Coexpression cluster:C2898

Full id: C2898_oral_giant_large_epidermoid_squamous_embryonic_renal

Phase1 CAGE Peaks

Hg19::chr7:55053219..55053226,+	p@chr7:55053219..55053226 +
Hg19::chr7:55053266..55053282,+	p@chr7:55053266..55053282 +
Hg19::chr7:55053327..55053342,+	p@chr7:55053327..55053342 +
Hg19::chr7:55053540..55053550,+	p@chr7:55053540..55053550 +

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	4.28e-09	253
bladder cell	4.90e-07	1
lower urinary tract cell	4.90e-07	1

Uber Anatomy

Ontology term	p-value	n
viscus	1.12e-11	18
pancreas	4.68e-10	10
mammalian vulva	7.50e-08	1
external female genitalia	7.50e-08	1
mucosa of oral region	2.01e-07	4
respiratory system mucosa	2.01e-07	4
body cavity	2.73e-07	46
urinary bladder urothelium	4.90e-07	1
wall of urinary bladder	4.90e-07	1
mucosa of urinary bladder	4.90e-07	1
body cavity or lining	8.95e-07	49

Disease

Ontology term	p-value	n
squamous cell carcinoma	1.27e-27	14
carcinoma	4.24e-21	106
cell type cancer	3.80e-16	143
disease of cellular proliferation	5.70e-12	239
cancer	3.53e-11	235
lung large cell carcinoma	2.33e-09	3
organ system benign neoplasm	1.25e-07	1
skin benign neoplasm	1.25e-07	1
integumentary system benign neoplasm	1.25e-07	1
dermis tumor	1.25e-07	1
cutaneous fibrous histiocytoma	1.25e-07	1
cystadenocarcinoma	1.72e-07	1
mucinous cystadenocarcinoma	1.72e-07	1
disease of anatomical entity	6.19e-07	39

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
CEBPB#1051	4	7.97114762582482	0.000247638578809083	0.00268707797737577
EP300#2033	4	6.7739417262232	0.000474845982144264	0.0043544156228962
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00195489570209549
FOSL2#2355	4	16.9302006045617	1.2165416097647e-05	0.000304394799190742
FOXA1#3169	4	11.0814197493855	6.62943068949433e-05	0.00107361003532346
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000724693571028395
JUN#3725	4	12.5128291923363	4.07770316866756e-05	0.000745181524466266
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00392641962419034
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00129967259574225
STAT3#6774	4	10.5194649971542	8.16377768286615e-05	0.00123531842570394
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0245070401222038
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114903240936102

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.