Coexpression cluster:C2548

Full id: C2548_salivary_immature_tongue_esophagus_amniotic_cervical_Corneal

Phase1 CAGE Peaks

Hg19::chr1:201252522..201252533,+	p2@PKP1
Hg19::chr1:201252623..201252640,+	p1@PKP1
Hg19::chr2:64681348..64681364,+	p1@LGALSL
Hg19::chr6:7541895..7541916,+	p1@DSP

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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p.value	FDR	nGenes	nPathway	Name
2.63387331172458e-05	0.0166724180632166	2	147	Apoptosis (Reactome):REACT_578

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:0005911	intercellular junction	0.00104122004525117
GO:0005882	intermediate filament	0.00104122004525117
GO:0045111	intermediate filament cytoskeleton	0.00104122004525117
GO:0019215	intermediate filament binding	0.00191331223659601
GO:0030054	cell junction	0.00206830683319861
GO:0030280	structural constituent of epidermis	0.00546596270161619
GO:0030057	desmosome	0.00546596270161619
GO:0044430	cytoskeletal part	0.00552645155524017
GO:0005913	cell-cell adherens junction	0.00552645155524017
GO:0001533	cornified envelope	0.00841609563968864
GO:0018149	peptide cross-linking	0.00882703254456832
GO:0005856	cytoskeleton	0.00882703254456832
GO:0030216	keratinocyte differentiation	0.00882703254456832
GO:0014704	intercalated disc	0.012838016257695
GO:0005912	adherens junction	0.0137653044832711
GO:0044459	plasma membrane part	0.0175034631324322
GO:0007275	multicellular organismal development	0.0175034631324322
GO:0005200	structural constituent of cytoskeleton	0.0180480957314749
GO:0030674	protein binding, bridging	0.0182357472300847
GO:0032403	protein complex binding	0.0182357472300847
GO:0043296	apical junction complex	0.0182357472300847
GO:0016327	apicolateral plasma membrane	0.0182357472300847
GO:0043232	intracellular non-membrane-bound organelle	0.0200027457430974
GO:0043228	non-membrane-bound organelle	0.0200027457430974
GO:0008544	epidermis development	0.0206233211507383
GO:0007398	ectoderm development	0.0214424247473283
GO:0032502	developmental process	0.0233615575638312
GO:0005886	plasma membrane	0.0283630958363565
GO:0032501	multicellular organismal process	0.0283630958363565
GO:0044446	intracellular organelle part	0.0309825493835566
GO:0044422	organelle part	0.0309825493835566
GO:0009888	tissue development	0.0363098561462876

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	3.30e-25	254
endodermal cell	4.80e-17	59
endo-epithelial cell	1.34e-15	43
epithelial cell of alimentary canal	2.81e-08	21
respiratory epithelial cell	4.45e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	4.07e-20	169
endoderm	4.07e-20	169
presumptive endoderm	4.07e-20	169
digestive system	6.22e-16	155
digestive tract	6.22e-16	155
primitive gut	6.22e-16	155
mixed endoderm/mesoderm-derived structure	9.61e-15	130
multi-cellular organism	4.16e-14	659
subdivision of digestive tract	5.16e-14	129
endodermal part of digestive tract	5.16e-14	129
respiratory system	3.10e-12	72
foregut	1.09e-11	98
organ	4.78e-11	511
immaterial anatomical entity	6.09e-11	126
multi-tissue structure	3.34e-10	347
adult organism	5.73e-10	115
subdivision of trunk	1.05e-09	113
organ part	1.29e-09	219
anatomical group	1.68e-09	626
anatomical system	1.88e-09	625
organism subdivision	2.27e-09	365
mesenchyme	4.33e-09	238
entire embryonic mesenchyme	4.33e-09	238
anatomical space	6.86e-09	104
endo-epithelium	1.57e-08	82
embryo	2.79e-08	612
respiratory tract	3.45e-08	53
trunk region element	4.14e-08	107
primordium	1.33e-07	168
embryonic structure	2.53e-07	605
developing anatomical structure	2.53e-07	605
exocrine gland	3.98e-07	31
exocrine system	3.98e-07	31
germ layer	4.70e-07	604
embryonic tissue	4.70e-07	604
presumptive structure	4.70e-07	604
epiblast (generic)	4.70e-07	604
gland	6.87e-07	59
respiratory primordium	8.19e-07	38
endoderm of foregut	8.19e-07	38
oral opening	8.34e-07	21

Disease

Ontology term	p-value	n
carcinoma	2.91e-15	106
cell type cancer	4.83e-10	143

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)
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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
BHLHE40#8553	2	22.4359067734887	0.00289146449685312	0.0156402351660888

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.