Coexpression cluster:C461

Full id: C461_oral_chorionic_squamous_amniotic_epidermoid_gall_bronchogenic

Phase1 CAGE Peaks

Hg19::chr10:128111291..128111299,-	p@chr10:128111291..128111299 -
Hg19::chr12:4116249..4116260,+	p@chr12:4116249..4116260 +
Hg19::chr12:4121031..4121079,+	p@chr12:4121031..4121079 +
Hg19::chr12:4136898..4136917,+	p@chr12:4136898..4136917 +
Hg19::chr12:4136920..4136943,+	p@chr12:4136920..4136943 +
Hg19::chr12:4140802..4140815,+	p@chr12:4140802..4140815 +
Hg19::chr13:114487620..114487623,-	p@chr13:114487620..114487623 -
Hg19::chr13:45390377..45390382,+	p@chr13:45390377..45390382 +
Hg19::chr14:81036045..81036050,-	p@chr14:81036045..81036050 -
Hg19::chr16:50451403..50451407,-	p@chr16:50451403..50451407 -
Hg19::chr20:60736437..60736455,-	p@chr20:60736437..60736455 -
Hg19::chr2:150999864..150999872,+	p@chr2:150999864..150999872 +
Hg19::chr3:52705394..52705398,+	p@chr3:52705394..52705398 +
Hg19::chr3:87039544..87039558,-	p@chr3:87039544..87039558 -
Hg19::chr3:87039601..87039605,-	p@chr3:87039601..87039605 -
Hg19::chr3:87039621..87039638,-	p@chr3:87039621..87039638 -
Hg19::chr3:87039662..87039723,-	p@chr3:87039662..87039723 -
Hg19::chr6:170533335..170533355,+	p@chr6:170533335..170533355 +
Hg19::chr7:106415430..106415437,+	p2@ENST00000490162
Hg19::chr7:106415457..106415472,+	p1@ENST00000490162
Hg19::chrX:29678307..29678312,+	p@chrX:29678307..29678312 +

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
bladder cell	3.30e-40	1
lower urinary tract cell	3.30e-40	1
epithelial cell of cervix	3.81e-21	2

Uber Anatomy

Ontology term	p-value	n
mammalian vulva	1.48e-40	1
external female genitalia	1.48e-40	1
urinary bladder urothelium	3.30e-40	1
wall of urinary bladder	3.30e-40	1
mucosa of urinary bladder	3.30e-40	1
uterine epithelium	3.81e-21	2
cervix epithelium	3.81e-21	2
urinary bladder	6.96e-21	2
lower urinary tract	6.96e-21	2
tongue	1.22e-14	3
gustatory system	1.22e-14	3
future tongue	1.22e-14	3
mucosa of oral region	2.53e-11	4
respiratory system mucosa	2.53e-11	4
urothelium	3.49e-09	5
mucosa	5.93e-09	20
uterine cervix	5.92e-08	6
neck of organ	5.92e-08	6
bile duct	6.78e-08	6
digestive system duct	6.78e-08	6
transitional epithelium	7.25e-08	6

Disease

Ontology term	p-value	n
squamous cell carcinoma	2.90e-26	14
carcinoma	5.66e-10	106
cervical cancer	2.74e-09	5
cell type cancer	1.55e-07	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	8	2.58054922903741	0.00755024888341394	0.0311220919262292
FOS#2353	7	2.99931843629814	0.00591679194613282	0.0265394190887376
JUN#3725	6	3.57509405495324	0.00493527413854895	0.0230619729644704
JUND#3727	11	3.66387158859911	4.44264141518177e-05	0.000787483073252153
SIRT6#51548	2	14.6322289514309	0.00818865229087286	0.0323308126646934
SMARCA4#6597	2	14.9300860293227	0.0078779247423581	0.03234383922349

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.