Coexpression cluster:C2379

Full id: C2379_smallcell_maxillary_malignant_kidney_pancreatic_signet_bronchioalveolar

Phase1 CAGE Peaks

Hg19::chr16:57653596..57653610,+	p10@GPR56
Hg19::chr16:57653625..57653669,+	p3@GPR56
Hg19::chr16:57653946..57653968,+	p4@GPR56
Hg19::chr16:57653997..57654022,+	p7@GPR56

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
epithelial cell	1.94e-38	253
endo-epithelial cell	1.25e-25	42
endodermal cell	4.27e-23	58
epithelial cell of alimentary canal	6.21e-13	20
respiratory epithelial cell	6.16e-11	13
kidney tubule cell	8.00e-08	10
nephron tubule epithelial cell	8.00e-08	10
general ecto-epithelial cell	2.14e-07	14
epithelial cell of tracheobronchial tree	4.57e-07	9
epithelial cell of lower respiratory tract	4.57e-07	9

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	9.26e-35	160
endoderm	9.26e-35	160
presumptive endoderm	9.26e-35	160
digestive system	2.38e-27	145
digestive tract	2.38e-27	145
primitive gut	2.38e-27	145
subdivision of digestive tract	1.99e-25	118
respiratory system	1.03e-21	74
foregut	1.70e-19	87
respiratory tract	1.72e-16	54
trunk region element	3.94e-14	101
renal system	4.81e-14	48
endo-epithelium	5.44e-14	82
immaterial anatomical entity	9.70e-14	117
urinary system structure	1.39e-13	47
respiratory primordium	2.37e-13	38
endoderm of foregut	2.37e-13	38
anatomical space	5.17e-13	95
segment of respiratory tract	3.48e-12	47
organ	1.44e-11	503
subdivision of trunk	7.10e-11	112
epithelial bud	9.57e-11	37
orifice	6.45e-10	36
thoracic cavity element	8.83e-10	34
thoracic cavity	8.83e-10	34
thoracic segment organ	2.69e-09	35
organism subdivision	2.76e-09	264
internal genitalia	7.08e-09	25
reproductive structure	1.15e-08	59
reproductive system	1.15e-08	59
epithelial fold	1.17e-08	47
oral opening	1.86e-08	22
reproductive organ	4.79e-08	48
organ part	5.13e-08	218
lung	6.84e-08	22
respiratory tube	6.84e-08	22
respiration organ	6.84e-08	22
pair of lungs	6.84e-08	22
lung primordium	6.84e-08	22
lung bud	6.84e-08	22
nephron tubule epithelium	8.00e-08	10
thoracic segment of trunk	1.54e-07	52
respiratory system epithelium	1.74e-07	28
primordium	1.76e-07	160
kidney	3.10e-07	26
kidney mesenchyme	3.10e-07	26
upper urinary tract	3.10e-07	26
kidney rudiment	3.10e-07	26
kidney field	3.10e-07	26
multi-cellular organism	3.59e-07	656
extraembryonic membrane	5.01e-07	14
membranous layer	5.01e-07	14
gland	5.12e-07	59
cavitated compound organ	6.24e-07	31
female organism	6.26e-07	41
embryo	6.47e-07	592

Disease

Ontology term	p-value	n
carcinoma	2.04e-27	106
cell type cancer	6.63e-19	143
squamous cell carcinoma	8.12e-11	14
adenocarcinoma	4.41e-09	25
cancer	8.40e-07	235

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	4	4.90738921487932	0.00172402235736179	0.0106434457043511
ESR1#2099	4	30.7686032961545	1.11467714392546e-06	4.60141368515537e-05

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.