Coexpression cluster:C1556

Full id: C1556_epididymis_seminal_Renal_ductus_kidney_rhabdomyosarcoma_renal

Phase1 CAGE Peaks

Hg19::chr10:102505147..102505162,+	p9@PAX2
Hg19::chr10:102505297..102505302,+	p11@PAX2
Hg19::chr10:102505493..102505546,+	p2@PAX2
Hg19::chr10:102505946..102505949,+	p14@PAX2
Hg19::chr10:102505954..102505973,+	p3@PAX2

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><br>

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Cell Type

Ontology term	p-value	n
kidney cell	1.58e-21	18
kidney epithelial cell	1.58e-21	18
kidney tubule cell	3.38e-18	12
nephron tubule epithelial cell	3.38e-18	12
epithelial cell of nephron	3.60e-18	16
kidney cortical cell	3.22e-13	13
renal cortical epithelial cell	3.22e-13	13
brush border epithelial cell	7.81e-07	3
kidney cortex tubule cell	7.81e-07	3
epithelial cell of proximal tubule	7.81e-07	3

Uber Anatomy

Ontology term	p-value	n
cavitated compound organ	2.36e-31	32
kidney	1.11e-29	27
kidney mesenchyme	1.11e-29	27
kidney rudiment	1.11e-29	27
kidney field	1.11e-29	27
mesonephros	1.13e-21	18
pronephros	1.13e-21	18
nephrogenic cord	1.13e-21	18
pronephric mesoderm	1.13e-21	18
rostral part of nephrogenic cord	1.13e-21	18
presumptive pronephric mesoderm	1.13e-21	18
excretory tube	6.38e-20	17
mesonephric epithelium	6.38e-20	17
mesonephric tubule	6.38e-20	17
nephric duct	6.38e-20	17
kidney epithelium	6.38e-20	17
renal duct	6.38e-20	17
mesonephric duct	6.38e-20	17
pronephric duct	6.38e-20	17
duct	6.54e-20	26
urogenital ridge	5.02e-19	20
urinary system structure	1.25e-18	44
renal tubule	3.38e-18	12
nephron tubule	3.38e-18	12
nephron tubule epithelium	3.38e-18	12
nephron epithelium	3.60e-18	16
nephron	3.60e-18	16
uriniferous tubule	3.60e-18	16
metanephric mesenchyme	3.60e-18	16
nephrogenic mesenchyme	3.60e-18	16
renal system	4.83e-18	45
intraembryonic coelom	6.82e-18	21
abdomen element	1.42e-14	55
abdominal segment element	1.42e-14	55
posterior neural tube	2.43e-14	15
chordal neural plate	2.43e-14	15
compound organ	1.95e-13	69
cortex of kidney	3.22e-13	13
renal parenchyma	3.22e-13	13
segmental subdivision of hindbrain	1.22e-12	12
hindbrain	1.22e-12	12
presumptive hindbrain	1.22e-12	12
cortex	1.44e-12	16
abdominal segment of trunk	2.12e-12	61
abdomen	2.12e-12	61
body cavity precursor	2.30e-12	63
intermediate mesoderm	2.57e-12	37
trunk region element	1.06e-11	107
segmental subdivision of nervous system	1.75e-11	13
anatomical cavity	2.66e-11	70
parenchyma	3.35e-11	17
male reproductive organ	1.04e-09	11
anatomical space	1.42e-08	104
regional part of metencephalon	2.27e-08	9
metencephalon	2.27e-08	9
future metencephalon	2.27e-08	9
testis	1.49e-07	8
brainstem	2.28e-07	8
male genital duct	3.52e-07	3
internal male genitalia	3.52e-07	3
subdivision of trunk	5.49e-07	113
renal cortex tubule	7.81e-07	3
region of nephron tubule	7.81e-07	3
proximal tubule	7.81e-07	3
immaterial anatomical entity	9.66e-07	126

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
CTBP2#1488	3	37.6302002035969	3.95343056005017e-05	0.000737439425363601
SUZ12#23512	2	20.0463123644252	0.00382407565415475	0.0188717401712549

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.