Coexpression cluster:C1399

Full id: C1399_Bronchial_Tracheal_bronchial_Lymphatic_salivary_Small_lung

Phase1 CAGE Peaks

Hg19::chr14:75033780..75033781,+	p@chr14:75033780..75033781 +
Hg19::chr17:38179565..38179597,-	p4@MED24
Hg19::chr17:38179600..38179634,-	p2@MED24
Hg19::chr17:38179639..38179652,-	p7@MED24
Hg19::chr1:95089255..95089279,-	p1@ENST00000435559
Hg19::chr6:6803656..6803661,+	p@chr6:6803656..6803661 +

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:0042809	vitamin D receptor binding	0.00964765100671141
GO:0016455	RNA polymerase II transcription mediator activity	0.00964765100671141
GO:0000119	mediator complex	0.00964765100671141
GO:0046966	thyroid hormone receptor binding	0.00964765100671141
GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	0.00964765100671141
GO:0030521	androgen receptor signaling pathway	0.00964765100671141
GO:0016251	general RNA polymerase II transcription factor activity	0.00964765100671141
GO:0006367	transcription initiation from RNA polymerase II promoter	0.00964765100671141
GO:0030518	steroid hormone receptor signaling pathway	0.00964765100671141
GO:0030522	intracellular receptor-mediated signaling pathway	0.00964765100671141
GO:0035257	nuclear hormone receptor binding	0.00964765100671141
GO:0051427	hormone receptor binding	0.00964765100671141
GO:0006352	transcription initiation	0.0142175909572589
GO:0016591	DNA-directed RNA polymerase II, holoenzyme	0.0166839077559671
GO:0003713	transcription coactivator activity	0.0253208524667373
GO:0003702	RNA polymerase II transcription factor activity	0.0330318466600978
GO:0065004	protein-DNA complex assembly	0.0330318466600978
GO:0003712	transcription cofactor activity	0.0330318466600978
GO:0016563	transcription activator activity	0.0330318466600978
GO:0008134	transcription factor binding	0.0437166742359254
GO:0044451	nucleoplasm part	0.0437166742359254
GO:0005654	nucleoplasm	0.0479151279663466

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	2.50e-20	254
endo-epithelial cell	5.69e-11	43
respiratory epithelial cell	4.79e-09	13
squamous epithelial cell	5.63e-07	62

Uber Anatomy

Ontology term	p-value	n
respiratory system	2.66e-14	72
endoderm-derived structure	1.44e-12	169
endoderm	1.44e-12	169
presumptive endoderm	1.44e-12	169
respiratory tract	2.56e-10	53
anatomical space	8.35e-09	104
digestive system	1.48e-08	155
digestive tract	1.48e-08	155
primitive gut	1.48e-08	155
thoracic cavity element	2.48e-08	34
thoracic cavity	2.48e-08	34
thoracic segment organ	8.32e-08	35
thoracic segment of trunk	1.71e-07	52
oral opening	2.91e-07	21
tracheobronchial tree	3.65e-07	14
lower respiratory tract	3.65e-07	14
orifice	5.95e-07	35
mixed endoderm/mesoderm-derived structure	8.27e-07	130
segment of respiratory tract	8.36e-07	46

Disease

Ontology term	p-value	n
carcinoma	4.10e-07	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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ESR1#2099	3	15.3843016480772	0.000637403909579904	0.005226491867207
NR3C1#2908	3	7.48651166558652	0.0051086696598407	0.0237574294507126
STAT3#6774	6	10.5194649971542	7.37398960627247e-07	3.26603944227943e-05
TFAP2A#7020	6	16.518634373045	4.91595718330683e-08	3.15755013694577e-06
TFAP2C#7022	6	10.8092286098602	6.2644941908553e-07	2.86327137329863e-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.