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Coexpression cluster:C247

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Full id: C247_pons_locus_medulla_spinal_paracentral_medial_occipital



Phase1 CAGE Peaks

Hg19::chr10:105037601..105037624,+p4@INA
Hg19::chr10:105037641..105037652,+p16@INA
Hg19::chr10:121578268..121578279,+p6@INPP5F
Hg19::chr10:79938937..79938973,+p@chr10:79938937..79938973
+
Hg19::chr10:88718397..88718424,+p3@SNCG
Hg19::chr12:107974646..107974657,+p6@BTBD11
Hg19::chr12:5019095..5019105,+p3@ENST00000542043
Hg19::chr12:5019108..5019119,+p1@ENST00000542043
Hg19::chr12:6579808..6579815,-p2@VAMP1
Hg19::chr12:6579833..6579850,-p1@VAMP1
Hg19::chr13:25946216..25946235,+p5@ATP8A2
Hg19::chr13:29646198..29646211,+p5@MTUS2
Hg19::chr15:43803143..43803158,+p2@MAP1A
Hg19::chr15:83378526..83378537,-p7@AP3B2
Hg19::chr16:29909708..29909739,-p@chr16:29909708..29909739
-
Hg19::chr16:31021916..31021920,-p3@STX1B
Hg19::chr16:67189374..67189388,-p@chr16:67189374..67189388
-
Hg19::chr17:7115127..7115145,-p@chr17:7115127..7115145
-
Hg19::chr18:5577640..5577652,-p14@EPB41L3
Hg19::chr18:5577655..5577670,-p17@EPB41L3
Hg19::chr18:70209396..70209407,-p@chr18:70209396..70209407
-
Hg19::chr1:202679535..202679553,-p2@SYT2
Hg19::chr1:202679556..202679619,-p1@SYT2
Hg19::chr1:202679624..202679645,-p3@SYT2
Hg19::chr1:7788387..7788404,+p@chr1:7788387..7788404
+
Hg19::chr21:31312275..31312287,-p3@GRIK1
Hg19::chr21:31312328..31312347,-p2@GRIK1
Hg19::chr21:31312348..31312362,-p4@GRIK1
Hg19::chr21:34100341..34100356,-p5@SYNJ1
Hg19::chr21:47851604..47851613,+p@chr21:47851604..47851613
+
Hg19::chr22:29876197..29876215,+p1@NEFH
Hg19::chr22:29886248..29886264,+p@chr22:29886248..29886264
+
Hg19::chr22:36635684..36635733,-p3@APOL2
Hg19::chr2:167005607..167005628,-p2@SCN1A
Hg19::chr2:196440724..196440739,+p15@SLC39A10
Hg19::chr2:218873244..218873256,-p@chr2:218873244..218873256
-
Hg19::chr3:10857905..10857920,+p1@SLC6A11
Hg19::chr3:56809534..56809564,-p9@ARHGEF3
Hg19::chr3:9745487..9745502,+p2@CPNE9
Hg19::chr4:9783252..9783264,+p1@DRD5
Hg19::chr5:142065223..142065256,-p6@FGF1
Hg19::chr5:161494723..161494732,+p15@GABRG2
Hg19::chr6:143929375..143929393,+p5@PHACTR2
Hg19::chr6:46293320..46293331,-p7@RCAN2
Hg19::chr6:72926685..72926703,+p18@RIMS1
Hg19::chr7:100493699..100493740,-p3@ACHE
Hg19::chr7:100493744..100493759,-p4@ACHE
Hg19::chr7:126892303..126892311,-p4@GRM8
Hg19::chr7:31092185..31092196,+p8@ADCYAP1R1
Hg19::chr7:38671067..38671081,-p4@AMPH
Hg19::chr7:752742..752786,-p5@PRKAR1B
Hg19::chr8:24771265..24771282,+p1@NEFM
Hg19::chr8:24814118..24814133,-p1@NEFL


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


p.valueFDRnGenesnPathwayName
1.68021345890663e-050.002658937798719745272Neuroactive ligand-receptor interaction (KEGG):04080
3.47189991265201e-050.00439542528941744353Amyotrophic lateral sclerosis (ALS) (KEGG):05014
0.00010614362777180.01119815272992495401Transmembrane transport of small molecules (Reactome):REACT_15518
1.1460283977764e-077.25435975792461e-056197Synaptic Transmission (Reactome):REACT_13685
1.24432917686229e-060.000262553456317944318Botulinum neurotoxicity (Reactome):REACT_11184
8.907224977488e-070.000262553456317944462{VAMP2,63} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0060053neurofilament cytoskeleton5.76452463698256e-09
GO:0005883neurofilament5.76452463698256e-09
GO:0044459plasma membrane part5.39356905720145e-07
GO:0030054cell junction5.39356905720145e-07
GO:0007268synaptic transmission6.66485268915385e-07
GO:0060052neurofilament cytoskeleton organization and biogenesis6.66485268915385e-07
GO:0051234establishment of localization1.10714024149718e-06
