Coexpression cluster:C3893

Full id: C3893_chorionic_testicular_squamous_clear_Esophageal_choriocarcinoma_Amniotic

Phase1 CAGE Peaks

Hg19::chr1:160990908..160990921,-	p4@F11R
Hg19::chr1:160990922..160990949,-	p1@F11R
Hg19::chr1:160990954..160990973,-	p3@F11R

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	9.01e-50	254
squamous epithelial cell	5.75e-15	62
endodermal cell	6.28e-14	59
endo-epithelial cell	1.66e-13	43
endothelial cell	1.40e-10	35
endothelial cell of vascular tree	6.70e-10	24
meso-epithelial cell	1.08e-09	44
lining cell	5.43e-09	57
barrier cell	5.43e-09	57
blood vessel endothelial cell	7.75e-08	18
embryonic blood vessel endothelial progenitor cell	7.75e-08	18

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	8.98e-13	169
endoderm	8.98e-13	169
presumptive endoderm	8.98e-13	169
subdivision of digestive tract	6.95e-11	129
endodermal part of digestive tract	6.95e-11	129
immaterial anatomical entity	4.96e-10	126
foregut	2.38e-09	98
endo-epithelium	3.85e-09	82
digestive system	3.88e-09	155
digestive tract	3.88e-09	155
primitive gut	3.88e-09	155
respiratory system	3.99e-09	72
mixed endoderm/mesoderm-derived structure	5.05e-09	130
anatomical space	3.02e-08	104
respiratory tract	3.64e-08	53
trunk region element	4.08e-08	107
endothelium	7.75e-08	18
blood vessel endothelium	7.75e-08	18
cardiovascular system endothelium	7.75e-08	18
respiratory primordium	3.67e-07	38
endoderm of foregut	3.67e-07	38
subdivision of trunk	6.02e-07	113
simple squamous epithelium	9.51e-07	22

Disease

Ontology term	p-value	n
carcinoma	2.13e-17	106
cell type cancer	8.11e-09	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
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660647510307249
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032552009455549
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322397157243563
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462531342010013
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00897966870337484
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128147734686223
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253614253928434
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186629997569068
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199793720733306
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.0024597080441292
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.001366981643696
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00484740591206848
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.02769391817119
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246649969672283
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000940638201367337
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109102551412904
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00629581706919523
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190381242499502
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242897555086032

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.