Coexpression cluster:C737

Full id: C737_rhabdomyosarcoma_skeletal_mesenchymal_Skeletal_Pericytes_tongue_diaphragm

Phase1 CAGE Peaks

Hg19::chr11:17741084..17741094,+	p3@MYOD1
Hg19::chr11:47470650..47470653,-	p5@RAPSN
Hg19::chr11:47470657..47470674,-	p2@RAPSN
Hg19::chr11:47470682..47470693,-	p1@RAPSN
Hg19::chr11:47470703..47470715,-	p3@RAPSN
Hg19::chr12:81102260..81102302,+	p@chr12:81102260..81102302 +
Hg19::chr16:31225409..31225428,+	p3@TRIM72
Hg19::chr16:31225432..31225453,+	p2@TRIM72
Hg19::chr17:7348374..7348435,+	p1@CHRNB1
Hg19::chr19:49223185..49223197,-	p6@MAMSTR
Hg19::chr2:233390890..233390903,+	p3@CHRND

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:0045211	postsynaptic membrane	6.79938374953971e-05
GO:0044456	synapse part	6.79938374953971e-05
GO:0005892	nicotinic acetylcholine-gated receptor-channel complex	6.79938374953971e-05
GO:0015464	acetylcholine receptor activity	0.000110207136155915
GO:0042166	acetylcholine binding	0.000110207136155915
GO:0004889	nicotinic acetylcholine-activated cation-selective channel activity	0.000110207136155915
GO:0042391	regulation of membrane potential	0.000173536456370901
GO:0043176	amine binding	0.000308677077309302
GO:0030054	cell junction	0.000329255168161089
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.000666112422770907
GO:0043235	receptor complex	0.00141713184631989
GO:0005230	extracellular ligand-gated ion channel activity	0.00184280447188266
GO:0030594	neurotransmitter receptor activity	0.00193503853896072
GO:0042165	neurotransmitter binding	0.00193503853896072
GO:0015276	ligand-gated ion channel activity	0.00194818366524397
GO:0022834	ligand-gated channel activity	0.00194818366524397
GO:0003012	muscle system process	0.00194818366524397
GO:0006936	muscle contraction	0.00194818366524397
GO:0048625	myoblast cell fate commitment	0.00328069494872328
GO:0007518	myoblast cell fate determination	0.00328069494872328
GO:0055082	cellular chemical homeostasis	0.00328069494872328
GO:0006873	cellular ion homeostasis	0.00328069494872328
GO:0050801	ion homeostasis	0.00397762027942711
GO:0007268	synaptic transmission	0.00439703107944435
GO:0032501	multicellular organismal process	0.00439703107944435
GO:0048878	chemical homeostasis	0.00449427535592236
GO:0003008	system process	0.00484422787117751
GO:0019226	transmission of nerve impulse	0.00497613463498123
GO:0019725	cellular homeostasis	0.00618997073618544
GO:0005515	protein binding	0.00658133782506141
GO:0005261	cation channel activity	0.00724649481992225
GO:0007271	synaptic transmission, cholinergic	0.00832867358554158
GO:0042592	homeostatic process	0.00886226726540242
GO:0046873	metal ion transmembrane transporter activity	0.00923617233921631
GO:0022836	gated channel activity	0.00923617233921631
GO:0044459	plasma membrane part	0.0114977939322784
GO:0007267	cell-cell signaling	0.0139263162510835
GO:0005216	ion channel activity	0.0142062424824373
GO:0022838	substrate specific channel activity	0.0142062424824373
GO:0045445	myoblast differentiation	0.0142062424824373
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0142062424824373
GO:0022803	passive transmembrane transporter activity	0.0142062424824373
GO:0015267	channel activity	0.0142062424824373
GO:0001709	cell fate determination	0.0146236309168168
GO:0043234	protein complex	0.0179716781370358
GO:0048741	skeletal muscle fiber development	0.0196191815942839
GO:0048747	muscle fiber development	0.0196191815942839
GO:0008324	cation transmembrane transporter activity	0.0196191815942839
GO:0042692	muscle cell differentiation	0.0208083176960963
GO:0065008	regulation of biological quality	0.0224398321940344
GO:0007519	skeletal muscle development	0.0290832469142844
GO:0045165	cell fate commitment	0.0302197586792451
GO:0005886	plasma membrane	0.0338623366681617
GO:0032991	macromolecular complex	0.0348690262537573
GO:0014706	striated muscle development	0.0348690262537573
GO:0050877	neurological system process	0.0348690262537573
GO:0015075	ion transmembrane transporter activity	0.0368473140920722
GO:0005887	integral to plasma membrane	0.0368473140920722
GO:0031226	intrinsic to plasma membrane	0.0370642587046981
GO:0006811	ion transport	0.037387762057121
GO:0022891	substrate-specific transmembrane transporter activity	0.0453015648225363

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
cell of skeletal muscle	3.13e-44	9
skeletal muscle myoblast	3.26e-21	4
skeletal muscle satellite cell	1.65e-15	3
muscle precursor cell	3.76e-14	58
myoblast	3.76e-14	58
multi-potent skeletal muscle stem cell	3.76e-14	58
contractile cell	6.47e-10	59
muscle cell	6.07e-09	55
electrically responsive cell	7.32e-08	61
electrically active cell	7.32e-08	61
smooth muscle cell of the brain vasculature	2.06e-07	3

Uber Anatomy

Ontology term	p-value	n
skeletal muscle tissue	9.28e-23	62
striated muscle tissue	9.28e-23	62
myotome	9.28e-23	62
muscle tissue	6.41e-22	64
musculature	6.41e-22	64
musculature of body	6.41e-22	64
somite	2.35e-19	71
presomitic mesoderm	2.35e-19	71
presumptive segmental plate	2.35e-19	71
dermomyotome	2.35e-19	71
trunk paraxial mesoderm	2.35e-19	71
paraxial mesoderm	4.98e-19	72
presumptive paraxial mesoderm	4.98e-19	72
dense mesenchyme tissue	1.03e-18	73
epithelial vesicle	2.98e-17	78
multilaminar epithelium	5.72e-16	83
trunk mesenchyme	2.55e-15	122
organism subdivision	5.05e-13	264
unilaminar epithelium	5.54e-13	148
muscle structure	1.31e-11	2
muscle organ	1.31e-11	2
throat	2.85e-11	2
open tracheal system trachea	9.16e-11	2
mesenchyme	1.60e-10	160
entire embryonic mesenchyme	1.60e-10	160
trunk	2.02e-10	199
chordate pharynx	4.00e-08	10
pharyngeal region of foregut	4.00e-08	10
tongue	6.57e-08	3
gustatory system	6.57e-08	3
future tongue	6.57e-08	3
multi-tissue structure	1.40e-07	342
pharynx	2.16e-07	11

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
USF1#7391	6	3.46990869665889	0.00339735017630123	0.0173351502375769

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.