3
sperm acrosome associated 3
chr1_+_99648658 1.59 ENSRNOT00000039531
Klk13
kallikrein related-peptidase 13
chr6_-_124429701 1.58 ENSRNOT00000037902
ENSRNOT00000080950
Ttc7b
tetratricopeptide repeat domain 7B
chr8_-_21384131 1.56 ENSRNOT00000071010
Zfp560
zinc finger protein 560
chrX_-_45000363 1.55 ENSRNOT00000035538
Cldn34e
claudin 34E
chr6_-_26051229 1.44 ENSRNOT00000005855
Bre
brain and reproductive organ-expressed (TNFRSF1A modulator)
chr3_+_18315320 1.44 ENSRNOT00000006954
AABR07051626.2

chr16_+_7088476 1.41 ENSRNOT00000024624
Glt8d1
glycosyltransferase 8 domain containing 1
chr10_+_10774639 1.26 ENSRNOT00000061208
Sept12
septin 12
chr20_+_3827086 1.24 ENSRNOT00000081588
Rxrb
retinoid X receptor beta
chr3_+_176865156 1.19 ENSRNOT00000019084
Zgpat
zinc finger CCCH-type and G-patch domain containing
chr6_-_92527711 1.17 ENSRNOT00000007529
Nin
ninein
chr1_-_100746021 0.97 ENSRNOT00000037973
Zfp473
zinc finger protein 473
chr1_+_255040426 0.94 ENSRNOT00000092151
Pcgf5
polycomb group ring finger 5
chr2_+_178117466 0.92 ENSRNOT00000065115
ENSRNOT00000084198
LOC499643
similar to hypothetical protein FLJ25371
chr11_-_84037938 0.81 ENSRNOT00000002327
Abcf3
ATP binding cassette subfamily F member 3
chr10_+_14216155 0.70 ENSRNOT00000020192
Hagh
hydroxyacyl glutathione hydrolase
chr4_+_147514120 0.61 ENSRNOT00000013146
Mkrn2
makorin, ring finger protein, 2
chr2_+_203768117 0.48 ENSRNOT00000080176
Igsf3
immunoglobulin superfamily, member 3
chr1_+_88182155 0.43 ENSRNOT00000083176
Yif1b
Yip1 interacting factor homolog B, membrane trafficking protein
chr2_-_62887048 0.17 ENSRNOT00000039234
RGD1306502
similar to hypothetical protein FLJ11193
chr15_+_34296922 0.15 ENSRNOT00000026430
Rec8
REC8 meiotic recombination protein
chr3_-_72219246 0.13 ENSRNOT00000009903
Smtnl1
smoothelin-like 1
chr12_-_21746236 0.12 ENSRNOT00000001869
LOC102550456
TSC22 domain family protein 4-like

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
5.4 26.9 GO:0050828 regulation of liquid surface tension(GO:0050828)
3.2 25.8 GO:0090240 negative regulation of cell adhesion mediated by integrin(GO:0033629) positive regulation of histone H4 acetylation(GO:0090240)
2.3 18.8 GO:0097118 neuroligin clustering involved in postsynaptic membrane assembly(GO:0097118)
2.0 2.0 GO:0097116 gephyrin clustering involved in postsynaptic density assembly(GO:0097116)
2.0 7.9 GO:2001288 positive regulation of caveolin-mediated endocytosis(GO:2001288)
1.7 13.7 GO:0019800 peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan(GO:0019800)
1.6 9.9 GO:0072656 maintenance of protein location in mitochondrion(GO:0072656)
1.6 6.4 GO:0050893 sensory processing(GO:0050893)
1.3 14.0 GO:0031284 positive regulation of guanylate cyclase activity(GO:0031284)
1.3 5.1 GO:0097117 guanylate kinase-associated protein clustering(GO:0097117)
1.2 6.1 GO:0061668 mitochondrial ribosome assembly(GO:0061668)
1.0 8.1 GO:0006620 posttranslational protein targeting to membrane(GO:0006620)
1.0 8.0 GO:0097210 response to gonadotropin-releasing hormone(GO:0097210) cellular response to gonadotropin-releasing hormone(GO:0097211)
0.8 3.4 GO:1904959 regulation of cytochrome-c oxidase activity(GO:1904959)
0.8 14.5 GO:2000311 regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity(GO:2000311)
0.7 11.8 GO:0097120 receptor localization to synapse(GO:0097120)
0.7 7.4 GO:0051823 regulation of synapse structural plasticity(GO:0051823)
0.6 20.9 GO:0001953 negative regulation of cell-matrix adhesion(GO:0001953)
0.5 7.1 GO:0051151 negative regulation of smooth muscle cell differentiation(GO:0051151)
0.4 2.0 GO:0031053 primary miRNA processing(GO:0031053)
0.3 3.7 GO:0015747 urate transport(GO:0015747)
0.3 19.2 GO:0035082 axoneme assembly(GO:0035082)
0.3 2.0 GO:0031584 activation of phospholipase D activity(GO:0031584) regulation of protein kinase C activity(GO:1900019) positive regulation of protein kinase C activity(GO:1900020)
0.3 11.9 GO:0007271 synaptic transmission, cholinergic(GO:0007271)
0.2 11.6 GO:0021762 substantia nigra development(GO:0021762)
0.2 1.0 GO:0006398 mRNA 3'-end processing by stem-loop binding and cleavage(GO:0006398)
0.2 3.1 GO:0048268 clathrin coat assembly(GO:0048268)
0.2 3.9 GO:0042832 defense response to protozoan(GO:0042832)
0.1 0.7 GO:0019243 methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione(GO:0019243) methylglyoxal catabolic process(GO:0051596) methylglyoxal catabolic process to lactate(GO:0061727)
0.1 1.2 GO:0034454 microtubule anchoring at centrosome(GO:0034454)
0.1 1.2 GO:0007175 negative regulation of epidermal growth factor-activated receptor activity(GO:0007175)
0.1 9.0 GO:0021549 cerebellum development(GO:0021549)
0.1 0.5 GO:0032808 lacrimal gland development(GO:0032808)
0.0 2.6 GO:0016239 positive regulation of macroautophagy(GO:0016239)
0.0 1.6 GO:0046854 phosphatidylinositol phosphorylation(GO:0046854)
0.0 4.1 GO:0035023 regulation of Rho protein signal transduction(GO:0035023)
0.0 1.4 GO:0045739 positive regulation of DNA repair(GO:0045739)
0.0 2.8 GO:0006888 ER to Golgi vesicle-mediated transport(GO:0006888)
0.0 4.2 GO:0006898 receptor-mediated endocytosis(GO:0006898)
0.0 0.1 GO:0070236 negative regulation of activation-induced cell death of T cells(GO:0070236)

