Coexpression cluster:C3662

Full id: C3662_breast_tridermal_rectal_bronchioalveolar_acute_stomach_embryonic

Phase1 CAGE Peaks

Hg19::chr17:57918299..57918329,+	p4@MIR21
Hg19::chr17:57918343..57918368,+	p6@MIR21
Hg19::chr17:57918422..57918461,+	p2@MIR21

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
CD14-positive, CD16-negative classical monocyte	1.35e-09	42
monopoietic cell	1.65e-09	63
monocyte	1.65e-09	63
monoblast	1.65e-09	63
promonocyte	1.65e-09	63
macrophage dendritic cell progenitor	4.93e-09	65
granulocyte monocyte progenitor cell	1.32e-08	71
myeloid lineage restricted progenitor cell	1.50e-08	70
classical monocyte	1.59e-08	45
myeloid leukocyte	4.30e-07	76

Uber Anatomy

Ontology term	p-value	n
mesoderm	3.47e-08	448
mesoderm-derived structure	3.47e-08	448
presumptive mesoderm	3.47e-08	448
bone marrow	7.85e-08	80
bone element	1.41e-07	86
immune system	7.42e-07	115

Disease

Ontology term	p-value	n
disease of cellular proliferation	5.46e-08	239
cancer	5.96e-08	235
cell type cancer	1.07e-07	143

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
BCL11A#53335	3	28.3694551036071	4.37778126761649e-05	0.00077756989423231
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000526863238998577
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139130428642322
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115159808907105
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00914411668635563
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387669210925286
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000737137832254018
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269374685531354
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.0088158659118078
POU5F1#5460	3	335.439201451906	2.63510205045339e-08	1.82135951718929e-06
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542270792403912

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.