Coexpression cluster:C3035

Full id: C3035_prostate_signet_epidermoid_Keratinocyte_giant_Mammary_mucinous

Phase1 CAGE Peaks

Hg19::chr10:6779293..6779312,+	p4@ENST00000417112
Hg19::chr10:6779326..6779351,+	p3@ENST00000417112
Hg19::chr10:6779369..6779400,+	p1@ENST00000417112

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	4.07e-39	253
endo-epithelial cell	5.42e-13	42
kidney tubule cell	8.62e-10	10
nephron tubule epithelial cell	8.62e-10	10
squamous epithelial cell	1.47e-08	63
epithelial cell of alimentary canal	3.04e-08	20
respiratory epithelial cell	4.42e-08	13
epithelial cell of nephron	4.53e-08	15
kidney cell	6.95e-08	17
kidney epithelial cell	6.95e-08	17
endodermal cell	8.96e-08	58
extraembryonic cell	4.27e-07	19

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.60e-17	160
endoderm	1.60e-17	160
presumptive endoderm	1.60e-17	160
organ part	7.48e-16	218
respiratory system	3.71e-14	74
respiratory tract	2.55e-12	54
urinary system structure	2.98e-12	47
renal system	8.65e-12	48
multi-tissue structure	2.37e-11	342
digestive system	2.60e-11	145
digestive tract	2.60e-11	145
primitive gut	2.60e-11	145
segment of respiratory tract	3.52e-11	47
respiratory primordium	1.51e-10	38
endoderm of foregut	1.51e-10	38
larynx	5.47e-10	9
nephron tubule epithelium	8.62e-10	10
extraembryonic membrane	3.20e-09	14
membranous layer	3.20e-09	14
organ	3.28e-09	503
excretory tube	1.20e-08	16
kidney epithelium	1.20e-08	16
organ segment	2.10e-08	98
organism subdivision	2.13e-08	264
nephron epithelium	4.53e-08	15
renal tubule	4.53e-08	15
nephron tubule	4.53e-08	15
nephron	4.53e-08	15
uriniferous tubule	4.53e-08	15
nephrogenic mesenchyme	4.53e-08	15
subdivision of digestive tract	1.46e-07	118
endo-epithelium	3.77e-07	82
upper respiratory tract	5.18e-07	19
foregut	6.06e-07	87

Disease

Ontology term	p-value	n
carcinoma	3.58e-15	106
squamous cell carcinoma	5.61e-14	14
cell type cancer	1.63e-08	143

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
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166791333242486
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00432637197318118
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00443009733261023
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156113252375403
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00307791343400666
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00482859016859612
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154388242812752
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00641388419256431

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.