Coexpression cluster:C397

Full id: C397_mesenchymal_Myoblast_rhabdomyosarcoma_Hepatic_Melanocyte_astrocytoma_Skeletal

Phase1 CAGE Peaks

Hg19::chr10:124611862..124611895,-	p@chr10:124611862..124611895 -
Hg19::chr11:16916978..16916996,-	p@chr11:16916978..16916996 -
Hg19::chr11:19619705..19619737,+	p@chr11:19619705..19619737 +
Hg19::chr11:47470490..47470498,-	p1@AB527888
Hg19::chr11:47470591..47470604,-	p4@RAPSN
Hg19::chr12:47414211..47414229,-	p@chr12:47414211..47414229 -
Hg19::chr12:81110684..81110700,+	p1@MYF5
Hg19::chr12:81112790..81112800,+	p@chr12:81112790..81112800 +
Hg19::chr12:81112806..81112813,+	p@chr12:81112806..81112813 +
Hg19::chr12:81112863..81112872,+	p@chr12:81112863..81112872 +
Hg19::chr13:66999851..66999857,-	p@chr13:66999851..66999857 -
Hg19::chr17:47572647..47572662,+	p1@NGFR
Hg19::chr17:47587813..47587828,+	p@chr17:47587813..47587828 +
Hg19::chr17:47589320..47589331,+	p@chr17:47589320..47589331 +
Hg19::chr17:55365619..55365632,+	p@chr17:55365619..55365632 +
Hg19::chr17:55365700..55365722,+	p@chr17:55365700..55365722 +
Hg19::chr18:37550533..37550548,+	p@chr18:37550533..37550548 +
Hg19::chr2:45419385..45419401,-	p1@ENST00000427020
Hg19::chr2:47452905..47452914,+	p1@ENST00000444361
Hg19::chr4:109810994..109811004,-	p@chr4:109810994..109811004 -
Hg19::chr4:12642027..12642049,-	p2@ENST00000509155
Hg19::chr4:3465027..3465050,+	p1@DOK7
Hg19::chr5:1278894..1278897,-	p@chr5:1278894..1278897 -
Hg19::chr6:39787581..39787589,-	p@chr6:39787581..39787589 -
Hg19::chr7:98258032..98258045,+	p@chr7:98258032..98258045 +
Hg19::chr7:98258764..98258767,+	p@chr7:98258764..98258767 +

