Coexpression cluster:C3110

Full id: C3110_spindle_mesodermal_bone_Preadipocyte_basal_Sertoli_mesenchymal

Phase1 CAGE Peaks

Hg19::chr11:12399071..12399185,+	p1@PARVA
Hg19::chr12:65672443..65672553,+	p1@MSRB3
Hg19::chr1:25071930..25071944,+	p1@CLIC4

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:0000318	protein-methionine-R-oxide reductase activity	0.0116556290380794
GO:0042995	cell projection	0.0116556290380794
GO:0030091	protein repair	0.0116556290380794
GO:0008113	peptide-methionine-(S)-S-oxide reductase activity	0.0174813849255237
GO:0005902	microvillus	0.0218311521137686
GO:0016671	oxidoreductase activity, acting on sulfur group of donors, disulfide as acceptor	0.0218311521137686
GO:0030336	negative regulation of cell migration	0.0218311521137686
GO:0051271	negative regulation of cell motility	0.0218311521137686
GO:0040013	negative regulation of locomotion	0.0218311521137686
GO:0005739	mitochondrion	0.0218311521137686
GO:0016667	oxidoreductase activity, acting on sulfur group of donors	0.0218311521137686
GO:0005925	focal adhesion	0.0218311521137686
GO:0005924	cell-substrate adherens junction	0.0218311521137686
GO:0030027	lamellipodium	0.0218311521137686
GO:0005247	voltage-gated chloride channel activity	0.0218311521137686
GO:0030055	cell-matrix junction	0.0218311521137686
GO:0022844	voltage-gated anion channel activity	0.0220860378853777
GO:0005912	adherens junction	0.0238017783027782
GO:0005856	cytoskeleton	0.0238017783027782
GO:0043168	anion binding	0.0238017783027782
GO:0031404	chloride ion binding	0.0238017783027782
GO:0030334	regulation of cell migration	0.0238017783027782
GO:0051270	regulation of cell motility	0.0244942442579686
GO:0031252	leading edge	0.0244942442579686
GO:0040012	regulation of locomotion	0.0244942442579686
GO:0040011	locomotion	0.0244942442579686
GO:0005254	chloride channel activity	0.026161140102132
GO:0016323	basolateral plasma membrane	0.026161140102132
GO:0006821	chloride transport	0.026161140102132
GO:0005253	anion channel activity	0.0290568016757411
GO:0005737	cytoplasm	0.0341057389528163

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
non-terminally differentiated cell	1.78e-35	180
fibroblast	8.30e-21	75
mesodermal cell	3.54e-20	119
muscle precursor cell	1.51e-16	57
myoblast	1.51e-16	57
multi-potent skeletal muscle stem cell	1.51e-16	57
muscle cell	1.79e-15	54
contractile cell	9.71e-15	59
smooth muscle cell	2.00e-13	42
smooth muscle myoblast	2.00e-13	42
electrically responsive cell	2.43e-12	60
electrically active cell	2.43e-12	60
vascular associated smooth muscle cell	5.86e-12	32
embryonic cell	5.17e-11	248
fat cell	5.85e-09	15
skin fibroblast	6.87e-09	23

Uber Anatomy

Ontology term	p-value	n
splanchnic layer of lateral plate mesoderm	6.19e-22	84
vasculature	2.24e-20	79
vascular system	2.24e-20	79
somite	5.19e-20	83
paraxial mesoderm	5.19e-20	83
presomitic mesoderm	5.19e-20	83
presumptive segmental plate	5.19e-20	83
trunk paraxial mesoderm	5.19e-20	83
presumptive paraxial mesoderm	5.19e-20	83
organism subdivision	5.78e-18	365
vessel	6.45e-18	69
trunk mesenchyme	8.45e-18	143
multi-cellular organism	9.50e-18	659
blood vessel	1.11e-17	60
epithelial tube open at both ends	1.11e-17	60
blood vasculature	1.11e-17	60
vascular cord	1.11e-17	60
dermomyotome	2.03e-17	70
circulatory system	5.60e-17	113
trunk	9.45e-17	216
muscle tissue	1.05e-16	63
musculature	1.05e-16	63
musculature of body	1.05e-16	63
skeletal muscle tissue	2.71e-16	61
striated muscle tissue	2.71e-16	61
myotome	2.71e-16	61
epithelial tube	3.03e-16	118
cardiovascular system	4.17e-16	110
multilaminar epithelium	6.12e-16	82
anatomical system	2.90e-14	625
multi-tissue structure	3.06e-14	347
anatomical group	5.52e-14	626
artery	8.17e-14	42
arterial blood vessel	8.17e-14	42
arterial system	8.17e-14	42
unilaminar epithelium	1.02e-13	138
cell layer	3.80e-13	312
anatomical cluster	7.41e-13	286
epithelium	8.65e-13	309
mesenchyme	1.28e-12	238
entire embryonic mesenchyme	1.28e-12	238
systemic artery	1.44e-11	33
systemic arterial system	1.44e-11	33
anatomical conduit	1.02e-10	241
primary circulatory organ	3.05e-10	27
surface structure	4.92e-10	95
heart	2.26e-09	24
primitive heart tube	2.26e-09	24
primary heart field	2.26e-09	24
anterior lateral plate mesoderm	2.26e-09	24
heart tube	2.26e-09	24
heart primordium	2.26e-09	24
cardiac mesoderm	2.26e-09	24
cardiogenic plate	2.26e-09	24
heart rudiment	2.26e-09	24
mesoderm	2.12e-08	448
mesoderm-derived structure	2.12e-08	448
presumptive mesoderm	2.12e-08	448
integument	2.57e-08	45
integumental system	2.57e-08	45
aorta	4.15e-08	21
aortic system	4.15e-08	21
embryonic structure	7.58e-08	605
developing anatomical structure	7.58e-08	605
tube	8.80e-08	194
germ layer	1.31e-07	604
embryonic tissue	1.31e-07	604
presumptive structure	1.31e-07	604
epiblast (generic)	1.31e-07	604
embryo	1.68e-07	612
skin of body	3.91e-07	40
compound organ	9.59e-07	69

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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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.