Coexpression cluster:C2613

Full id: C2613_tonsil_trachea_salivary_hepatocellular_throat_tongue_breast

Phase1 CAGE Peaks

Hg19::chr20:31595419..31595426,+	p2@BPIFB2
Hg19::chr20:31595501..31595519,+	p1@BPIFB2
Hg19::chr20:31608346..31608355,+	p@chr20:31608346..31608355 +
Hg19::chr20:31612754..31612763,+	p@chr20:31612754..31612763 +

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
peptide hormone secreting cell	1.06e-09	1
enteroendocrine cell	1.06e-09	1
type D enteroendocrine cell	1.06e-09	1
somatostatin secreting cell	1.06e-09	1
pancreatic D cell	1.06e-09	1
progenitor cell of endocrine pancreas	1.06e-09	1
metabolising cell	5.52e-07	12
endopolyploid cell	5.52e-07	12
parenchymal cell	5.52e-07	12
polyploid cell	5.52e-07	12
hepatocyte	5.52e-07	12

Uber Anatomy

Ontology term	p-value	n
open tracheal system trachea	3.76e-18	2
major salivary gland	6.82e-18	2
throat	2.85e-17	2
oral opening	1.69e-13	22
saliva-secreting gland	1.95e-13	6
gland of oral region	1.95e-13	6
gland of foregut	1.95e-13	6
oral gland	1.95e-13	6
oral cavity	1.95e-13	6
exocrine gland	8.24e-13	31
exocrine system	8.24e-13	31
tongue	3.77e-12	3
gustatory system	3.77e-12	3
future tongue	3.77e-12	3
foregut	5.32e-12	87
subdivision of digestive tract	2.13e-11	118
orifice	9.67e-11	36
mouth	3.99e-10	29
stomodeum	3.99e-10	29
tonsil	4.09e-10	1
mucosa-associated lymphoid tissue	4.09e-10	1
lymphoid tissue	4.09e-10	1
tonsillar ring	4.09e-10	1
adult organism	4.55e-10	114
parotid gland	6.88e-10	1
cheek	6.88e-10	1
parotid gland primordium	6.88e-10	1
submandibular gland	9.70e-10	1
submandibular gland primordium	9.70e-10	1
penis	1.62e-09	1
intromittent organ	1.62e-09	1
lateral plate mesenchyme	1.62e-09	1
undifferentiated genital tubercle	1.62e-09	1
somatopleure	1.62e-09	1
digestive system	7.84e-09	145
digestive tract	7.84e-09	145
primitive gut	7.84e-09	145
gland of gut	2.92e-08	10
chordate pharynx	3.30e-08	10
pharyngeal region of foregut	3.30e-08	10
gland	3.54e-08	59
respiratory system	5.93e-08	74
endoderm-derived structure	8.86e-08	160
endoderm	8.86e-08	160
presumptive endoderm	8.86e-08	160
anterior region of body	1.21e-07	62
craniocervical region	1.21e-07	62
pharynx	1.67e-07	11

Disease

Ontology term	p-value	n
somatostatinoma	1.06e-09	1
vascular disease	1.76e-09	1
ischemia	1.76e-09	1
extrinsic cardiomyopathy	1.76e-09	1
myocardial ischemia	1.76e-09	1
myocardial infarction	1.76e-09	1

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
BHLHE40#8553	2	22.4359067734887	0.00289146449685312	0.0156410452471561
FOSL2#2355	3	12.6976504534213	0.00078756857297571	0.00616726956534529
FOXA2#3170	2	12.3152318763326	0.00936191628546724	0.0353488494193027
HNF4A#3172	2	11.5661451814768	0.0105758568176249	0.0390749605609343
HNF4G#3174	2	14.3767112632234	0.00692416998043918	0.0293083159839138
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123859882906981
RXRA#6256	2	10.0373085695666	0.0139170380592011	0.0488828121969766

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.