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0042488	positive regulation of odontogenesis of dentine-containing teeth	0.0049452490286118
GO:0048635	negative regulation of muscle development	0.0049452490286118
GO:0005030	neurotrophin receptor activity	0.0049452490286118
GO:0042482	positive regulation of odontogenesis	0.0049452490286118
GO:0007517	muscle development	0.00510368093955047
GO:0042481	regulation of odontogenesis	0.00565146362241504
GO:0048406	nerve growth factor binding	0.00565146362241504
GO:0042487	regulation of odontogenesis of dentine-containing teeth	0.00659308309224691
GO:0048634	regulation of muscle development	0.00659308309224691
GO:0021675	nerve development	0.00719213669429478
GO:0016048	detection of temperature stimulus	0.00719213669429478
GO:0043121	neurotrophin binding	0.0082406260734007
GO:0009887	organ morphogenesis	0.0084756982616971
GO:0043588	skin development	0.0084756982616971
GO:0030054	cell junction	0.010513208766455
GO:0048704	embryonic skeletal morphogenesis	0.0109850757914487
GO:0044459	plasma membrane part	0.0109850757914487
GO:0005035	death receptor activity	0.0109850757914487
GO:0048706	embryonic skeletal development	0.01285083614425
GO:0001952	regulation of cell-matrix adhesion	0.01285083614425
GO:0048705	skeletal morphogenesis	0.01412055080712
GO:0001756	somitogenesis	0.016172306480016
GO:0042475	odontogenesis of dentine-containing teeth	0.016327839596185
GO:0005158	insulin receptor binding	0.0189383805889956
GO:0042476	odontogenesis	0.0197582979184786
GO:0035282	segmentation	0.0197582979184786
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0197582979184786
GO:0009266	response to temperature stimulus	0.0204621440366349
GO:0005886	plasma membrane	0.0278112583159776
GO:0032501	multicellular organismal process	0.0278112583159776
GO:0009582	detection of abiotic stimulus	0.0278112583159776
GO:0030198	extracellular matrix organization and biogenesis	0.0278112583159776
GO:0009653	anatomical structure morphogenesis	0.0278112583159776
GO:0009581	detection of external stimulus	0.0290268206664025
GO:0009952	anterior/posterior pattern formation	0.0298661743075181
GO:0048513	organ development	0.0298661743075181
GO:0007411	axon guidance	0.0298661743075181
GO:0030155	regulation of cell adhesion	0.0338838289822843
GO:0007519	skeletal muscle development	0.0338838289822843
GO:0051093	negative regulation of developmental process	0.0379508218150131
GO:0051606	detection of stimulus	0.0384626346065112
GO:0043062	extracellular structure organization and biogenesis	0.0389706572423428
GO:0003002	regionalization	0.0389706572423428
GO:0014706	striated muscle development	0.0389706572423428
GO:0019838	growth factor binding	0.0389706572423428
GO:0048598	embryonic morphogenesis	0.0389876890311985
GO:0009792	embryonic development ending in birth or egg hatching	0.0389876890311985
GO:0043009	chordate embryonic development	0.0389876890311985
GO:0007160	cell-matrix adhesion	0.0397702834627644
GO:0032403	protein complex binding	0.0397702834627644
GO:0031589	cell-substrate adhesion	0.0397702834627644
GO:0048731	system development	0.0405695329663668
GO:0007409	axonogenesis	0.0423359748223512
GO:0048667	neuron morphogenesis during differentiation	0.0429322859394706
GO:0048812	neurite morphogenesis	0.0429322859394706
GO:0007389	pattern specification process	0.0434856550912361
GO:0000904	cellular morphogenesis during differentiation	0.0434856550912361
GO:0031175	neurite development	0.0436226376512858
GO:0008544	epidermis development	0.0436226376512858
GO:0048869	cellular developmental process	0.0436226376512858
GO:0030154	cell differentiation	0.0436226376512858
GO:0007398	ectoderm development	0.0462836611723014
GO:0045211	postsynaptic membrane	0.0464787764579897
GO:0048666	neuron development	0.0472774191380379
GO:0044456	synapse part	0.0483627566764478
GO:0048856	anatomical structure development	0.0483627566764478
GO:0009628	response to abiotic stimulus	0.0483627566764478

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>

---

Cell Type

Ontology term	p-value	n
skeletal muscle myoblast	1.69e-45	4
cell of skeletal muscle	2.78e-35	9
muscle precursor cell	1.48e-16	58
myoblast	1.48e-16	58
multi-potent skeletal muscle stem cell	1.48e-16	58
non-terminally differentiated cell	8.87e-09	106
skeletal muscle satellite cell	6.78e-08	3
mesodermal cell	8.44e-08	121

Uber Anatomy

Ontology term	p-value	n
skeletal muscle tissue	4.30e-20	62
striated muscle tissue	4.30e-20	62
myotome	4.30e-20	62
muscle tissue	1.86e-19	64
musculature	1.86e-19	64
musculature of body	1.86e-19	64
somite	1.63e-17	71
presomitic mesoderm	1.63e-17	71
presumptive segmental plate	1.63e-17	71
dermomyotome	1.63e-17	71
trunk paraxial mesoderm	1.63e-17	71
paraxial mesoderm	2.88e-17	72
presumptive paraxial mesoderm	2.88e-17	72
dense mesenchyme tissue	5.01e-17	73
epithelial vesicle	6.46e-16	78
multilaminar epithelium	6.12e-15	83
trunk mesenchyme	4.78e-10	122
unilaminar epithelium	3.32e-08	148
mesenchyme	1.49e-07	160
entire embryonic mesenchyme	1.49e-07	160
musculoskeletal system	3.60e-07	167

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

---

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

---

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

---

This analysis result is provided for C0 - C305 clusters.