Coexpression cluster:C2074

Full id: C2074_Mesenchymal_Osteoblast_Adipocyte_mature_Chondrocyte_Synoviocyte_Preadipocyte

Phase1 CAGE Peaks

Hg19::chr10:81892415..81892447,+	p2@PLAC9
Hg19::chr10:81892478..81892493,+	p1@PLAC9
Hg19::chr5:158527633..158527660,+	p1@ENST00000523301
Hg19::chr5:158527667..158527701,+	p1@ENST00000499583 p1@uc003lxm.1

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
fibroblast	1.12e-19	76
contractile cell	8.07e-16	59
muscle precursor cell	9.74e-16	58
myoblast	9.74e-16	58
multi-potent skeletal muscle stem cell	9.74e-16	58
muscle cell	4.21e-15	55
electrically responsive cell	2.58e-14	61
electrically active cell	2.58e-14	61
non-terminally differentiated cell	3.31e-13	106
fat cell	4.52e-12	15
smooth muscle cell	2.01e-11	43
smooth muscle myoblast	2.01e-11	43
vascular associated smooth muscle cell	1.23e-08	32
mesodermal cell	4.17e-08	121
preadipocyte	6.23e-08	12

Uber Anatomy

Ontology term	p-value	n
dense mesenchyme tissue	1.45e-20	73
somite	2.87e-20	71
presomitic mesoderm	2.87e-20	71
presumptive segmental plate	2.87e-20	71
dermomyotome	2.87e-20	71
trunk paraxial mesoderm	2.87e-20	71
paraxial mesoderm	3.31e-20	72
presumptive paraxial mesoderm	3.31e-20	72
muscle tissue	4.48e-18	64
musculature	4.48e-18	64
musculature of body	4.48e-18	64
skeletal muscle tissue	1.71e-17	62
striated muscle tissue	1.71e-17	62
myotome	1.71e-17	62
epithelial vesicle	2.14e-17	78
multilaminar epithelium	5.58e-16	83
splanchnic layer of lateral plate mesoderm	2.14e-14	83
multi-tissue structure	1.01e-13	342
structure with developmental contribution from neural crest	1.64e-12	132
trunk mesenchyme	5.70e-12	122
mesenchyme	2.38e-11	160
entire embryonic mesenchyme	2.38e-11	160
cell layer	4.62e-11	309
adult organism	4.70e-11	114
epithelium	1.42e-10	306
circulatory system	1.62e-10	112
primary circulatory organ	2.11e-10	27
multi-cellular organism	2.37e-10	656
vasculature	2.91e-10	78
vascular system	2.91e-10	78
cardiovascular system	7.98e-10	109
anatomical cluster	9.01e-10	373
organism subdivision	1.04e-09	264
adipose tissue	1.30e-09	14
heart	1.31e-09	24
primitive heart tube	1.31e-09	24
primary heart field	1.31e-09	24
anterior lateral plate mesoderm	1.31e-09	24
heart tube	1.31e-09	24
heart primordium	1.31e-09	24
cardiac mesoderm	1.31e-09	24
cardiogenic plate	1.31e-09	24
heart rudiment	1.31e-09	24
epithelial tube open at both ends	2.73e-09	59
blood vessel	2.73e-09	59
blood vasculature	2.73e-09	59
vascular cord	2.73e-09	59
unilaminar epithelium	3.71e-09	148
artery	4.55e-09	42
arterial blood vessel	4.55e-09	42
arterial system	4.55e-09	42
tissue	4.20e-08	773
vessel	5.48e-08	68
anatomical conduit	8.21e-08	240
systemic artery	8.89e-08	33
systemic arterial system	8.89e-08	33
surface structure	1.19e-07	99
trunk	8.37e-07	199
anatomical system	9.43e-07	624

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
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321109008508911

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.