GO:0019226transmission of nerve impulse1.19931140373097e-06
GO:0051179localization2.90696985444759e-06
GO:0006810transport4.32552140686666e-06
GO:0007267cell-cell signaling4.32552140686666e-06
GO:0045104intermediate filament cytoskeleton organization and biogenesis1.20627154453211e-05
GO:0045103intermediate filament-based process1.39099149236477e-05
GO:0045110intermediate filament bundle assembly3.35002810673953e-05
GO:0005887integral to plasma membrane6.93337190746111e-05
GO:0005886plasma membrane6.93337190746111e-05
GO:0032501multicellular organismal process6.93337190746111e-05
GO:0031226intrinsic to plasma membrane6.93337190746111e-05
GO:0030424axon0.000123706784522979
GO:0045109intermediate filament organization0.0002341018288924
GO:0030135coated vesicle0.000267933225744423
GO:0016192vesicle-mediated transport0.000418809417604697
GO:0008088axon cargo transport0.000568172251123635
GO:0007275multicellular organismal development0.000568172251123635
GO:0005856cytoskeleton0.000698920488850127
GO:0007399nervous system development0.000902372266977661
GO:0008021synaptic vesicle0.000920014325211797
GO:0006836neurotransmitter transport0.00102372330387087
GO:0044425membrane part0.00102372330387087
GO:0043005neuron projection0.00108511220980445
GO:0005882intermediate filament0.00112117144533564
GO:0045111intermediate filament cytoskeleton0.00112117144533564
GO:0005200structural constituent of cytoskeleton0.0011391566271197
GO:0050804regulation of synaptic transmission0.00164217168261946
GO:0050877neurological system process0.00192181601951179
GO:0051969regulation of transmission of nerve impulse0.00192181601951179
GO:0048489synaptic vesicle transport0.00192181601951179
GO:0016044membrane organization and biogenesis0.00192883952669166
GO:0007270nerve-nerve synaptic transmission0.00203660384954451
GO:0022892substrate-specific transporter activity0.00205606845313884
GO:0015075ion transmembrane transporter activity0.00214531373740093
GO:0044430cytoskeletal part0.00214531373740093
GO:0030136clathrin-coated vesicle0.00214531373740093
GO:0042995cell projection0.00241759306773508
GO:0005230extracellular ligand-gated ion channel activity0.00301010924667021
GO:0031644regulation of neurological process0.00301895377699923
GO:0016023cytoplasmic membrane-bound vesicle0.00335209651229851
GO:0031988membrane-bound vesicle0.00346540054964109
GO:0007154cell communication0.00365036465590875
GO:0042165neurotransmitter binding0.00365036465590875
GO:0048856anatomical structure development0.00384311493099898
GO:0022891substrate-specific transmembrane transporter activity0.0040609291840681
GO:0003008system process0.00427800408195558
GO:0051649establishment of cellular localization0.00446159307994661
GO:0044456synapse part0.00450748968317031
GO:0022834ligand-gated channel activity0.0045637709753216
GO:0015276ligand-gated ion channel activity0.0045637709753216
GO:0016043cellular component organization and biogenesis0.0045637709753216
GO:0051641cellular localization0.00466686851699799
GO:0048731system development0.00486533136937667
GO:0032502developmental process0.00514003969057503
GO:0022857transmembrane transporter activity0.00526040200093909
GO:0031410cytoplasmic vesicle0.00531710148004648
GO:0005234extracellular-glutamate-gated ion channel activity0.00531710148004648
GO:0031982vesicle0.00553543088521537
GO:0045761regulation of adenylate cyclase activity0.00569918910307809
GO:0051339regulation of lyase activity0.00580484496877022
GO:0031279regulation of cyclase activity0.00580484496877022
GO:0005515protein binding0.00627792290736801
GO:0010324membrane invagination0.00627792290736801
GO:0006897endocytosis0.00627792290736801
