Coexpression cluster:C1119

Full id: C1119_nonsmall_smallcell_argyrophil_small_duodenum_esophagus_cerebellum

Phase1 CAGE Peaks

Hg19::chr10:5406920..5406934,+	p2@UCN3
Hg19::chr10:5406935..5406962,+	p1@UCN3
Hg19::chr10:5407062..5407072,+	p3@UCN3
Hg19::chr10:5407085..5407093,+	p5@UCN3
Hg19::chr2:241836244..241836276,-	p2@C2orf54
Hg19::chr6:18208375..18208387,+	p@chr6:18208375..18208387 +
Hg19::chr8:141018677..141018706,-	p5@TRAPPC9

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:0007189	G-protein signaling, adenylate cyclase activating pathway	0.0100553396915107
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0100553396915107
GO:0019933	cAMP-mediated signaling	0.0100553396915107
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0100553396915107
GO:0019935	cyclic-nucleotide-mediated signaling	0.0100553396915107
GO:0005179	hormone activity	0.0149044311001217
GO:0019932	second-messenger-mediated signaling	0.0157776992817614

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
endodermal cell	9.48e-08	59

Uber Anatomy

Ontology term	p-value	n
adult organism	2.84e-25	115
subdivision of digestive tract	3.01e-16	129
endodermal part of digestive tract	3.01e-16	129
digestive system	3.47e-15	155
digestive tract	3.47e-15	155
primitive gut	3.47e-15	155
endoderm-derived structure	5.14e-15	169
endoderm	5.14e-15	169
presumptive endoderm	5.14e-15	169
neural tube	4.32e-12	57
neural rod	4.32e-12	57
future spinal cord	4.32e-12	57
neural keel	4.32e-12	57
mixed endoderm/mesoderm-derived structure	6.39e-12	130
endo-epithelium	3.71e-11	82
foregut	7.87e-11	98
multi-tissue structure	4.01e-10	347
regional part of brain	1.71e-09	59
thoracic cavity element	1.94e-09	34
thoracic cavity	1.94e-09	34
thoracic segment organ	5.20e-09	35
organ part	8.29e-09	219
anatomical conduit	1.13e-08	241
organism subdivision	1.42e-08	365
lung	1.66e-08	22
respiratory tube	1.66e-08	22
respiration organ	1.66e-08	22
pair of lungs	1.66e-08	22
lung primordium	1.66e-08	22
lung bud	1.66e-08	22
anterior region of body	1.83e-08	129
craniocervical region	1.83e-08	129
neural plate	3.78e-08	86
presumptive neural plate	3.78e-08	86
organ	4.44e-08	511
neurectoderm	5.67e-08	90
tube	7.22e-08	194
organ segment	9.30e-08	97
trunk region element	9.39e-08	107
posterior neural tube	1.21e-07	15
chordal neural plate	1.21e-07	15
segmental subdivision of nervous system	1.28e-07	13
central nervous system	1.40e-07	82
respiratory system	1.96e-07	72
brain	2.07e-07	69
future brain	2.07e-07	69
head	3.90e-07	123
regional part of forebrain	5.08e-07	41
forebrain	5.08e-07	41
future forebrain	5.08e-07	41
respiratory tract	8.48e-07	53
epithelial bud	8.72e-07	37
anterior neural tube	9.77e-07	42

Disease

Ontology term	p-value	n
carcinoma	7.64e-08	106

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.