Coexpression cluster:C3509

Full id: C3509_Fibroblast_Keratocytes_Myoblast_tridermal_Smooth_optic_embryonic

Phase1 CAGE Peaks

Hg19::chr15:71146436..71146447,-	p3@LARP6
Hg19::chr15:71146461..71146475,-	p2@LARP6
Hg19::chr15:71146480..71146531,-	p1@LARP6

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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No GOStat results

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
contractile cell	7.87e-18	59
muscle precursor cell	3.06e-17	58
myoblast	3.06e-17	58
multi-potent skeletal muscle stem cell	3.06e-17	58
muscle cell	1.62e-16	55
smooth muscle cell	3.46e-16	43
smooth muscle myoblast	3.46e-16	43
non-terminally differentiated cell	1.08e-15	106
vascular associated smooth muscle cell	2.55e-14	32
electrically responsive cell	5.44e-14	61
electrically active cell	5.44e-14	61
fibroblast	5.61e-14	76
mesodermal cell	1.47e-13	121
embryonic cell	1.96e-11	250

Uber Anatomy

Ontology term	p-value	n
cell layer	2.78e-20	309
epithelium	7.62e-20	306
multi-tissue structure	1.16e-17	342
dense mesenchyme tissue	4.00e-16	73
paraxial mesoderm	7.30e-16	72
presumptive paraxial mesoderm	7.30e-16	72
somite	9.59e-16	71
presomitic mesoderm	9.59e-16	71
presumptive segmental plate	9.59e-16	71
dermomyotome	9.59e-16	71
trunk paraxial mesoderm	9.59e-16	71
anatomical cluster	1.07e-15	373
epithelial vesicle	2.06e-15	78
skeletal muscle tissue	3.57e-15	62
striated muscle tissue	3.57e-15	62
myotome	3.57e-15	62
anatomical conduit	6.08e-15	240
tube	1.10e-14	192
multilaminar epithelium	1.88e-14	83
muscle tissue	4.00e-14	64
musculature	4.00e-14	64
musculature of body	4.00e-14	64
structure with developmental contribution from neural crest	5.35e-14	132
mesenchyme	1.41e-13	160
entire embryonic mesenchyme	1.41e-13	160
multi-cellular organism	3.80e-13	656
artery	9.62e-13	42
arterial blood vessel	9.62e-13	42
arterial system	9.62e-13	42
organism subdivision	1.04e-12	264
trunk mesenchyme	5.48e-12	122
splanchnic layer of lateral plate mesoderm	8.24e-12	83
anatomical system	1.40e-11	624
trunk	1.40e-11	199
systemic artery	1.41e-11	33
systemic arterial system	1.41e-11	33
anatomical group	2.61e-11	625
vasculature	3.00e-11	78
vascular system	3.00e-11	78
epithelial tube open at both ends	1.02e-10	59
blood vessel	1.02e-10	59
blood vasculature	1.02e-10	59
vascular cord	1.02e-10	59
unilaminar epithelium	9.48e-10	148
vessel	1.05e-09	68
epithelial tube	1.39e-09	117
circulatory system	3.91e-09	112
cardiovascular system	8.99e-09	109
neural plate	4.26e-08	82
presumptive neural plate	4.26e-08	82
neurectoderm	5.53e-08	86
embryo	9.28e-08	592
ectoderm-derived structure	1.98e-07	171
ectoderm	1.98e-07	171
presumptive ectoderm	1.98e-07	171
developing anatomical structure	3.91e-07	581
ecto-epithelium	5.08e-07	104
brain	6.69e-07	68
future brain	6.69e-07	68
nervous system	7.12e-07	89

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324599364023192

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.