Coexpression cluster:C1393

Full id: C1393_thyroid_lung_throat_Alveolar_small_nonsmall_papillary

Phase1 CAGE Peaks

Hg19::chr14:36983118..36983142,-	p3@SFTA3
Hg19::chr14:36986015..36986024,-	p@chr14:36986015..36986024 -
Hg19::chr14:36988729..36988748,-	p2@ENST00000521945
Hg19::chr14:36988882..36988895,-	p13@NKX2-1
Hg19::chr14:36989573..36989577,-	p18@NKX2-1
Hg19::chr9:138336075..138336099,-	p@chr9:138336075..138336099 -

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:0021798	forebrain dorsal/ventral pattern formation	0.00523960908983869
GO:0021871	forebrain regionalization	0.00523960908983869
GO:0030878	thyroid gland development	0.00589456022606853
GO:0007492	endoderm development	0.00589456022606853
GO:0009953	dorsal/ventral pattern formation	0.0109555462787536
GO:0035270	endocrine system development	0.0109555462787536
GO:0001764	neuron migration	0.0109555462787536
GO:0030324	lung development	0.0109555462787536
GO:0030323	respiratory tube development	0.0109555462787536
GO:0030900	forebrain development	0.0109555462787536
GO:0048732	gland development	0.0109555462787536
GO:0003002	regionalization	0.0189935829506652
GO:0035295	tube development	0.0227595519839868
GO:0007389	pattern specification process	0.0227595519839868
GO:0007420	brain development	0.0227595519839868
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0227595519839868
GO:0005667	transcription factor complex	0.030190128565261
GO:0045893	positive regulation of transcription, DNA-dependent	0.030190128565261
GO:0016477	cell migration	0.030190128565261
GO:0007417	central nervous system development	0.030190128565261
GO:0048699	generation of neurons	0.030190128565261
GO:0022008	neurogenesis	0.0311353693992338
GO:0045941	positive regulation of transcription	0.0311353693992338
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0311353693992338
GO:0009888	tissue development	0.0311353693992338
GO:0016563	transcription activator activity	0.0311353693992338
GO:0009887	organ morphogenesis	0.0330433411955956
GO:0031325	positive regulation of cellular metabolic process	0.0330433411955956
GO:0051674	localization of cell	0.0330433411955956
GO:0006928	cell motility	0.0330433411955956
GO:0009893	positive regulation of metabolic process	0.0330433411955956
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0346305413281526
GO:0044451	nucleoplasm part	0.0358833834637438
GO:0005654	nucleoplasm	0.0399905458474453
GO:0006366	transcription from RNA polymerase II promoter	0.0479049973928109

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><br>

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Cell Type

Ontology term	p-value	n
respiratory epithelial cell	4.51e-09	13

Uber Anatomy

Ontology term	p-value	n
respiratory tract	9.40e-18	53
respiratory primordium	5.64e-17	38
endoderm of foregut	5.64e-17	38
respiratory system	4.04e-16	72
thoracic segment organ	2.36e-10	35
segment of respiratory tract	1.02e-09	46
thoracic cavity element	2.83e-09	34
thoracic cavity	2.83e-09	34
endoderm-derived structure	1.76e-08	169
endoderm	1.76e-08	169
presumptive endoderm	1.76e-08	169
lung	2.74e-08	22
respiratory tube	2.74e-08	22
respiration organ	2.74e-08	22
pair of lungs	2.74e-08	22
lung primordium	2.74e-08	22
lung bud	2.74e-08	22
thyroid gland	4.28e-08	5
pharyngeal pouch	4.28e-08	5
thyroid diverticulum	4.28e-08	5
pharyngeal pouch 2	4.28e-08	5
thyroid primordium	4.28e-08	5
digestive system	2.39e-07	155
digestive tract	2.39e-07	155
primitive gut	2.39e-07	155
male genital duct	3.01e-07	3
internal male genitalia	3.01e-07	3
larynx	3.11e-07	9

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
CTBP2#1488	3	31.3585001696641	7.81255347077474e-05	0.00120308946023923
SUZ12#23512	2	16.7052603036876	0.00566023468207957	0.0255610001280628

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.