Coexpression cluster:C1375

Full id: C1375_cerebellum_Pericytes_extraskeletal_neuroblastoma_teratocarcinoma_neuroectodermal_H9

Phase1 CAGE Peaks

Hg19::chr13:100633838..100633854,-	p@chr13:100633838..100633854 -
Hg19::chr13:100634004..100634025,+	p2@ZIC2
Hg19::chr13:100634088..100634099,+	p5@ZIC2
Hg19::chr13:100634111..100634118,+	p8@ZIC2
Hg19::chr13:100634130..100634143,+	p3@ZIC2
Hg19::chr3:147124697..147124729,+	p@chr3:147124697..147124729 +

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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No GOStat results

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
neural cell	4.01e-11	25
neurectodermal cell	5.44e-09	59
neuronal stem cell	5.35e-07	8

Uber Anatomy

Ontology term	p-value	n
central nervous system	3.08e-38	82
regional part of nervous system	4.77e-37	94
nervous system	4.77e-37	94
brain	5.87e-30	69
future brain	5.87e-30	69
neurectoderm	5.51e-27	90
regional part of brain	3.48e-25	59
neural tube	7.54e-25	57
neural rod	7.54e-25	57
future spinal cord	7.54e-25	57
neural keel	7.54e-25	57
neural plate	4.55e-24	86
presumptive neural plate	4.55e-24	86
ectoderm	8.95e-24	173
presumptive ectoderm	8.95e-24	173
ectoderm-derived structure	2.12e-21	169
head	1.30e-17	123
anterior region of body	1.86e-16	129
craniocervical region	1.86e-16	129
regional part of forebrain	1.97e-16	41
forebrain	1.97e-16	41
future forebrain	1.97e-16	41
anterior neural tube	1.05e-15	42
pre-chordal neural plate	1.86e-15	61
telencephalon	2.30e-14	34
regional part of telencephalon	5.86e-14	33
gray matter	7.75e-14	34
brain grey matter	7.75e-14	34
cerebral hemisphere	1.58e-13	32
cerebral cortex	4.77e-12	25
pallium	4.77e-12	25
posterior neural tube	8.35e-11	15
chordal neural plate	8.35e-11	15
regional part of cerebral cortex	2.12e-10	22
segmental subdivision of nervous system	4.12e-10	13
segmental subdivision of hindbrain	7.00e-10	12
hindbrain	7.00e-10	12
presumptive hindbrain	7.00e-10	12
neocortex	1.40e-09	20
regional part of metencephalon	8.86e-08	9
metencephalon	8.86e-08	9
future metencephalon	8.86e-08	9
cerebellum	9.27e-07	6
rhombic lip	9.27e-07	6

Disease

Ontology term	p-value	n
cancer	2.89e-35	235
disease of cellular proliferation	2.32e-33	239
cell type cancer	7.59e-33	143
carcinoma	1.06e-23	106
organ system cancer	8.03e-11	137
adenocarcinoma	6.98e-09	25
germ cell and embryonal cancer	3.79e-07	22
germ cell cancer	3.79e-07	22

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
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.010131840544153
HEY1#23462	5	3.36675920258809	0.00442382704520303	0.0209485410462008
HMGN3#9324	4	5.45236514890039	0.00272961688233377	0.0149867762366763
TAF1#6872	5	2.78587190478774	0.0107863634029041	0.0397893828565943
TAF7#6879	5	9.5275578374366	2.84599232912077e-05	0.000599985048165209
ZBTB7A#51341	5	6.12659108989658	0.000247607282141475	0.00268897337418878
ZNF263#10127	5	6.8515346975089	0.000143460795381412	0.00186749370669815

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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This analysis result is provided for C0 - C305 clusters.