Coexpression cluster:C1326

Full id: C1326_mesenchymal_CD14_Fibroblast_Smooth_Preadipocyte_Endothelial_Renal

Phase1 CAGE Peaks

Hg19::chr11:102668601..102668604,-	p14@MMP1
Hg19::chr13:43938419..43938424,-	p@chr13:43938419..43938424 -
Hg19::chr13:43938433..43938456,-	p@chr13:43938433..43938456 -
Hg19::chr5:110407337..110407343,+	p9@TSLP
Hg19::chr5:110407408..110407415,+	p3@TSLP
Hg19::chr5:99385675..99385684,-	p@chr5:99385675..99385684 -

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:0004232	interstitial collagenase activity	0.00412079823606691
GO:0005615	extracellular space	0.00412079823606691
GO:0008133	collagenase activity	0.00412079823606691
GO:0044421	extracellular region part	0.00432581913920992
GO:0030574	collagen catabolic process	0.00432581913920992
GO:0044256	protein digestion	0.00432581913920992
GO:0044254	multicellular organismal protein catabolic process	0.00432581913920992
GO:0044266	multicellular organismal macromolecule catabolic process	0.00432581913920992
GO:0044259	multicellular organismal macromolecule metabolic process	0.00432581913920992
GO:0044268	multicellular organismal protein metabolic process	0.00432581913920992
GO:0032963	collagen metabolic process	0.00432581913920992
GO:0044243	multicellular organismal catabolic process	0.00432581913920992
GO:0044236	multicellular organismal metabolic process	0.00437322683744746
GO:0007586	digestion	0.0167553098487676
GO:0004222	metalloendopeptidase activity	0.0325440067988259
GO:0005125	cytokine activity	0.047689218626343

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
vascular associated smooth muscle cell	3.20e-13	32
muscle precursor cell	1.42e-11	57
myoblast	1.42e-11	57
multi-potent skeletal muscle stem cell	1.42e-11	57
non-terminally differentiated cell	8.37e-11	180
smooth muscle cell	1.06e-10	42
smooth muscle myoblast	1.06e-10	42
multi fate stem cell	1.78e-10	430
muscle cell	1.85e-10	54
contractile cell	5.51e-10	59
somatic stem cell	5.83e-10	436
electrically responsive cell	1.27e-09	60
electrically active cell	1.27e-09	60
stem cell	2.65e-09	444
cardiocyte	4.65e-08	16
somatic cell	8.11e-08	591
cardiac mesenchymal cell	1.90e-07	4
migratory trunk neural crest cell	1.90e-07	4

Uber Anatomy

Ontology term	p-value	n
artery	1.99e-23	42
arterial blood vessel	1.99e-23	42
arterial system	1.99e-23	42
blood vessel	3.56e-18	60
epithelial tube open at both ends	3.56e-18	60
blood vasculature	3.56e-18	60
vascular cord	3.56e-18	60
systemic artery	1.07e-17	33
systemic arterial system	1.07e-17	33
splanchnic layer of lateral plate mesoderm	2.84e-17	84
vessel	2.18e-15	69
vasculature	4.82e-14	79
vascular system	4.82e-14	79
epithelial tube	2.28e-13	118
cardiovascular system	1.47e-12	110
dermomyotome	3.11e-12	70
circulatory system	6.80e-12	113
somite	3.29e-11	83
paraxial mesoderm	3.29e-11	83
presomitic mesoderm	3.29e-11	83
presumptive segmental plate	3.29e-11	83
trunk paraxial mesoderm	3.29e-11	83
presumptive paraxial mesoderm	3.29e-11	83
lateral plate mesoderm	3.73e-11	216
skeletal muscle tissue	2.74e-10	61
striated muscle tissue	2.74e-10	61
myotome	2.74e-10	61
multilaminar epithelium	9.14e-10	82
muscle tissue	1.03e-09	63
musculature	1.03e-09	63
musculature of body	1.03e-09	63
musculoskeletal system	1.45e-09	167
aorta	2.16e-09	21
aortic system	2.16e-09	21
unilaminar epithelium	1.66e-08	138
mesoderm	1.53e-07	448
mesoderm-derived structure	1.53e-07	448
presumptive mesoderm	1.53e-07	448

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
GATA2#2624	3	6.372465866777	0.00805882130874255	0.0318820879072602

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.