Coexpression cluster:C1785

Full id: C1785_Cardiac_umbilical_colon_uterus_throat_trachea_Smooth

Phase1 CAGE Peaks

Hg19::chr17:48262709..48262724,-	p27@COL1A1
Hg19::chr2:189876607..189876629,+	p6@AF130082
Hg19::chr2:189876978..189876985,+	p21@AF130082
Hg19::chr2:189876995..189877006,+	p13@AF130082
Hg19::chr2:189877092..189877097,+	p20@AF130082

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:0005584	collagen type I	0.00341457671023196
GO:0008147	structural constituent of bone	0.00341457671023196
GO:0051591	response to cAMP	0.00443894972330154
GO:0005583	fibrillar collagen	0.00443894972330154
GO:0031960	response to corticosteroid stimulus	0.00443894972330154
GO:0009612	response to mechanical stimulus	0.00469504297656894
GO:0042542	response to hydrogen peroxide	0.00469504297656894
GO:0043434	response to peptide hormone stimulus	0.00469504297656894
GO:0000302	response to reactive oxygen species	0.00512186506534793
GO:0048545	response to steroid hormone stimulus	0.00597550924290592
GO:0007584	response to nutrient	0.00597550924290592
GO:0010035	response to inorganic substance	0.00597550924290592
GO:0005581	collagen	0.0070425644648534
GO:0031667	response to nutrient levels	0.0070425644648534
GO:0010033	response to organic substance	0.0070425644648534
GO:0009991	response to extracellular stimulus	0.0070425644648534
GO:0009725	response to hormone stimulus	0.00763258323463613
GO:0001503	ossification	0.00790744080264242
GO:0031214	biomineral formation	0.00790744080264242
GO:0046849	bone remodeling	0.00819498410455669
GO:0048771	tissue remodeling	0.00853644177557988
GO:0006979	response to oxidative stress	0.00853644177557989
GO:0005201	extracellular matrix structural constituent	0.00853644177557989
GO:0044420	extracellular matrix part	0.00853644177557989
GO:0007605	sensory perception of sound	0.00853644177557989
GO:0050954	sensory perception of mechanical stimulus	0.00853644177557989
GO:0008544	epidermis development	0.00853644177557989
GO:0006817	phosphate transport	0.00859531378782526
GO:0007398	ectoderm development	0.00859531378782526
GO:0009628	response to abiotic stimulus	0.00939008595313787
GO:0001501	skeletal development	0.0115104279425561
GO:0015698	inorganic anion transport	0.0138717178853173
GO:0009888	tissue development	0.0157794832821325
GO:0006820	anion transport	0.0162192393736018
GO:0005578	proteinaceous extracellular matrix	0.0205362399286807
GO:0009719	response to endogenous stimulus	0.0250876538848987
GO:0042221	response to chemical stimulus	0.0271781848963057
GO:0009605	response to external stimulus	0.0284398297049582
GO:0044421	extracellular region part	0.0398367282860395
GO:0007600	sensory perception	0.0405480984340045
GO:0048513	organ development	0.0475125856874959
GO:0006950	response to stress	0.0496739611893268

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
muscle cell	4.50e-07	55
contractile cell	6.33e-07	59

Uber Anatomy

Ontology term	p-value	n
skeletal muscle tissue	2.39e-07	62
striated muscle tissue	2.39e-07	62
myotome	2.39e-07	62
muscle tissue	6.29e-07	64
musculature	6.29e-07	64
musculature of body	6.29e-07	64
intestine	7.38e-07	17
mesenchyme	9.40e-07	160
entire embryonic mesenchyme	9.40e-07	160

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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No analysis results for this cluster

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.