Coexpression cluster:C3224

Full id: C3224_Fibroblast_Dendritic_basal_chronic_leiomyoma_Renal_Aortic

Phase1 CAGE Peaks

Hg19::chr12:105724535..105724548,+	p3@C12orf75
Hg19::chr12:105724590..105724612,+	p4@C12orf75
Hg19::chr12:105724613..105724666,+	p2@C12orf75

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

---

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>

---

Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	1.16e-15	180
fibroblast	7.67e-15	75
skin fibroblast	2.17e-11	23
somatic cell	6.17e-11	591
native cell	8.86e-11	722
smooth muscle cell	9.68e-10	42
smooth muscle myoblast	9.68e-10	42
vascular associated smooth muscle cell	1.27e-08	32
muscle precursor cell	6.24e-08	57
myoblast	6.24e-08	57
multi-potent skeletal muscle stem cell	6.24e-08	57
contractile cell	8.57e-08	59
multi fate stem cell	1.07e-07	430
somatic stem cell	2.14e-07	436
muscle cell	2.46e-07	54
animal cell	3.16e-07	679
eukaryotic cell	3.16e-07	679
T cell	3.47e-07	25
pro-T cell	3.47e-07	25
lymphocyte	4.67e-07	53
common lymphoid progenitor	4.67e-07	53
lymphoid lineage restricted progenitor cell	5.52e-07	52
stem cell	8.16e-07	444

Uber Anatomy

Ontology term	p-value	n
somite	1.19e-12	83
paraxial mesoderm	1.19e-12	83
presomitic mesoderm	1.19e-12	83
presumptive segmental plate	1.19e-12	83
trunk paraxial mesoderm	1.19e-12	83
presumptive paraxial mesoderm	1.19e-12	83
trunk mesenchyme	3.57e-10	143
dermomyotome	5.77e-10	70
multilaminar epithelium	2.69e-09	82
integument	3.99e-08	45
integumental system	3.99e-08	45
surface structure	4.85e-08	95
skin of body	9.43e-08	40
skeletal muscle tissue	2.70e-07	61
striated muscle tissue	2.70e-07	61
myotome	2.70e-07	61
artery	6.88e-07	42
arterial blood vessel	6.88e-07	42
arterial system	6.88e-07	42
muscle tissue	8.93e-07	63
musculature	8.93e-07	63
musculature of body	8.93e-07	63

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00435907362259917
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00895163002010695
MAX#4149	3	6.45255550900712	0.00372191383426551	0.018590700604374
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268733044425877
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172425698890611
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275655181495951
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245608799601426
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247514948684
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00613411303231012

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.