GO:0060181female receptivity0.00655659780821679
GO:0045924regulation of female receptivity0.00655659780821679
GO:0033596TSC1-TSC2 complex0.00655659780821679
GO:0060180female mating behavior0.00655659780821679
GO:0050795regulation of behavior0.00655659780821679
GO:0032222regulation of synaptic transmission, cholinergic0.00655659780821679
GO:0032223negative regulation of synaptic transmission, cholinergic0.00655659780821679
GO:0008090retrograde axon cargo transport0.00655659780821679
GO:0001589dopamine D5 receptor activity0.00655659780821679
GO:0033693neurofilament bundle assembly0.00655659780821679
GO:0022836gated channel activity0.00783831692333591
GO:0046907intracellular transport0.00911087086016492
GO:0001507acetylcholine catabolic process in synaptic cleft0.0110593733437102
GO:0043237laminin-1 binding0.0110593733437102
GO:0003990acetylcholinesterase activity0.0110593733437102
GO:0033057reproductive behavior in a multicellular organism0.0110593733437102
GO:0019896axon transport of mitochondrion0.0110593733437102
GO:0031133regulation of axon diameter0.0110593733437102
GO:0050805negative regulation of synaptic transmission0.0110593733437102
GO:0006581acetylcholine catabolic process0.0110593733437102
GO:0001994norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure0.0110593733437102
GO:0030818negative regulation of cAMP biosynthetic process0.0110593733437102
GO:0030815negative regulation of cAMP metabolic process0.0110593733437102
GO:0051966regulation of synaptic transmission, glutamatergic0.0110593733437102
GO:0001588dopamine D1 receptor-like receptor activity0.0110593733437102
GO:0019932second-messenger-mediated signaling0.0111195460700301
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0117553069406724
GO:0001505regulation of neurotransmitter levels0.0136251482154584
GO:0032940secretion by cell0.0142129165712312
GO:0016020membrane0.0142129165712312
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0142129165712312
GO:0043236laminin binding0.0142129165712312
GO:0008291acetylcholine metabolic process0.0142129165712312
GO:0030800negative regulation of cyclic nucleotide metabolic process0.0142129165712312
GO:0030346protein phosphatase 2B binding0.0142129165712312
GO:0030809negative regulation of nucleotide biosynthetic process0.0142129165712312
GO:0001992regulation of systemic arterial blood pressure by vasopressin0.0142129165712312
GO:0030803negative regulation of cyclic nucleotide biosynthetic process0.0142129165712312
GO:0051970negative regulation of transmission of nerve impulse0.0142129165712312
GO:0042220response to cocaine0.0142129165712312
GO:0014073response to tropane0.0142129165712312
GO:0019933cAMP-mediated signaling0.0147949686011322
GO:0005216ion channel activity0.0167255681365211
GO:0008066glutamate receptor activity0.0168727651275069
GO:0007010cytoskeleton organization and biogenesis0.0168727651275069
GO:0022838substrate specific channel activity0.0169913913045988
GO:0022803passive transmembrane transporter activity0.0171090747376351
GO:0015267channel activity0.0171090747376351
GO:0004104cholinesterase activity0.0171090747376351
GO:0035249synaptic transmission, glutamatergic0.0171090747376351
GO:0007191dopamine receptor, adenylate cyclase activating pathway0.0171090747376351
GO:0002076osteoblast development0.0171090747376351
GO:0050840extracellular matrix binding0.0171090747376351
GO:0043228non-membrane-bound organelle0.0177843020348907
GO:0043232intracellular non-membrane-bound organelle0.0177843020348907
GO:0008306associative learning0.0199303464299923
GO:0008035high-density lipoprotein binding0.0199303464299923
GO:0030817regulation of cAMP biosynthetic process0.0199303464299923
