Coexpression cluster:C271

Full id: C271_pineal_spinal_locus_globus_medulla_thalamus_cerebellum

Phase1 CAGE Peaks

Hg19::chr10:103599591..103599635,-	p3@KCNIP2
Hg19::chr10:64133934..64133954,+	p6@ZNF365
Hg19::chr10:94000157..94000191,-	p6@CPEB3
Hg19::chr11:131240498..131240532,+	p1@NTM
Hg19::chr11:131240536..131240547,+	p4@NTM
Hg19::chr11:131240548..131240559,+	p10@NTM
Hg19::chr11:131240565..131240572,+	p13@NTM
Hg19::chr12:131201033..131201041,-	p3@RIMBP2
Hg19::chr12:22487588..22487616,-	p3@ST8SIA1
Hg19::chr12:22487618..22487648,-	p1@ST8SIA1
Hg19::chr12:26274116..26274141,-	p2@AK094422
Hg19::chr12:71314617..71314622,-	p16@PTPRR
Hg19::chr14:32547434..32547446,+	p11@ARHGAP5
Hg19::chr15:79575073..79575138,+	p1@ANKRD34C
Hg19::chr17:55757077..55757089,+	p@chr17:55757077..55757089 +
Hg19::chr17:7554234..7554251,+	p1@ATP1B2
Hg19::chr17:7556683..7556703,+	p@chr17:7556683..7556703 +
Hg19::chr17:7556754..7556788,+	p@chr17:7556754..7556788 +
Hg19::chr17:7557938..7557979,+	p@chr17:7557938..7557979 +
Hg19::chr17:7559125..7559140,+	p@chr17:7559125..7559140 +
Hg19::chr17:7559212..7559223,+	p@chr17:7559212..7559223 +
Hg19::chr17:7559305..7559325,+	p@chr17:7559305..7559325 +
Hg19::chr17:7559346..7559354,+	p@chr17:7559346..7559354 +
Hg19::chr17:7559648..7559652,+	p16@ATP1B2
Hg19::chr17:7560487..7560497,+	p11@ATP1B2
Hg19::chr17:7560507..7560534,+	p2@ATP1B2
Hg19::chr17:7560542..7560578,+	p4@ATP1B2
Hg19::chr17:7560589..7560611,+	p8@ATP1B2
Hg19::chr17:7560617..7560658,+	p5@ATP1B2
Hg19::chr17:7560779..7560820,+	p3@ATP1B2
Hg19::chr19:30715705..30715726,+	p@chr19:30715705..30715726 +
Hg19::chr19:52452374..52452419,+	p1@ENST00000500242 p1@uc002pyb.2 p1@uc002pyc.2
Hg19::chr1:10436637..10436646,+	p@chr1:10436637..10436646 +
Hg19::chr1:197237352..197237414,+	p2@CRB1
Hg19::chr1:216680100..216680145,-	p@chr1:216680100..216680145 -
Hg19::chr2:220154660..220154662,-	p@chr2:220154660..220154662 -
Hg19::chr4:170581337..170581344,+	p10@CLCN3
Hg19::chr4:187112411..187112444,+	p7@CYP4V2
Hg19::chr6:87646995..87647024,+	p2@HTR1E
Hg19::chr7:128864848..128864913,+	p1@AHCYL2
Hg19::chr7:130152491..130152507,+	p@chr7:130152491..130152507 +
Hg19::chr9:35829208..35829308,+	p1@TMEM8B
Hg19::chr9:99449322..99449347,+	p1@ENST00000423924
Hg19::chrX:144899314..144899392,+	p1@SLITRK2
Hg19::chrX:144899416..144899486,+	p3@SLITRK2
Hg19::chrX:144899488..144899501,+	p4@SLITRK2
Hg19::chrX:144903040..144903070,+	p2@SLITRK2

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

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No results for this coexpression

