Coexpression cluster:C4558

Full id: C4558_mature_heart_mesodermal_lung_skin_diaphragm_eye

Phase1 CAGE Peaks

Hg19::chr6:131291472..131291492,-	p2@EPB41L2
Hg19::chr6:131291507..131291537,-	p6@EPB41L2
Hg19::chr9:95298256..95298282,-	p1@ECM2

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:0008091	spectrin	0.0101237505259809
GO:0030866	cortical actin cytoskeleton organization and biogenesis	0.0101237505259809
GO:0030865	cortical cytoskeleton organization and biogenesis	0.0101237505259809
GO:0030864	cortical actin cytoskeleton	0.0101237505259809
GO:0030863	cortical cytoskeleton	0.012653011472308
GO:0005178	integrin binding	0.0162633670782013
GO:0044448	cell cortex part	0.0162633670782013
GO:0005938	cell cortex	0.0202331933385269
GO:0005200	structural constituent of cytoskeleton	0.0208036560891747
GO:0007160	cell-matrix adhesion	0.0208036560891747
GO:0032403	protein complex binding	0.0208036560891747
GO:0031589	cell-substrate adhesion	0.0208036560891747
GO:0019898	extrinsic to membrane	0.0208036560891747
GO:0030036	actin cytoskeleton organization and biogenesis	0.0437120020465577
GO:0030029	actin filament-based process	0.0437120020465577
GO:0015629	actin cytoskeleton	0.0466293410899719

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
fibroblast	1.07e-12	76
muscle precursor cell	5.29e-09	58
myoblast	5.29e-09	58
multi-potent skeletal muscle stem cell	5.29e-09	58
muscle cell	5.61e-08	55
contractile cell	1.67e-07	59
fat cell	2.75e-07	15

Uber Anatomy

Ontology term	p-value	n
adult organism	5.30e-31	114
structure with developmental contribution from neural crest	2.08e-15	132
neural tube	1.00e-13	56
neural rod	1.00e-13	56
future spinal cord	1.00e-13	56
neural keel	1.00e-13	56
multi-tissue structure	1.45e-13	342
regional part of nervous system	4.55e-12	53
regional part of brain	4.55e-12	53
regional part of forebrain	1.43e-11	41
forebrain	1.43e-11	41
anterior neural tube	1.43e-11	41
future forebrain	1.43e-11	41
muscle tissue	1.81e-11	64
musculature	1.81e-11	64
musculature of body	1.81e-11	64
neurectoderm	2.12e-11	86
neural plate	2.66e-11	82
presumptive neural plate	2.66e-11	82
skeletal muscle tissue	1.04e-10	62
striated muscle tissue	1.04e-10	62
myotome	1.04e-10	62
anatomical cluster	1.58e-10	373
anatomical conduit	1.61e-10	240
multi-cellular organism	2.14e-10	656
brain	2.47e-10	68
future brain	2.47e-10	68
tube	4.07e-10	192
tissue	5.71e-10	773
primary circulatory organ	5.81e-10	27
central nervous system	5.96e-10	81
cell layer	1.13e-09	309
heart	1.68e-09	24
primitive heart tube	1.68e-09	24
primary heart field	1.68e-09	24
anterior lateral plate mesoderm	1.68e-09	24
heart tube	1.68e-09	24
heart primordium	1.68e-09	24
cardiac mesoderm	1.68e-09	24
cardiogenic plate	1.68e-09	24
heart rudiment	1.68e-09	24
dense mesenchyme tissue	2.26e-09	73
epithelium	2.63e-09	306
paraxial mesoderm	2.73e-09	72
presumptive paraxial mesoderm	2.73e-09	72
telencephalon	3.91e-09	34
nervous system	4.34e-09	89
somite	6.05e-09	71
presomitic mesoderm	6.05e-09	71
presumptive segmental plate	6.05e-09	71
dermomyotome	6.05e-09	71
trunk paraxial mesoderm	6.05e-09	71
brain grey matter	6.23e-09	34
gray matter	6.23e-09	34
regional part of telencephalon	2.85e-08	32
cerebral hemisphere	4.31e-08	32
anatomical system	1.43e-07	624
organ system subdivision	1.61e-07	223
anatomical group	1.92e-07	625
regional part of cerebral cortex	2.85e-07	22
pre-chordal neural plate	4.70e-07	61
ecto-epithelium	4.90e-07	104
trunk mesenchyme	7.32e-07	122
mesenchyme	7.93e-07	160
entire embryonic mesenchyme	7.93e-07	160
multilaminar epithelium	8.68e-07	83
epithelial vesicle	9.00e-07	78

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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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.