Coexpression cluster:C3864

Full id: C3864_small_Intestinal_serous_choriocarcinoma_Hepatocyte_rectal_Prostate

Phase1 CAGE Peaks

Hg19::chr1:151483855..151483871,+	p2@CGN
Hg19::chr1:151483881..151483912,+	p1@CGN
Hg19::chr1:151483924..151483940,+	p3@CGN

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	1.53e-15	253
endodermal cell	8.40e-13	58
endo-epithelial cell	3.02e-10	42

Uber Anatomy

Ontology term	p-value	n
organ system subdivision	7.30e-21	223
endoderm-derived structure	6.55e-20	160
endoderm	6.55e-20	160
presumptive endoderm	6.55e-20	160
subdivision of digestive tract	3.44e-18	118
digestive system	5.53e-18	145
digestive tract	5.53e-18	145
primitive gut	5.53e-18	145
adult organism	4.21e-16	114
endo-epithelium	2.26e-15	82
trunk region element	2.43e-14	101
anatomical cluster	2.13e-12	373
immaterial anatomical entity	2.77e-12	117
foregut	3.52e-12	87
organ	1.70e-11	503
organ part	1.78e-11	218
multi-tissue structure	6.61e-11	342
subdivision of trunk	1.08e-09	112
anatomical space	4.49e-09	95
neural tube	1.28e-08	56
neural rod	1.28e-08	56
future spinal cord	1.28e-08	56
neural keel	1.28e-08	56
gastrointestinal system	1.64e-08	25
abdomen element	1.65e-08	54
abdominal segment element	1.65e-08	54
anatomical conduit	4.67e-08	240
regional part of nervous system	5.78e-08	53
regional part of brain	5.78e-08	53
gut epithelium	7.69e-08	54
embryo	1.14e-07	592
lung	2.52e-07	22
respiratory tube	2.52e-07	22
respiration organ	2.52e-07	22
pair of lungs	2.52e-07	22
lung primordium	2.52e-07	22
lung bud	2.52e-07	22
ectoderm-derived structure	2.78e-07	171
ectoderm	2.78e-07	171
presumptive ectoderm	2.78e-07	171
urinary system structure	3.79e-07	47
central nervous system	5.43e-07	81
nervous system	7.39e-07	89
intestine	7.67e-07	17
renal system	8.44e-07	48
ecto-epithelium	8.45e-07	104
epithelial bud	9.42e-07	37

Disease

Ontology term	p-value	n
carcinoma	1.84e-22	106
cell type cancer	5.58e-19	143
adenocarcinoma	1.27e-09	25
cancer	2.56e-09	235
disease of cellular proliferation	5.12e-09	239
squamous cell carcinoma	3.03e-07	14

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325436175995409
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322296631957756
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320708783572263
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186558340822065
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294560680113183
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172950973720172
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190309788127463
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421657145651973
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329477970865951
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140232254958388

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.