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

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GO ID	GO name	FDR corrected p-value
GO:0044425	membrane part	0.0157114682679854
GO:0016020	membrane	0.0157114682679854
GO:0016021	integral to membrane	0.0157114682679854
GO:0016324	apical plasma membrane	0.0157114682679854
GO:0031224	intrinsic to membrane	0.0157114682679854
GO:0032501	multicellular organismal process	0.0157114682679854
GO:0048388	endosomal lumen acidification	0.0157114682679854
GO:0045163	clustering of voltage-gated potassium channels	0.0157114682679854
GO:0045177	apical part of cell	0.0191512452993784
GO:0009653	anatomical structure morphogenesis	0.01982022288438
GO:0005250	A-type (transient outward) potassium channel activity	0.01982022288438
GO:0032989	cellular structure morphogenesis	0.01982022288438
GO:0000902	cell morphogenesis	0.01982022288438
GO:0048856	anatomical structure development	0.01982022288438
GO:0019904	protein domain specific binding	0.0229795800062908
GO:0032502	developmental process	0.0229795800062908
GO:0050877	neurological system process	0.0229795800062908
GO:0030955	potassium ion binding	0.0229795800062908
GO:0044459	plasma membrane part	0.0229795800062908
GO:0015271	outward rectifier potassium channel activity	0.0229795800062908
GO:0003828	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity	0.0229795800062908
GO:0009986	cell surface	0.0229795800062908
GO:0048666	neuron development	0.0237715222228541
GO:0045161	neuronal ion channel clustering	0.0253099614812186
GO:0007267	cell-cell signaling	0.0253099614812186
GO:0045851	pH reduction	0.0296281311295286
GO:0051453	regulation of cellular pH	0.0296281311295286
GO:0051452	cellular pH reduction	0.0296281311295286
GO:0046923	ER retention sequence binding	0.0296281311295286
GO:0003008	system process	0.0296281311295286
GO:0007032	endosome organization and biogenesis	0.0304581850844502
GO:0005513	detection of calcium ion	0.0304581850844502
GO:0030182	neuron differentiation	0.0304581850844502
GO:0031420	alkali metal ion binding	0.0313964221689795
GO:0007601	visual perception	0.0313964221689795
GO:0050953	sensory perception of light stimulus	0.0313964221689795
GO:0006688	glycosphingolipid biosynthetic process	0.0330198688334164
GO:0042551	neuron maturation	0.0330198688334164
GO:0048699	generation of neurons	0.0339901125499411
GO:0006813	potassium ion transport	0.0367104905655899
GO:0030641	cellular hydrogen ion homeostasis	0.0367104905655899
GO:0022008	neurogenesis	0.0368328655832253
GO:0004993	serotonin receptor activity	0.0379126926495747
GO:0030004	cellular monovalent inorganic cation homeostasis	0.0400758765880435
GO:0009247	glycolipid biosynthetic process	0.0400758765880435
GO:0055067	monovalent inorganic cation homeostasis	0.0400758765880435
GO:0007268	synaptic transmission	0.0400758765880435
GO:0031901	early endosome membrane	0.0409695555806811
GO:0005391	sodium:potassium-exchanging ATPase activity	0.0409695555806811
GO:0042169	SH2 domain binding	0.0409695555806811
GO:0009593	detection of chemical stimulus	0.0409695555806811
GO:0022832	voltage-gated channel activity	0.0409695555806811
GO:0005244	voltage-gated ion channel activity	0.0409695555806811
GO:0019198	transmembrane receptor protein phosphatase activity	0.0409695555806811
GO:0005001	transmembrane receptor protein tyrosine phosphatase activity	0.0409695555806811
GO:0006687	glycosphingolipid metabolic process	0.0409695555806811
GO:0012505	endomembrane system	0.0409695555806811
GO:0016043	cellular component organization and biogenesis	0.0409695555806811
GO:0019226	transmission of nerve impulse	0.0409695555806811
GO:0030165	PDZ domain binding	0.041745255595325
GO:0005048	signal sequence binding	0.0424104566331044
GO:0030148	sphingolipid biosynthetic process	0.0424104566331044
GO:0000139	Golgi membrane	0.0465679210758911
GO:0005100	Rho GTPase activator activity	0.046927511566585

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>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.14e-51	115
regional part of nervous system	2.41e-38	94
nervous system	2.41e-38	94
central nervous system	5.10e-38	82
neural tube	1.41e-34	57
neural rod	1.41e-34	57
future spinal cord	1.41e-34	57
neural keel	1.41e-34	57
neurectoderm	2.90e-33	90
neural plate	1.65e-32	86
presumptive neural plate	1.65e-32	86
ectoderm	1.06e-31	173
presumptive ectoderm	1.06e-31	173
brain	3.24e-31	69
future brain	3.24e-31	69
ectoderm-derived structure	9.60e-31	169
regional part of brain	4.80e-30	59
anterior region of body	2.11e-27	129
craniocervical region	2.11e-27	129
anterior neural tube	1.78e-26	42
regional part of forebrain	3.34e-26	41
forebrain	3.34e-26	41
future forebrain	3.34e-26	41
head	3.74e-26	123
pre-chordal neural plate	4.81e-25	61
gray matter	4.77e-22	34
brain grey matter	4.77e-22	34
telencephalon	7.50e-22	34
regional part of telencephalon	2.82e-21	33
cerebral hemisphere	1.01e-20	32
cerebral cortex	2.26e-16	25
pallium	2.26e-16	25
regional part of cerebral cortex	2.84e-15	22
neocortex	5.74e-14	20
organ	4.25e-12	511
multi-cellular organism	1.75e-09	659
posterior neural tube	3.78e-09	15
chordal neural plate	3.78e-09	15
embryo	1.09e-08	612
organism subdivision	4.79e-08	365
segmental subdivision of nervous system	8.09e-08	13
segmental subdivision of hindbrain	2.72e-07	12
hindbrain	2.72e-07	12
presumptive hindbrain	2.72e-07	12
nucleus of brain	3.90e-07	9
neural nucleus	3.90e-07	9
basal ganglion	4.06e-07	9
nuclear complex of neuraxis	4.06e-07	9
aggregate regional part of brain	4.06e-07	9
collection of basal ganglia	4.06e-07	9
cerebral subcortex	4.06e-07	9
embryonic structure	4.51e-07	605
developing anatomical structure	4.51e-07	605
germ layer	7.75e-07	604
embryonic tissue	7.75e-07	604
presumptive structure	7.75e-07	604
epiblast (generic)	7.75e-07	604

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

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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

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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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