Coexpression cluster:C1455

Full id: C1455_Tracheal_Corneal_Keratinocyte_Mammary_Urothelial_Bronchial_Esophageal

Phase1 CAGE Peaks

Hg19::chr19:45281118..45281181,+	p1@CBLC
Hg19::chr19:45281215..45281224,+	p2@CU688574
Hg19::chr19:45281245..45281260,+	p1@CU688574
Hg19::chr1:26856236..26856292,+	p2@RPS6KA1
Hg19::chr22:37915562..37915598,-	p3@CARD10
Hg19::chr22:40390930..40390994,+	p1@FAM83F

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:0007175	negative regulation of epidermal growth factor receptor activity	0.00847707066194942
GO:0042059	negative regulation of epidermal growth factor receptor signaling pathway	0.00847707066194942
GO:0032449	CBM complex	0.00847707066194942
GO:0007176	regulation of epidermal growth factor receptor activity	0.0158169451647997
GO:0007250	activation of NF-kappaB-inducing kinase	0.0158169451647997
GO:0042058	regulation of epidermal growth factor receptor signaling pathway	0.0158169451647997
GO:0065009	regulation of a molecular function	0.0158169451647997
GO:0030159	receptor signaling complex scaffold activity	0.0188285090913903
GO:0032947	protein complex scaffold	0.0188285090913903
GO:0007173	epidermal growth factor receptor signaling pathway	0.0277273132276541
GO:0006468	protein amino acid phosphorylation	0.0277273132276541
GO:0007165	signal transduction	0.0277273132276541
GO:0007154	cell communication	0.0323588363159623
GO:0016310	phosphorylation	0.032800513276824
GO:0019538	protein metabolic process	0.032800513276824
GO:0032147	activation of protein kinase activity	0.0370140841269794
GO:0006793	phosphorus metabolic process	0.0385749904955098
GO:0006796	phosphate metabolic process	0.0385749904955098
GO:0009968	negative regulation of signal transduction	0.0462629851426927

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	1.13e-41	254
endodermal cell	3.47e-16	59
endo-epithelial cell	7.96e-16	43
respiratory epithelial cell	1.43e-07	13
epithelial cell of alimentary canal	3.83e-07	21

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.09e-20	169
endoderm	2.09e-20	169
presumptive endoderm	2.09e-20	169
subdivision of digestive tract	5.80e-16	129
endodermal part of digestive tract	5.80e-16	129
digestive system	1.22e-15	155
digestive tract	1.22e-15	155
primitive gut	1.22e-15	155
mixed endoderm/mesoderm-derived structure	3.26e-14	130
foregut	1.09e-12	98
trunk region element	2.65e-11	107
immaterial anatomical entity	4.10e-11	126
respiratory system	5.92e-11	72
anatomical space	4.39e-10	104
respiratory tract	1.74e-09	53
endo-epithelium	4.72e-09	82
renal system	1.27e-08	45
urinary system structure	2.10e-08	44
primordium	3.06e-08	168
respiratory primordium	1.33e-07	38
endoderm of foregut	1.33e-07	38
abdomen element	2.86e-07	55
abdominal segment element	2.86e-07	55
segment of respiratory tract	4.40e-07	46
kidney	7.43e-07	27
kidney mesenchyme	7.43e-07	27
kidney rudiment	7.43e-07	27
kidney field	7.43e-07	27

Disease

Ontology term	p-value	n
carcinoma	5.06e-22	106
cell type cancer	7.41e-14	143
cancer	8.62e-12	235
disease of cellular proliferation	7.96e-11	239
squamous cell carcinoma	1.39e-07	14
adenocarcinoma	2.01e-07	25

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
HEY1#23462	5	3.36675920258809	0.00442382704520303	0.0209523410627164
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380336971519365
STAT3#6774	3	5.25973249857712	0.0137766205807855	0.0484743776307749
TAF1#6872	5	2.78587190478774	0.0107863634029041	0.0397950052082767
USF1#7391	4	4.24099951813864	0.00700536775082942	0.0296076080502154
USF2#7392	4	8.66146492337973	0.000463535508143562	0.0042679348439571

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.