GO:0008089anterograde axon cargo transport0.0199303464299923
GO:0001993regulation of systemic arterial blood pressure by norepinephrine-epinephrine0.0199303464299923
GO:0004439phosphoinositide 5-phosphatase activity0.0199303464299923
GO:0042439ethanolamine and derivative metabolic process0.0199303464299923
GO:0046903secretion0.0220853584299826
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0220853584299826
GO:0031594neuromuscular junction0.0222341222275618
GO:0019098reproductive behavior0.0222341222275618
GO:0030802regulation of cyclic nucleotide biosynthetic process0.0222341222275618
GO:0030808regulation of nucleotide biosynthetic process0.0222341222275618
GO:0007617mating behavior0.0222341222275618
GO:0045980negative regulation of nucleotide metabolic process0.0222341222275618
GO:0048488synaptic vesicle endocytosis0.0222341222275618
GO:0030814regulation of cAMP metabolic process0.0222341222275618
GO:0019935cyclic-nucleotide-mediated signaling0.0224568120805291
GO:0022607cellular component assembly0.0245546746794124
GO:0031645negative regulation of neurological process0.0245546746794124
GO:0003084positive regulation of systemic arterial blood pressure0.0245546746794124
GO:0005332gamma-aminobutyric acid:sodium symporter activity0.0245546746794124
GO:0001963synaptic transmission, dopaminergic0.0245546746794124
GO:0030799regulation of cyclic nucleotide metabolic process0.0245546746794124
GO:0008503benzodiazepine receptor activity0.0245546746794124
GO:0009611response to wounding0.0254724008806108
GO:0006869lipid transport0.0257109825227417
GO:0004445inositol-polyphosphate 5-phosphatase activity0.0259850654483273
GO:0045776negative regulation of blood pressure0.0259850654483273
GO:0042135neurotransmitter catabolic process0.0259850654483273
GO:0050886endocrine process0.0259850654483273
GO:0001990regulation of systemic arterial blood pressure by hormone0.0259850654483273
GO:0015185L-gamma-aminobutyric acid transmembrane transporter activity0.0259850654483273
GO:0016079synaptic vesicle exocytosis0.0259850654483273
GO:0043279response to alkaloid0.0259850654483273
GO:0015277kainate selective glutamate receptor activity0.0259850654483273
GO:0046030inositol trisphosphate phosphatase activity0.0259850654483273
GO:0030594neurotransmitter receptor activity0.0260856382739532
GO:0045211postsynaptic membrane0.0286922244060811
GO:0031526brush border membrane0.0286922244060811
GO:0001540beta-amyloid binding0.0313005149388685
GO:0006140regulation of nucleotide metabolic process0.0313005149388685
GO:0045777positive regulation of blood pressure0.0313005149388685
GO:0045184establishment of protein localization0.0324215379354728
GO:0042402biogenic amine catabolic process0.033619649627795
GO:0014070response to organic cyclic substance0.033619649627795
GO:0031253cell projection membrane0.033619649627795
GO:0046873metal ion transmembrane transporter activity0.0348795867831052
GO:0042577lipid phosphatase activity0.0348795867831052
GO:0003044regulation of systemic arterial blood pressure mediated by a chemical signal0.0348795867831052
GO:0051705behavioral interaction between organisms0.0348795867831052
GO:0007271synaptic transmission, cholinergic0.0348795867831052
GO:0042734presynaptic membrane0.0348795867831052
GO:0005283sodium:amino acid symporter activity0.0348795867831052
GO:0007618mating0.0348795867831052
GO:0008104protein localization0.0348795867831052
GO:0007018microtubule-based movement0.0367252912294252
GO:0005416cation:amino acid symporter activity0.0367252912294252
GO:0030866cortical actin cytoskeleton organization and biogenesis0.0367252912294252
GO:0004999vasoactive intestinal polypeptide receptor activity0.0367252912294252