Gene overrepresentation in cellular component category:

Log-likelihood per target  Total log-likelihood Term Description
3.2 19.2 GO:0005879 axonemal microtubule(GO:0005879)
1.9 18.8 GO:0036057 filtration diaphragm(GO:0036056) slit diaphragm(GO:0036057)
0.5 2.0 GO:0044307 germinal vesicle(GO:0042585) dendritic branch(GO:0044307)
0.4 6.4 GO:0017146 NMDA selective glutamate receptor complex(GO:0017146)
0.3 9.9 GO:0097228 sperm principal piece(GO:0097228)
0.3 10.0 GO:0032281 AMPA glutamate receptor complex(GO:0032281)
0.3 1.4 GO:0070552 BRISC complex(GO:0070552)
0.3 3.7 GO:0030127 COPII vesicle coat(GO:0030127)
0.2 26.9 GO:0005902 microvillus(GO:0005902)
0.2 12.7 GO:0015030 Cajal body(GO:0015030)
0.2 1.2 GO:0036449 microtubule minus-end(GO:0036449)
0.2 2.0 GO:0097470 ribbon synapse(GO:0097470)
0.2 12.5 GO:0005905 clathrin-coated pit(GO:0005905)
0.2 3.1 GO:0030131 clathrin adaptor complex(GO:0030131) clathrin-coated vesicle membrane(GO:0030665)
0.1 11.6 GO:0031594 neuromuscular junction(GO:0031594)
0.1 1.3 GO:0097227 septin complex(GO:0031105) sperm annulus(GO:0097227)
0.1 8.0 GO:0014704 intercalated disc(GO:0014704)
0.1 5.1 GO:0060170 ciliary membrane(GO:0060170)
0.1 6.1 GO:0005762 organellar large ribosomal subunit(GO:0000315) mitochondrial large ribosomal subunit(GO:0005762)
0.1 8.1 GO:0032587 ruffle membrane(GO:0032587)
0.1 29.5 GO:0016324 apical plasma membrane(GO:0016324)
0.1 21.1 GO:0005578 proteinaceous extracellular matrix(GO:0005578)
0.0 3.4 GO:0005758 mitochondrial intermembrane space(GO:0005758)
0.0 0.2 GO:0034991 nuclear meiotic cohesin complex(GO:0034991)
0.0 2.6 GO:0001650 fibrillar center(GO:0001650)
0.0 1.5 GO:0005923 bicellular tight junction(GO:0005923)
0.0 0.9 GO:0031519 PcG protein complex(GO:0031519)
0.0 16.5 GO:0036477 somatodendritic compartment(GO:0036477)
0.0 1.7 GO:0001669 acrosomal vesicle(GO:0001669)

Gene overrepresentation in molecular function category:

Log-likelihood per target  Total log-likelihood Term Description
4.7 18.8 GO:0070699 type II activin receptor binding(GO:0070699)
2.0 14.0 GO:0010853 cyclase activator activity(GO:0010853) guanylate cyclase activator activity(GO:0030250)
1.6 11.5 GO:0030160 GKAP/Homer scaffold activity(GO:0030160)
1.6 20.9 GO:0030215 semaphorin receptor binding(GO:0030215)
0.9 7.9 GO:0019871 sodium channel inhibitor activity(GO:0019871)
0.6 2.6 GO:0047179 platelet-activating factor acetyltransferase activity(GO:0047179)
0.6 11.9 GO:0033130 acetylcholine receptor binding(GO:0033130)
0.5 2.0 GO:0032296 ribonuclease III activity(GO:0004525) double-stranded RNA-specific ribonuclease activity(GO:0032296)
0.5 2.7 GO:0019158 glucokinase activity(GO:0004340) hexokinase activity(GO:0004396) fructokinase activity(GO:0008865) mannokinase activity(GO:0019158)
0.4 8.0 GO:0005388 calcium-transporting ATPase activity(GO:0005388)
0.4 3.4 GO:0016531 copper chaperone activity(GO:0016531)
0.3 11.9 GO:0005158 insulin receptor binding(GO:0005158)
0.3 11.8 GO:0046875 ephrin receptor binding(GO:0046875)
0.3 25.8 GO:0002039 p53 binding(GO:0002039)
0.3 11.6 GO:0042169 SH2 domain binding(GO:0042169)
0.3 3.7 GO:0015347 sodium-independent organic anion transmembrane transporter activity(GO:0015347)
0.3 7.4 GO:0005540 hyaluronic acid binding(GO:0005540)
0.2 7.2 GO:0030742 GTP-dependent protein binding(GO:0030742)
0.2 4.2 GO:0030247 pattern binding(GO:0001871) polysaccharide binding(GO:0030247)
0.2 10.0 GO:0005245 voltage-gated calcium channel activity(GO:0005245)
0.2 2.0 GO:0042043 neurexin family protein binding(GO:0042043)
0.1 6.2 GO:0005227 calcium activated cation channel activity(GO:0005227)
0.1 0.7 GO:0004416 hydroxyacylglutathione hydrolase activity(GO:0004416)
0.1 1.7 GO:0003796 lysozyme activity(GO:0003796)
0.0 4.1 GO:0005089 Rho guanyl-nucleotide exchange factor activity(GO:0005089)
0.0 3.1 GO:0030276 clathrin binding(GO:0030276)
0.0 2.0 GO:0005080 protein kinase C binding(GO:0005080)
0.0 4.6 GO:0004702 receptor signaling protein serine/threonine kinase activity(GO:0004702)
0.0 1.4 GO:0005164 tumor necrosis factor receptor binding(GO:0005164)
0.0 2.5 GO:0051213 dioxygenase activity(GO:0051213)
0.0 8.1 GO:0008017 microtubule binding(GO:0008017)
0.0 8.5 GO:0019904 protein domain specific binding(GO:0019904)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target  Total log-likelihood Term Description
0.4 4.2 SA FAS SIGNALING The TNF-type receptor Fas induces apoptosis on ligand binding.
0.4 7.4 PID SYNDECAN 3 PATHWAY Syndecan-3-mediated signaling events
0.4 54.8 NABA ECM AFFILIATED Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins
0.3 17.0 PID RET PATHWAY Signaling events regulated by Ret tyrosine kinase
0.1 7.9 PID TRKR PATHWAY Neurotrophic factor-mediated Trk receptor signaling
0.1 11.0 ST INTEGRIN SIGNALING PATHWAY Integrin Signaling Pathway
0.1 2.6 PID LIS1 PATHWAY Lissencephaly gene (LIS1) in neuronal migration and development
0.1 4.1 PID RHOA REG PATHWAY Regulation of RhoA activity
0.1 3.1 PID HNF3A PATHWAY FOXA1 transcription factor network
0.1 13.7 NABA ECM GLYCOPROTEINS Genes encoding structural ECM glycoproteins
0.0 2.7 PID HIF1 TFPATHWAY HIF-1-alpha transcription factor network
0.0 0.7 PID P73PATHWAY p73 transcription factor network

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Log-likelihood per target  Total log-likelihood Term Description
1.2 20.9 REACTOME OTHER SEMAPHORIN INTERACTIONS Genes involved in Other semaphorin interactions
0.7 18.8 REACTOME NEPHRIN INTERACTIONS Genes involved in Nephrin interactions
0.5 7.4 REACTOME CS DS DEGRADATION Genes involved in CS/DS degradation
0.3 10.0 REACTOME TRAFFICKING OF AMPA RECEPTORS Genes involved in Trafficking of AMPA receptors
0.2 2.0 REACTOME REGULATION OF INSULIN SECRETION BY ACETYLCHOLINE Genes involved in Regulation of Insulin Secretion by Acetylcholine
0.2 3.7 REACTOME ANTIGEN PRESENTATION FOLDING ASSEMBLY AND PEPTIDE LOADING OF CLASS I MHC Genes involved in Antigen Presentation: Folding, assembly and peptide loading of class I MHC
0.1 4.1 REACTOME SEMA4D INDUCED CELL MIGRATION AND GROWTH CONE COLLAPSE Genes involved in Sema4D induced cell migration and growth-cone collapse
0.1 2.0 REACTOME MICRORNA MIRNA BIOGENESIS Genes involved in MicroRNA (miRNA) Biogenesis
0.1 3.4 REACTOME MITOCHONDRIAL PROTEIN IMPORT Genes involved in Mitochondrial Protein Import
0.1 2.7 REACTOME GLUCOSE TRANSPORT Genes involved in Glucose transport