Coexpression cluster:C257

Full id: C257_pineal_insula_frontal_occipital_temporal_medial_paracentral

Phase1 CAGE Peaks

Hg19::chr11:107462012..107462019,+	p5@ELMOD1
Hg19::chr11:73309049..73309054,-	p5@FAM168A
Hg19::chr11:74952393..74952412,+	p@chr11:74952393..74952412 +
Hg19::chr11:795358..795372,-	p9@SLC25A22
Hg19::chr11:84148843..84148867,-	p21@DLG2
Hg19::chr11:84148869..84148881,-	p35@DLG2
Hg19::chr12:130303241..130303258,-	p@chr12:130303241..130303258 -
Hg19::chr12:57735443..57735464,-	p18@R3HDM2
Hg19::chr12:57735499..57735520,-	p10@R3HDM2
Hg19::chr12:57736218..57736229,-	p@chr12:57736218..57736229 -
Hg19::chr12:57736233..57736245,-	p@chr12:57736233..57736245 -
Hg19::chr12:81992111..81992164,-	p1@PPFIA2
Hg19::chr14:72399114..72399238,+	p1@RGS6
Hg19::chr19:46580848..46580895,-	p1@ENST00000366172 p1@uc002pdz.1
Hg19::chr1:110082487..110082535,+	p1@GPR61
Hg19::chr1:177133980..177133992,-	p7@ASTN1
Hg19::chr1:204640767..204640771,-	p@chr1:204640767..204640771 -
Hg19::chr1:217262933..217262968,-	p3@ESRRG
Hg19::chr1:217262969..217262995,-	p7@ESRRG
Hg19::chr1:50489619..50489650,-	p2@AGBL4
Hg19::chr1:77334255..77334267,+	p7@ST6GALNAC5
Hg19::chr2:210444126..210444140,+	p14@MAP2
Hg19::chr2:210444142..210444194,+	p6@MAP2
Hg19::chr2:215275814..215275834,+	p1@VWC2L
Hg19::chr2:219824420..219824431,+	p3@CDK5R2
Hg19::chr2:220174072..220174149,-	p1@PTPRN
Hg19::chr2:48667898..48667981,+	p1@PPP1R21
Hg19::chr2:50574708..50574743,-	p17@NRXN1
Hg19::chr3:118753716..118753731,-	p7@IGSF11
Hg19::chr3:124103560..124103577,+	p8@KALRN
Hg19::chr3:127347780..127347822,-	p@chr3:127347780..127347822 -
Hg19::chr3:158991085..158991096,+	p26@SCHIP1
Hg19::chr3:64211112..64211152,-	p4@PRICKLE2
Hg19::chr3:64211156..64211179,-	p11@PRICKLE2
Hg19::chr5:138210931..138210938,-	p6@LRRTM2
Hg19::chr5:138210954..138210965,-	p4@LRRTM2
Hg19::chr5:138210977..138210999,-	p2@LRRTM2
Hg19::chr5:146435485..146435499,-	p8@PPP2R2B
Hg19::chr5:146435501..146435530,-	p3@PPP2R2B
Hg19::chr5:146435572..146435581,-	p24@PPP2R2B
Hg19::chr5:161494848..161494859,+	p9@GABRG2
Hg19::chr5:161494946..161494955,+	p10@GABRG2
Hg19::chr5:161494956..161494967,+	p8@GABRG2
Hg19::chr5:71403323..71403340,+	p3@MAP1B
Hg19::chr5:74162339..74162405,-	p2@FAM169A
Hg19::chr6:84418484..84418496,-	p3@SNAP91
Hg19::chr7:14942830..14942867,-	p4@DGKB
Hg19::chr7:14942923..14942941,-	p6@DGKB
Hg19::chr7:31023427..31023491,+	p1@GHRHR
Hg19::chr7:39125494..39125510,+	p4@POU6F2
Hg19::chr7:39125511..39125560,+	p1@POU6F2

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:0031114	regulation of microtubule depolymerization	0.0132628609623142
GO:0007026	negative regulation of microtubule depolymerization	0.0132628609623142
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0132628609623142
GO:0007019	microtubule depolymerization	0.0132628609623142
GO:0031110	regulation of microtubule polymerization or depolymerization	0.015800510186969
GO:0031109	microtubule polymerization or depolymerization	0.015800510186969
GO:0044464	cell part	0.015800510186969
GO:0051261	protein depolymerization	0.0261605814414009
GO:0005515	protein binding	0.0261605814414009
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0261605814414009
GO:0007402	ganglion mother cell fate determination	0.0261605814414009
GO:0016533	cyclin-dependent protein kinase 5 activator complex	0.0410943584387354
GO:0048664	neuron fate determination	0.0410943584387354
GO:0016534	cyclin-dependent protein kinase 5 activator activity	0.0410943584387354

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>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	1.29e-11	180
neural cell	6.65e-09	25

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	3.81e-42	94
nervous system	3.81e-42	94
central nervous system	9.40e-41	82
adult organism	6.81e-34	115
brain	1.17e-33	69
future brain	1.17e-33	69
neural tube	1.30e-33	57
neural rod	1.30e-33	57
future spinal cord	1.30e-33	57
neural keel	1.30e-33	57
neurectoderm	4.40e-32	90
neural plate	9.50e-32	86
presumptive neural plate	9.50e-32	86
regional part of brain	2.01e-29	59
regional part of forebrain	4.98e-27	41
forebrain	4.98e-27	41
future forebrain	4.98e-27	41
anterior neural tube	8.38e-27	42
ectoderm	1.52e-25	173
presumptive ectoderm	1.52e-25	173
ectoderm-derived structure	6.29e-25	169
telencephalon	1.15e-22	34
gray matter	1.17e-22	34
brain grey matter	1.17e-22	34
pre-chordal neural plate	1.38e-22	61
head	2.32e-22	123
organism subdivision	5.59e-22	365
regional part of telencephalon	5.62e-22	33
anterior region of body	9.72e-22	129
craniocervical region	9.72e-22	129
cerebral hemisphere	1.32e-21	32
cerebral cortex	2.68e-17	25
pallium	2.68e-17	25
tube	8.95e-17	194
regional part of cerebral cortex	4.98e-16	22
neocortex	8.35e-15	20
epithelium	3.38e-14	309
cell layer	1.10e-13	312
multi-tissue structure	1.83e-13	347
anatomical conduit	2.06e-12	241
multi-cellular organism	9.98e-11	659
anatomical cluster	1.03e-09	286
posterior neural tube	5.44e-08	15
chordal neural plate	5.44e-08	15
embryo	1.27e-07	612
anatomical group	4.20e-07	626
anatomical system	4.23e-07	625
segmental subdivision of nervous system	7.07e-07	13
basal ganglion	7.16e-07	9
nuclear complex of neuraxis	7.16e-07	9
aggregate regional part of brain	7.16e-07	9
collection of basal ganglia	7.16e-07	9
cerebral subcortex	7.16e-07	9
nucleus of brain	8.32e-07	9
neural nucleus	8.32e-07	9

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CTBP2#1488	4	4.91898041877083	0.00889265822188434	0.0337343479000174
RAD21#5885	11	2.23343868333372	0.00845143374874908	0.0328004195200894

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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