Coexpression cluster:C725

Full id: C725_Mast_cord_mycosis_mesenchymal_Endothelial_hepatic_Mesenchymal

Phase1 CAGE Peaks

Hg19::chr10:64576035..64576046,-	p2@EGR2
Hg19::chr12:93966545..93966557,+	p25@SOCS2
Hg19::chr16:72128270..72128282,-	p5@TXNL4B
Hg19::chr1:173174598..173174624,-	p4@TNFSF4
Hg19::chr1:173174630..173174644,-	p7@TNFSF4
Hg19::chr1:173174664..173174677,-	p6@TNFSF4
Hg19::chr1:173174681..173174702,-	p5@TNFSF4
Hg19::chr1:173174706..173174733,-	p3@TNFSF4
Hg19::chr1:173174759..173174799,-	p2@TNFSF4
Hg19::chr1:173176462..173176477,-	p1@TNFSF4
Hg19::chr2:191185566..191185602,-	p@chr2:191185566..191185602 -

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

---

GO ID	GO name	FDR corrected p-value
GO:0005148	prolactin receptor binding	0.012546365820773
GO:0008269	JAK pathway signal transduction adaptor activity	0.012546365820773
GO:0008268	receptor signaling protein tyrosine kinase signaling protein activity	0.012546365820773
GO:0032868	response to insulin stimulus	0.012546365820773
GO:0005131	growth hormone receptor binding	0.012546365820773
GO:0005125	cytokine activity	0.012546365820773
GO:0007638	mechanosensory behavior	0.0154378789766626
GO:0048168	regulation of neuronal synaptic plasticity	0.0202595321431702
GO:0005159	insulin-like growth factor receptor binding	0.0220084121224001
GO:0048167	regulation of synaptic plasticity	0.0249249009211236
GO:0009612	response to mechanical stimulus	0.0249249009211236
GO:0007267	cell-cell signaling	0.0249249009211236
GO:0050803	regulation of synapse structure and activity	0.0249249009211236
GO:0043434	response to peptide hormone stimulus	0.0282827880332297
GO:0007422	peripheral nervous system development	0.0287944772484493
GO:0065008	regulation of biological quality	0.0388055118302518
GO:0005164	tumor necrosis factor receptor binding	0.0388055118302518
GO:0007259	JAK-STAT cascade	0.0388055118302518
GO:0032813	tumor necrosis factor receptor superfamily binding	0.0388055118302518
GO:0007611	learning and/or memory	0.03905990040876
GO:0005102	receptor binding	0.03905990040876
GO:0005070	SH3/SH2 adaptor activity	0.0400389898549058
GO:0005126	hematopoietin/interferon-class (D200-domain) cytokine receptor binding	0.0449198938933818
GO:0060090	molecular adaptor activity	0.0449198938933818

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>disease_data<br>

---

Cell Type

Ontology term	p-value	n
circulating cell	1.50e-10	6
endothelial cell of artery	9.27e-07	9

Uber Anatomy

Ontology term	p-value	n
blood	8.34e-22	15
haemolymphatic fluid	8.34e-22	15
organism substance	8.34e-22	15
cardiovascular system	4.96e-15	109
circulatory system	2.56e-14	112
lateral plate mesoderm	9.05e-07	203
endothelial tube	9.27e-07	9
arterial system endothelium	9.27e-07	9
endothelium of artery	9.27e-07	9

Disease

Ontology term	p-value	n
ovarian cancer	2.36e-09	14

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
CEBPB#1051	6	4.34789870499535	0.00102243427262561	0.00724584467657907
EP300#2033	6	3.69487730521265	0.00244128806655223	0.0137462629061165
FOXA1#3169	7	7.05181256779074	1.15697264990643e-05	0.000294571103324177
FOXA2#3170	6	13.4347984105447	1.73076139279195e-06	6.52324031403099e-05
HDAC2#3066	6	7.31761103815978	5.69712326977083e-05	0.000950330389988174
HEY1#23462	7	2.57097975470363	0.00712682984021317	0.0296340718112045
HNF4A#3172	6	12.6176129252475	2.49318000901648e-06	8.78196380983718e-05
HNF4G#3174	6	15.6836850144255	7.0138286269284e-07	3.1438508496471e-05
SP1#6667	6	3.10820802444049	0.00601132120248979	0.0269483785494626
USF1#7391	7	4.0482268127687	0.000433910736700334	0.0040508807929066

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.