GO:0017156calcium ion-dependent exocytosis0.0367252912294252
GO:0006886intracellular protein transport0.0378025738124215
GO:0030865cortical cytoskeleton organization and biogenesis0.0383055765245929
GO:0042982amyloid precursor protein metabolic process0.0383055765245929
GO:0030552cAMP binding0.0383055765245929
GO:0042219amino acid derivative catabolic process0.0383055765245929
GO:0044464cell part0.0383055765245929
GO:0033036macromolecule localization0.0389750845834086
GO:0007194negative regulation of adenylate cyclase activity0.0401888459378791
GO:0051350negative regulation of lyase activity0.0401888459378791
GO:0031280negative regulation of cyclase activity0.0401888459378791
GO:0030705cytoskeleton-dependent intracellular transport0.0405545026518932
GO:0003073regulation of systemic arterial blood pressure0.0419964870842404
GO:0042310vasoconstriction0.0419964870842404
GO:0050714positive regulation of protein secretion0.0419964870842404
GO:0016021integral to membrane0.0432250967315281
GO:0030137COPI-coated vesicle0.0433088025382806
GO:0050435beta-amyloid metabolic process0.0433088025382806
GO:0007212dopamine receptor signaling pathway0.0433088025382806
GO:0019903protein phosphatase binding0.0433088025382806
GO:0007612learning0.0433088025382806
GO:0008289lipid binding0.0434730328223996
GO:0031224intrinsic to membrane0.0438426697017679
GO:0001518voltage-gated sodium channel complex0.0451813700461926
GO:0004012phospholipid-translocating ATPase activity0.0463462548699017
GO:0006171cAMP biosynthetic process0.0463462548699017
GO:0015247aminophospholipid transporter activity0.0463462548699017
GO:0035240dopamine binding0.0463462548699017
GO:0004952dopamine receptor activity0.0463462548699017
GO:0005518collagen binding0.0463462548699017
GO:0007601visual perception0.0469904287170701
GO:0050953sensory perception of light stimulus0.0469904287170701
GO:0006892post-Golgi vesicle-mediated transport0.0497964531035081
GO:0007215glutamate signaling pathway0.0497964531035081
GO:0051047positive regulation of secretion0.0497964531035081
GO:0016208AMP binding0.0497964531035081



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system1.05e-3982
regional part of nervous system4.89e-3594
nervous system4.89e-3594
neural tube2.15e-3357
neural rod2.15e-3357
future spinal cord2.15e-3357
neural keel2.15e-3357
brain9.18e-3369
future brain9.18e-3369
regional part of brain3.01e-3159
adult organism3.50e-31115
ectoderm3.44e-26173
presumptive ectoderm3.44e-26173
ectoderm-derived structure1.56e-25169
anterior neural tube5.41e-2542
regional part of forebrain7.48e-2541
forebrain7.48e-2541
future forebrain7.48e-2541
neurectoderm6.65e-2490
neural plate2.02e-2386
presumptive neural plate2.02e-2386
anterior region of body4.73e-23129
craniocervical region4.73e-23129
head5.54e-22123
gray matter6.82e-2134
brain grey matter6.82e-2134
telencephalon7.98e-2134
regional part of telencephalon3.92e-2033
cerebral hemisphere1.04e-1932
pre-chordal neural plate1.61e-1661
regional part of cerebral cortex1.50e-1522
cerebral cortex1.75e-1525
pallium1.75e-1525
neocortex2.25e-1420
posterior neural tube1.94e-0915
chordal neural plate1.94e-0915
organism subdivision4.27e-09365
segmental subdivision of nervous system3.81e-0813
segmental subdivision of hindbrain1.27e-0712
hindbrain1.27e-0712
presumptive hindbrain1.27e-0712
nucleus of brain7.07e-079
neural nucleus7.07e-079
basal ganglion9.78e-079
nuclear complex of neuraxis9.78e-079
aggregate regional part of brain9.78e-079
collection of basal ganglia9.78e-079
cerebral subcortex9.78e-079


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


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