Coexpression cluster:C2293

Full id: C2293_large_lung_nonsmall_throat_trachea_bronchioalveolar_thyroid

Phase1 CAGE Peaks

Hg19::chr14:36982935..36982943,-	p9@SFTA3
Hg19::chr14:36982948..36982964,-	p7@SFTA3
Hg19::chr8:55471706..55471714,+	p3@RP1
Hg19::chr8:55471724..55471729,+	p8@RP1

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:0007603	phototransduction, visible light	0.00508440105755542
GO:0007602	phototransduction	0.00508440105755542
GO:0050962	detection of light stimulus during sensory perception	0.00508440105755542
GO:0050908	detection of light stimulus during visual perception	0.00508440105755542
GO:0009584	detection of visible light	0.00508440105755542
GO:0009583	detection of light stimulus	0.00508440105755542
GO:0006228	UTP biosynthetic process	0.00508440105755542
GO:0046051	UTP metabolic process	0.00508440105755542
GO:0004550	nucleoside diphosphate kinase activity	0.00508440105755542
GO:0046036	CTP metabolic process	0.00508440105755542
GO:0009209	pyrimidine ribonucleoside triphosphate biosynthetic process	0.00508440105755542
GO:0009208	pyrimidine ribonucleoside triphosphate metabolic process	0.00508440105755542
GO:0006241	CTP biosynthetic process	0.00508440105755542
GO:0006183	GTP biosynthetic process	0.00508440105755542
GO:0046039	GTP metabolic process	0.00508440105755542
GO:0009220	pyrimidine ribonucleotide biosynthetic process	0.00508440105755542
GO:0009218	pyrimidine ribonucleotide metabolic process	0.00508440105755542
GO:0005929	cilium	0.00508440105755542
GO:0009582	detection of abiotic stimulus	0.00508440105755542
GO:0050906	detection of stimulus during sensory perception	0.00508440105755542
GO:0009581	detection of external stimulus	0.00508440105755542
GO:0009147	pyrimidine nucleoside triphosphate metabolic process	0.00508440105755542
GO:0006221	pyrimidine nucleotide biosynthetic process	0.0051551405505301
GO:0006220	pyrimidine nucleotide metabolic process	0.00626398210290828
GO:0016776	phosphotransferase activity, phosphate group as acceptor	0.00626398210290828
GO:0051606	detection of stimulus	0.00671140939597316
GO:0009416	response to light stimulus	0.00671140939597316
GO:0019205	nucleobase, nucleoside, nucleotide kinase activity	0.00727069351230425
GO:0009314	response to radiation	0.00779140631026768
GO:0009206	purine ribonucleoside triphosphate biosynthetic process	0.00820283370618941
GO:0009145	purine nucleoside triphosphate biosynthetic process	0.00820283370618941
GO:0009201	ribonucleoside triphosphate biosynthetic process	0.00820283370618941
GO:0009142	nucleoside triphosphate biosynthetic process	0.00820283370618941
GO:0009205	purine ribonucleoside triphosphate metabolic process	0.00820283370618941
GO:0009144	purine nucleoside triphosphate metabolic process	0.00820283370618941
GO:0009199	ribonucleoside triphosphate metabolic process	0.00820283370618941
GO:0009152	purine ribonucleotide biosynthetic process	0.00859263778726866
GO:0009141	nucleoside triphosphate metabolic process	0.00859263778726866
GO:0009150	purine ribonucleotide metabolic process	0.00859263778726866
GO:0009260	ribonucleotide biosynthetic process	0.00859263778726866
GO:0006164	purine nucleotide biosynthetic process	0.00859263778726866
GO:0009628	response to abiotic stimulus	0.00859263778726866
GO:0006163	purine nucleotide metabolic process	0.00859263778726866
GO:0009259	ribonucleotide metabolic process	0.00859263778726866
GO:0007601	visual perception	0.0108452485166813
GO:0050953	sensory perception of light stimulus	0.0108452485166813
GO:0005625	soluble fraction	0.0111380836784235
GO:0009165	nucleotide biosynthetic process	0.0118847874720358
GO:0042995	cell projection	0.0142902798703374
GO:0009117	nucleotide metabolic process	0.0152125279642058
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0160986094661578
GO:0009605	response to external stimulus	0.0272328342798141
GO:0000267	cell fraction	0.0380735300325018
GO:0007600	sensory perception	0.0393570304084845

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
brush border epithelial cell	4.95e-10	3
kidney cortex tubule cell	4.95e-10	3
epithelial cell of proximal tubule	4.95e-10	3
lung fibroblast	1.41e-08	1

Uber Anatomy

Ontology term	p-value	n
thyroid gland	1.52e-22	5
pharyngeal pouch	1.52e-22	5
thyroid diverticulum	1.52e-22	5
pharyngeal pouch 2	1.52e-22	5
thyroid primordium	1.52e-22	5
throat	2.36e-15	2
lung	2.72e-15	22
respiratory tube	2.72e-15	22
respiration organ	2.72e-15	22
pair of lungs	2.72e-15	22
lung primordium	2.72e-15	22
lung bud	2.72e-15	22
epithelial bud	4.39e-14	37
endo-epithelium	4.91e-14	82
thoracic cavity element	1.86e-12	34
thoracic cavity	1.86e-12	34
thoracic segment organ	4.55e-12	35
respiratory primordium	5.04e-11	38
endoderm of foregut	5.04e-11	38
epithelial fold	8.77e-11	47
entire pharyngeal arch endoderm	2.37e-10	11
early pharyngeal endoderm	2.37e-10	11
renal cortex tubule	4.95e-10	3
region of nephron tubule	4.95e-10	3
proximal tubule	4.95e-10	3
lower lobe of right lung	1.13e-08	1
right lung lobe	1.13e-08	1
lower lobe of lung	1.13e-08	1
lobe of lung	1.13e-08	1
right lung	1.13e-08	1
digestive system	6.87e-08	145
digestive tract	6.87e-08	145
primitive gut	6.87e-08	145
trunk region element	7.85e-08	101
thoracic segment of trunk	9.64e-08	52
respiratory tract	2.06e-07	54
endoderm-derived structure	6.86e-07	160
endoderm	6.86e-07	160
presumptive endoderm	6.86e-07	160
subdivision of trunk	7.50e-07	112

Disease

Ontology term	p-value	n
papillary adenocarcinoma	4.72e-08	1
lung cancer	7.62e-08	15
lung carcinoma	9.96e-08	9
respiratory system cancer	2.33e-07	16

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	2	31.3585001696641	0.00149267688204723	0.00953828199242111
SUZ12#23512	2	25.0578904555315	0.00232525671652061	0.0131853342500107

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.