Coexpression cluster:C1028

Full id: C1028_Alveolar_Renal_iPS_teratocarcinoma_H9_HES3GFP_choriocarcinoma

Phase1 CAGE Peaks

Hg19::chr14:104033742..104033743,+	p1@ENST00000364314
Hg19::chr16:3064836..3064855,+	p@chr16:3064836..3064855 +
Hg19::chr16:3068178..3068191,-	p1@CLDN6
Hg19::chr16:3068393..3068407,+	p@chr16:3068393..3068407 +
Hg19::chr19:18557270..18557282,-	p2@ELL
Hg19::chr22:47030082..47030087,+	p@chr22:47030082..47030087 +
Hg19::chr2:234322838..234322854,+	p@chr2:234322838..234322854 +
Hg19::chr4:25679305..25679316,+	p@chr4:25679305..25679316 +

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:0008159	positive transcription elongation factor activity	0.0152784505458963
GO:0006368	RNA elongation from RNA polymerase II promoter	0.0152784505458963
GO:0003711	transcription elongation regulator activity	0.0152784505458963
GO:0006354	RNA elongation	0.0152784505458963
GO:0016338	calcium-independent cell-cell adhesion	0.0152784505458963
GO:0016607	nuclear speck	0.0374541676159651
GO:0005923	tight junction	0.0374541676159651
GO:0043296	apical junction complex	0.0374541676159651
GO:0016327	apicolateral plasma membrane	0.0374541676159651
GO:0016604	nuclear body	0.0374541676159651

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
epithelial cell of nephron	2.17e-09	16
kidney tubule cell	9.79e-08	12
nephron tubule epithelial cell	9.79e-08	12
kidney cell	1.43e-07	18
kidney epithelial cell	1.43e-07	18
kidney cortical cell	1.74e-07	13
renal cortical epithelial cell	1.74e-07	13

Uber Anatomy

Ontology term	p-value	n
nephron epithelium	2.17e-09	16
nephron	2.17e-09	16
uriniferous tubule	2.17e-09	16
metanephric mesenchyme	2.17e-09	16
nephrogenic mesenchyme	2.17e-09	16
excretory tube	3.23e-09	17
mesonephric epithelium	3.23e-09	17
mesonephric tubule	3.23e-09	17
nephric duct	3.23e-09	17
kidney epithelium	3.23e-09	17
renal duct	3.23e-09	17
mesonephric duct	3.23e-09	17
pronephric duct	3.23e-09	17
mesonephros	3.70e-09	18
pronephros	3.70e-09	18
nephrogenic cord	3.70e-09	18
pronephric mesoderm	3.70e-09	18
rostral part of nephrogenic cord	3.70e-09	18
presumptive pronephric mesoderm	3.70e-09	18
urogenital ridge	4.83e-08	20
renal tubule	9.79e-08	12
nephron tubule	9.79e-08	12
nephron tubule epithelium	9.79e-08	12
cortex of kidney	1.74e-07	13
renal parenchyma	1.74e-07	13
duct	3.83e-07	26
tube	6.64e-07	194

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)
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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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No analysis results for this cluster

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.