Coexpression cluster:C3685

Full id: C3685_Fibroblast_Pericytes_Mesenchymal_Meningeal_Trabecular_Adipocyte_Saos2

Phase1 CAGE Peaks

Hg19::chr17:75315534..75315612,+	p4@SEPT9
Hg19::chr17:75315994..75316022,+	p7@SEPT9
Hg19::chr17:75316024..75316071,+	p16@SEPT9

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	2.70e-22	76
multi fate stem cell	1.40e-19	427
somatic stem cell	2.56e-18	433
contractile cell	3.74e-18	59
muscle precursor cell	1.75e-17	58
myoblast	1.75e-17	58
multi-potent skeletal muscle stem cell	1.75e-17	58
muscle cell	9.77e-17	55
non-terminally differentiated cell	1.03e-16	106
stem cell	3.34e-16	441
smooth muscle cell	1.37e-14	43
smooth muscle myoblast	1.37e-14	43
electrically responsive cell	3.54e-12	61
electrically active cell	3.54e-12	61
vascular associated smooth muscle cell	4.67e-12	32
somatic cell	2.33e-11	588
connective tissue cell	1.11e-10	361
skin fibroblast	2.33e-10	23
motile cell	2.43e-09	386
mesenchymal cell	2.60e-09	354
mesodermal cell	6.46e-07	121

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	1.22e-21	78
dense mesenchyme tissue	9.02e-21	73
somite	9.61e-21	71
presomitic mesoderm	9.61e-21	71
presumptive segmental plate	9.61e-21	71
dermomyotome	9.61e-21	71
trunk paraxial mesoderm	9.61e-21	71
paraxial mesoderm	1.62e-20	72
presumptive paraxial mesoderm	1.62e-20	72
skeletal muscle tissue	5.61e-17	62
striated muscle tissue	5.61e-17	62
myotome	5.61e-17	62
muscle tissue	7.17e-17	64
musculature	7.17e-17	64
musculature of body	7.17e-17	64
multilaminar epithelium	3.91e-16	83
trunk mesenchyme	2.04e-13	122
mesenchyme	3.26e-12	160
entire embryonic mesenchyme	3.26e-12	160
musculoskeletal system	7.78e-12	167
connective tissue	9.64e-12	371
mesoderm	1.00e-10	315
mesoderm-derived structure	1.00e-10	315
presumptive mesoderm	1.00e-10	315
integument	1.19e-09	46
integumental system	1.19e-09	46
skin of body	6.27e-09	41
splanchnic layer of lateral plate mesoderm	3.68e-08	83
tissue	1.92e-07	773
surface structure	3.07e-07	99
artery	8.82e-07	42
arterial blood vessel	8.82e-07	42
arterial system	8.82e-07	42

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
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321832516779798
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.00062756399572275
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.0043349133084072
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719794030107325
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00484229551738379
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00613193640689185
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00615328641530908

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.