Coexpression cluster:C1471

Full id: C1471_salivary_kidney_submaxillary_parotid_adenocarcinoma_trachea_ductus

Phase1 CAGE Peaks

Hg19::chr1:217311090..217311097,-	p26@ESRRG
Hg19::chr7:138482733..138482757,+	p1@TMEM213
Hg19::chr7:138482916..138482927,-	p3@ATP6V0A4
Hg19::chr7:138482933..138482946,-	p2@ATP6V0A4
Hg19::chr7:138482949..138482954,-	p10@ATP6V0A4
Hg19::chr7:138484401..138484416,-	p8@ATP6V0A4

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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GO ID	GO name	FDR corrected p-value
GO:0050682	AF-2 domain binding	0.0159284217538759
GO:0033176	proton-transporting V-type ATPase complex	0.0159284217538759
GO:0016471	vacuolar proton-transporting V-type ATPase complex	0.0159284217538759
GO:0031526	brush border membrane	0.0159284217538759
GO:0031253	cell projection membrane	0.0159284217538759
GO:0005903	brush border	0.0277491655280892
GO:0016439	tRNA-pseudouridine synthase activity	0.0297538403539397
GO:0006885	regulation of pH	0.0297538403539397
GO:0009982	pseudouridine synthase activity	0.0297538403539397
GO:0007588	excretion	0.0303949284521266
GO:0044463	cell projection part	0.0309189706234276
GO:0005774	vacuolar membrane	0.0327946621331735
GO:0044437	vacuolar part	0.0327946621331735
GO:0016324	apical plasma membrane	0.0327946621331735
GO:0016866	intramolecular transferase activity	0.0327946621331735
GO:0005496	steroid binding	0.0334955096926417
GO:0045177	apical part of cell	0.0334955096926417
GO:0031214	biomineral formation	0.0334955096926417
GO:0001503	ossification	0.0334955096926417
GO:0046849	bone remodeling	0.0347094355554021
GO:0048771	tissue remodeling	0.0348443475486375
GO:0016469	proton-transporting two-sector ATPase complex	0.0348443475486375
GO:0003707	steroid hormone receptor activity	0.0348443475486375
GO:0019904	protein domain specific binding	0.0348443475486375
GO:0050954	sensory perception of mechanical stimulus	0.0348443475486375
GO:0007605	sensory perception of sound	0.0348443475486375
GO:0015992	proton transport	0.0348443475486375
GO:0006818	hydrogen transport	0.0348443475486375
GO:0004879	ligand-dependent nuclear receptor activity	0.0381184060088978
GO:0015078	hydrogen ion transmembrane transporter activity	0.0486706314057502
GO:0001501	skeletal development	0.0486706314057502
GO:0015077	monovalent inorganic cation transmembrane transporter activity	0.0487734568188069
GO:0045893	positive regulation of transcription, DNA-dependent	0.0487734568188069
GO:0005773	vacuole	0.0494544620923417

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><br>

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Cell Type

Ontology term	p-value	n
brush border epithelial cell	3.30e-09	3
kidney cortex tubule cell	3.30e-09	3
epithelial cell of proximal tubule	3.30e-09	3
embryonic stem cell	2.64e-08	5

Uber Anatomy

Ontology term	p-value	n
adult organism	2.10e-12	115
renal cortex tubule	3.30e-09	3
region of nephron tubule	3.30e-09	3
proximal tubule	3.30e-09	3
male genital duct	3.58e-09	3
internal male genitalia	3.58e-09	3
compound organ	3.29e-08	69
male reproductive organ	4.29e-08	11
anatomical space	2.40e-07	104
major salivary gland	5.04e-07	2
duct of male reproductive system	5.94e-07	4
open tracheal system trachea	6.31e-07	2
intraembryonic coelom	8.79e-07	21

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	4	3.57350424871668	0.0131663500723851	0.0466113160641954
NANOG#79923	4	19.4965189873418	1.9383725252986e-05	0.000437239067321081
RAD21#5885	4	6.90335593030422	0.0011108515162536	0.00771435743772925

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.