Coexpression cluster:C3396

Full id: C3396_brain_occipital_duodenum_temporal_parietal_small_Neurons

Phase1 CAGE Peaks

Hg19::chr14:103988483..103988543,-	p3@CKB
Hg19::chr3:127347988..127348000,+	p2@PODXL2
Hg19::chr3:127348005..127348063,+	p1@PODXL2

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:0055064	chloride ion homeostasis	0.000883080183680678
GO:0055083	monovalent inorganic anion homeostasis	0.000883080183680678
GO:0030644	cellular chloride ion homeostasis	0.000883080183680678
GO:0030320	cellular monovalent inorganic anion homeostasis	0.000883080183680678
GO:0004111	creatine kinase activity	0.00282573181120752
GO:0055081	anion homeostasis	0.00302748067160046
GO:0030002	cellular anion homeostasis	0.00302748067160046
GO:0016775	phosphotransferase activity, nitrogenous group as acceptor	0.0141228361494071
GO:0005539	glycosaminoglycan binding	0.0407066168659049
GO:0030247	polysaccharide binding	0.0407066168659049
GO:0001871	pattern binding	0.0407066168659049
GO:0007420	brain development	0.0408329421154592

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
epithelial cell	3.37e-07	254

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	7.18e-34	94
nervous system	7.18e-34	94
central nervous system	2.85e-32	82
neural tube	1.41e-28	57
neural rod	1.41e-28	57
future spinal cord	1.41e-28	57
neural keel	1.41e-28	57
neurectoderm	1.41e-27	90
brain	2.40e-26	69
future brain	2.40e-26	69
neural plate	5.10e-26	86
presumptive neural plate	5.10e-26	86
regional part of brain	2.34e-24	59
regional part of forebrain	7.36e-23	41
forebrain	7.36e-23	41
future forebrain	7.36e-23	41
anterior neural tube	6.16e-22	42
pre-chordal neural plate	1.65e-20	61
ectoderm	2.65e-20	173
presumptive ectoderm	2.65e-20	173
gray matter	8.27e-20	34
brain grey matter	8.27e-20	34
telencephalon	1.18e-19	34
regional part of telencephalon	4.68e-19	33
cerebral hemisphere	5.43e-19	32
ectoderm-derived structure	5.59e-19	169
adult organism	3.39e-17	115
head	3.30e-16	123
cerebral cortex	2.92e-15	25
pallium	2.92e-15	25
anterior region of body	5.06e-15	129
craniocervical region	5.06e-15	129
regional part of cerebral cortex	2.70e-14	22
organ part	8.11e-14	219
neocortex	3.29e-13	20
multi-tissue structure	2.12e-11	347
epithelium	1.19e-10	309
tube	1.29e-10	194
cell layer	1.76e-10	312
organ segment	1.37e-08	97
anatomical cluster	2.15e-08	286
organism subdivision	6.15e-08	365
anatomical conduit	7.52e-08	241
posterior neural tube	8.62e-08	15
chordal neural plate	8.62e-08	15
embryo	3.70e-07	612
segmental subdivision of nervous system	6.22e-07	13

Disease

Ontology term	p-value	n
cell type cancer	1.54e-15	143
carcinoma	7.70e-14	106
cancer	5.09e-10	235
disease of cellular proliferation	1.04e-09	239

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324277742634985
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321182501597923
NFYA#4800	2	12.2837204665537	0.00851601140372443	0.0324635440009335
NFYB#4801	2	11.1731955023576	0.0102546713505453	0.0381134384761423
SETDB1#9869	2	26.880017452007	0.00181446890796441	0.0108915063094945
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203097569470126

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.