Coexpression cluster:C3700

Full id: C3700_occipital_brain_temporal_duodenum_parietal_Renal_Neurons

Phase1 CAGE Peaks

Hg19::chr17:79989519..79989570,+	p1@RAC3
Hg19::chr17:79989572..79989600,+	p2@RAC3
Hg19::chr17:79989607..79989618,+	p4@RAC3

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
embryonic cell	3.65e-25	248
epithelial cell	6.60e-19	254
neurectodermal cell	1.71e-12	59
ectodermal cell	7.11e-12	71
mesodermal cell	3.00e-11	119
non-terminally differentiated cell	6.06e-11	180
neural cell	3.59e-09	25
endothelial cell	9.45e-09	35
electrically responsive cell	1.27e-08	60
electrically active cell	1.27e-08	60
epithelial cell of nephron	2.19e-08	16
migratory neural crest cell	2.29e-08	41
meso-epithelial cell	2.45e-08	44
contractile cell	5.88e-08	59
kidney cell	1.10e-07	18
kidney epithelial cell	1.10e-07	18
endothelial cell of vascular tree	1.18e-07	24
blood vessel endothelial cell	2.69e-07	18
embryonic blood vessel endothelial progenitor cell	2.69e-07	18
columnar/cuboidal epithelial cell	6.66e-07	27
kidney cortical cell	8.95e-07	13
renal cortical epithelial cell	8.95e-07	13

Uber Anatomy

Ontology term	p-value	n
cell layer	3.57e-20	312
epithelium	2.28e-19	309
multi-tissue structure	5.38e-14	347
organism subdivision	8.77e-13	365
ectoderm	2.50e-11	173
presumptive ectoderm	2.50e-11	173
ectoderm-derived structure	1.02e-10	169
vasculature	6.22e-10	79
vascular system	6.22e-10	79
tube	6.80e-10	194
organ part	9.10e-10	219
regional part of nervous system	3.22e-09	94
nervous system	3.22e-09	94
anatomical cluster	6.20e-09	286
anatomical conduit	1.72e-08	241
nephron epithelium	2.19e-08	16
nephron	2.19e-08	16
uriniferous tubule	2.19e-08	16
metanephric mesenchyme	2.19e-08	16
nephrogenic mesenchyme	2.19e-08	16
unilaminar epithelium	4.51e-08	138
trunk	5.60e-08	216
excretory tube	5.75e-08	17
mesonephric epithelium	5.75e-08	17
mesonephric tubule	5.75e-08	17
nephric duct	5.75e-08	17
kidney epithelium	5.75e-08	17
renal duct	5.75e-08	17
mesonephric duct	5.75e-08	17
pronephric duct	5.75e-08	17
embryo	1.88e-07	612
mesonephros	2.19e-07	18
pronephros	2.19e-07	18
nephrogenic cord	2.19e-07	18
pronephric mesoderm	2.19e-07	18
rostral part of nephrogenic cord	2.19e-07	18
presumptive pronephric mesoderm	2.19e-07	18
endothelium	2.69e-07	18
blood vessel endothelium	2.69e-07	18
cardiovascular system endothelium	2.69e-07	18
head	3.12e-07	123
trunk mesenchyme	3.39e-07	143
simple squamous epithelium	3.90e-07	22
epithelial tube	4.39e-07	118
kidney	4.60e-07	27
kidney mesenchyme	4.60e-07	27
kidney rudiment	4.60e-07	27
kidney field	4.60e-07	27
central nervous system	4.72e-07	82
cortex of kidney	8.95e-07	13
renal parenchyma	8.95e-07	13

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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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.