Coexpression cluster:C2414

Full id: C2414_kidney_smallcell_seminal_somatostatinoma_ductus_small_Fibroblast

Phase1 CAGE Peaks

Hg19::chr17:46667561..46667572,-	p4@HOXB3
Hg19::chr17:46667594..46667619,-	p1@HOXB3
Hg19::chr17:46667628..46667642,-	p2@HOXB3
Hg19::chr17:46668194..46668198,+	p1@ENST00000429755 p1@ENST00000487849 p1@ENST00000492897

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:0030878	thyroid gland development	0.008242081714353
GO:0035270	endocrine system development	0.0180540837552494
GO:0048732	gland development	0.0180540837552494

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	4.94e-13	16
kidney tubule cell	9.79e-13	12
nephron tubule epithelial cell	9.79e-13	12
kidney cell	5.42e-11	18
kidney epithelial cell	5.42e-11	18
kidney cortical cell	4.62e-10	13
renal cortical epithelial cell	4.62e-10	13

Uber Anatomy

Ontology term	p-value	n
intraembryonic coelom	6.90e-17	21
cavitated compound organ	1.25e-15	32
kidney	1.80e-15	27
kidney mesenchyme	1.80e-15	27
kidney rudiment	1.80e-15	27
kidney field	1.80e-15	27
abdominal segment of trunk	1.88e-15	61
abdomen	1.88e-15	61
mesonephros	3.43e-15	18
pronephros	3.43e-15	18
nephrogenic cord	3.43e-15	18
pronephric mesoderm	3.43e-15	18
rostral part of nephrogenic cord	3.43e-15	18
presumptive pronephric mesoderm	3.43e-15	18
excretory tube	4.18e-14	17
mesonephric epithelium	4.18e-14	17
mesonephric tubule	4.18e-14	17
nephric duct	4.18e-14	17
kidney epithelium	4.18e-14	17
renal duct	4.18e-14	17
mesonephric duct	4.18e-14	17
pronephric duct	4.18e-14	17
renal system	4.28e-14	45
subdivision of trunk	9.60e-14	113
urinary system structure	1.79e-13	44
urogenital ridge	4.91e-13	20
nephron epithelium	4.94e-13	16
nephron	4.94e-13	16
uriniferous tubule	4.94e-13	16
metanephric mesenchyme	4.94e-13	16
nephrogenic mesenchyme	4.94e-13	16
renal tubule	9.79e-13	12
nephron tubule	9.79e-13	12
nephron tubule epithelium	9.79e-13	12
trunk region element	3.35e-12	107
trunk	9.47e-12	216
abdomen element	9.89e-12	55
abdominal segment element	9.89e-12	55
duct	1.17e-11	26
body cavity precursor	1.88e-11	63
intermediate mesoderm	3.45e-11	37
anatomical space	1.82e-10	104
cortex of kidney	4.62e-10	13
renal parenchyma	4.62e-10	13
immaterial anatomical entity	2.59e-09	126
anatomical cavity	3.45e-09	70
large intestine	4.93e-09	11
mesenchyme	1.85e-08	238
entire embryonic mesenchyme	1.85e-08	238
cavity lining	3.34e-08	12
serous membrane	3.34e-08	12
parenchyma	4.78e-08	17
gastrointestinal system	4.84e-08	35
cortex	1.81e-07	16
internal genitalia	2.12e-07	25
trunk mesenchyme	2.30e-07	143
colon	4.12e-07	9

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.