Coexpression cluster:C449

Full id: C449_epidermoid_anaplastic_occipital_oral_middle_Wilms_parietal

Phase1 CAGE Peaks

Hg19::chr11:69988499..69988503,-	p@chr11:69988499..69988503 -
Hg19::chr17:39678090..39678101,-	p4@KRT15
Hg19::chr19:51512580..51512608,-	p@chr19:51512580..51512608 -
Hg19::chr2:72258505..72258535,+	p@chr2:72258505..72258535 +
Hg19::chr3:193809263..193809278,+	p1@ENST00000457815
Hg19::chr4:23975557..23975561,-	p@chr4:23975557..23975561 -
Hg19::chr4:23981805..23981809,-	p@chr4:23981805..23981809 -
Hg19::chr4:24010751..24010757,-	p@chr4:24010751..24010757 -
Hg19::chr4:24053554..24053559,-	p@chr4:24053554..24053559 -
Hg19::chr4:24055928..24055932,-	p@chr4:24055928..24055932 -
Hg19::chr4:24059076..24059080,-	p@chr4:24059076..24059080 -
Hg19::chr4:24105215..24105219,-	p@chr4:24105215..24105219 -
Hg19::chr4:24125531..24125534,-	p@chr4:24125531..24125534 -
Hg19::chr4:24188430..24188435,-	p@chr4:24188430..24188435 -
Hg19::chr4:24202276..24202277,-	p@chr4:24202276..24202277 -
Hg19::chr4:24208460..24208464,-	p@chr4:24208460..24208464 -
Hg19::chr4:24232569..24232574,-	p@chr4:24232569..24232574 -
Hg19::chr5:84943573..84943591,-	p@chr5:84943573..84943591 -
Hg19::chr6:43706592..43706595,-	p@chr6:43706592..43706595 -
Hg19::chr6:43706642..43706655,-	p@chr6:43706642..43706655 -
Hg19::chr7:55088621..55088630,+	p@chr7:55088621..55088630 +
Hg19::chr9:135687993..135687996,+	p@chr9:135687993..135687996 +

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:0005200	structural constituent of cytoskeleton	0.0333451077357824
GO:0008544	epidermis development	0.0333451077357824
GO:0007398	ectoderm development	0.0333451077357824
GO:0045111	intermediate filament cytoskeleton	0.0333451077357824
GO:0005882	intermediate filament	0.0333451077357824
GO:0009888	tissue development	0.0359119274696809

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
endo-epithelial cell	9.68e-11	43
endodermal cell	1.05e-10	59
respiratory epithelial cell	3.45e-07	13

Uber Anatomy

Ontology term	p-value	n
neural tube	4.86e-26	57
neural rod	4.86e-26	57
future spinal cord	4.86e-26	57
neural keel	4.86e-26	57
central nervous system	5.86e-26	82
adult organism	2.05e-24	115
regional part of nervous system	4.96e-23	94
nervous system	4.96e-23	94
anterior neural tube	9.23e-23	42
regional part of forebrain	1.66e-22	41
forebrain	1.66e-22	41
future forebrain	1.66e-22	41
brain	2.02e-21	69
future brain	2.02e-21	69
regional part of brain	2.37e-20	59
ectoderm-derived structure	4.35e-20	169
ectoderm	2.28e-19	173
presumptive ectoderm	2.28e-19	173
gray matter	2.59e-19	34
brain grey matter	2.59e-19	34
telencephalon	8.37e-19	34
neural plate	1.67e-18	86
presumptive neural plate	1.67e-18	86
cerebral hemisphere	3.41e-18	32
regional part of telencephalon	4.73e-18	33
neurectoderm	2.38e-17	90
anterior region of body	1.05e-16	129
craniocervical region	1.05e-16	129
regional part of cerebral cortex	1.12e-16	22
head	1.42e-16	123
neocortex	3.67e-15	20
pre-chordal neural plate	2.16e-14	61
cerebral cortex	2.22e-13	25
pallium	2.22e-13	25
organ part	1.01e-12	219
organ	2.78e-12	511
endoderm-derived structure	1.45e-11	169
endoderm	1.45e-11	169
presumptive endoderm	1.45e-11	169
multi-tissue structure	5.95e-10	347
embryo	7.91e-10	612
anatomical conduit	8.00e-10	241
digestive system	8.47e-10	155
digestive tract	8.47e-10	155
primitive gut	8.47e-10	155
anatomical system	1.54e-09	625
germ layer	1.57e-09	604
embryonic tissue	1.57e-09	604
presumptive structure	1.57e-09	604
epiblast (generic)	1.57e-09	604
anatomical group	2.14e-09	626
embryonic structure	2.18e-09	605
developing anatomical structure	2.18e-09	605
organism subdivision	2.70e-09	365
endo-epithelium	8.96e-09	82
subdivision of digestive tract	1.03e-08	129
endodermal part of digestive tract	1.03e-08	129
respiratory system	1.29e-08	72
epithelium	2.07e-08	309
multi-cellular organism	5.08e-08	659
cell layer	5.82e-08	312
tube	6.73e-08	194
anatomical cluster	8.21e-08	286
nucleus of brain	1.55e-07	9
neural nucleus	1.55e-07	9
basal ganglion	1.67e-07	9
nuclear complex of neuraxis	1.67e-07	9
aggregate regional part of brain	1.67e-07	9
collection of basal ganglia	1.67e-07	9
cerebral subcortex	1.67e-07	9
respiratory tract	4.09e-07	53
temporal lobe	9.07e-07	7

Disease

Ontology term	p-value	n
carcinoma	3.31e-09	106
squamous cell carcinoma	3.13e-07	14
cell type cancer	9.33e-07	143

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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This analysis result is provided for C0 - C305 clusters.