Coexpression cluster:C4020

Full id: C4020_thyroid_parotid_squamous_ductus_salivary_Neutrophils_seminal

Phase1 CAGE Peaks

Hg19::chr20:24911239..24911260,+	p@chr20:24911239..24911260 +
Hg19::chr20:24911267..24911310,+	p@chr20:24911267..24911310 +
Hg19::chr20:24911311..24911333,+	p@chr20:24911311..24911333 +

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
endo-epithelial cell	1.62e-15	43
endodermal cell	4.13e-12	59
epithelial cell	2.41e-08	254
epithelial cell of alimentary canal	2.57e-08	21

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	7.40e-22	169
endoderm	7.40e-22	169
presumptive endoderm	7.40e-22	169
digestive system	2.72e-18	155
digestive tract	2.72e-18	155
primitive gut	2.72e-18	155
subdivision of digestive tract	9.31e-16	129
endodermal part of digestive tract	9.31e-16	129
mixed endoderm/mesoderm-derived structure	1.03e-13	130
adult organism	2.00e-12	115
respiratory system	6.81e-12	72
endo-epithelium	4.93e-11	82
foregut	1.26e-09	98
orifice	2.17e-09	35
anatomical space	2.88e-09	104
immaterial anatomical entity	3.97e-09	126
respiratory tract	5.11e-08	53
neck	9.78e-08	10
oral opening	1.66e-07	21
mucosa	3.27e-07	12
thoracic cavity element	3.34e-07	34
thoracic cavity	3.34e-07	34
epithelial bud	4.90e-07	37
thoracic segment organ	7.92e-07	35

Disease

Ontology term	p-value	n
squamous cell carcinoma	2.97e-12	14
carcinoma	1.60e-08	106
adenocarcinoma	7.77e-08	25

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279836232037363
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00581914811850257
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000852188146858361
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269892514607731
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246876541097991

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.