Coexpression cluster:C425

Full id: C425_iPS_HES3GFP_H9_teratocarcinoma_testicular_hepatocellular_Wilms

Phase1 CAGE Peaks

Hg19::chr13:48611649..48611658,+	p4@NUDT15
Hg19::chr13:48611665..48611708,+	p3@NUDT15
Hg19::chr13:93868779..93868791,+	p@chr13:93868779..93868791 +
Hg19::chr15:74643092..74643103,+	p@chr15:74643092..74643103 +
Hg19::chr1:178235815..178235824,-	p@chr1:178235815..178235824 -
Hg19::chr1:196539193..196539198,-	p@chr1:196539193..196539198 -
Hg19::chr1:226411361..226411366,+	p1@MIXL1
Hg19::chr2:82240962..82240967,-	p@chr2:82240962..82240967 -
Hg19::chr3:162430587..162430591,+	p@chr3:162430587..162430591 +
Hg19::chr3:54673186..54673191,-	p@chr3:54673186..54673191 -
Hg19::chr4:111540901..111540905,+	p@chr4:111540901..111540905 +
Hg19::chr4:88852761..88852767,+	p@chr4:88852761..88852767 +
Hg19::chr4:88853035..88853041,+	p@chr4:88853035..88853041 +
Hg19::chr6:160649974..160649978,+	p@chr6:160649974..160649978 +
Hg19::chr7:125557914..125557920,+	p1@ENST00000411856
Hg19::chr7:125564060..125564062,+	p@chr7:125564060..125564062 +
Hg19::chr7:125566765..125566770,+	p@chr7:125566765..125566770 +
Hg19::chr8:21899898..21899901,+	p1@FGF17
Hg19::chr8:81213028..81213032,+	p1@ENST00000472088
Hg19::chr9:14722725..14722738,-	p1@CER1
Hg19::chr9:5098356..5098369,+	p1@ENST00000431069
Hg19::chr9:6020363..6020368,+	p@chr9:6020363..6020368 +
Hg19::chrY:15863548..15863573,+	p1@KALP
Hg19::chrY:21589521..21589522,+	p@chrY:21589521..21589522 +

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:0007167	enzyme linked receptor protein signaling pathway	0.0152323781567815
GO:0042074	cell migration involved in gastrulation	0.0152323781567815
GO:0042127	regulation of cell proliferation	0.0152323781567815
GO:0007275	multicellular organismal development	0.0152323781567815
GO:0030514	negative regulation of BMP signaling pathway	0.0152323781567815
GO:0030510	regulation of BMP signaling pathway	0.0152323781567815
GO:0009948	anterior/posterior axis specification	0.0152323781567815
GO:0005615	extracellular space	0.0152323781567815
GO:0008543	fibroblast growth factor receptor signaling pathway	0.0165573613962069
GO:0030509	BMP signaling pathway	0.0165573613962069
GO:0009798	axis specification	0.0165573613962069
GO:0008283	cell proliferation	0.0194524233922925
GO:0007369	gastrulation	0.0194524233922925
GO:0032502	developmental process	0.0217456776068593
GO:0044421	extracellular region part	0.0237867142250612
GO:0032501	multicellular organismal process	0.0271211765237296
GO:0005102	receptor binding	0.0271211765237296
GO:0009952	anterior/posterior pattern formation	0.0308668156604865
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.0403700043055772
GO:0003002	regionalization	0.0438810523001729
GO:0009968	negative regulation of signal transduction	0.0499201251580985

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><br>disease_data<br>

---

Cell Type

Ontology term	p-value	n
epithelial cell	9.06e-07	254

Disease

Ontology term	p-value	n
carcinoma	3.25e-13	106
cell type cancer	7.36e-12	143
cancer	4.47e-09	235
disease of cellular proliferation	3.01e-08	239

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
NANOG#79923	6	7.31119462025316	0.000126097651829232	0.00167978477798382

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.