Coexpression cluster:C1276

Full id: C1276_mesothelioma_CD14_leiomyoma_bile_Mesothelial_migratory_mesenchymal

Phase1 CAGE Peaks

Hg19::chr5:179247896..179247913,+	p1@SQSTM1
Hg19::chr5:179249956..179250009,+	p4@SQSTM1
Hg19::chr5:179251175..179251193,+	p@chr5:179251175..179251193 +
Hg19::chr5:179260060..179260092,+	p@chr5:179260060..179260092 +
Hg19::chr5:179260110..179260123,+	p@chr5:179260110..179260123 +
Hg19::chr5:179260160..179260190,+	p@chr5:179260160..179260190 +
Hg19::chr5:179260699..179260713,+	p@chr5:179260699..179260713 +

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
animal cell	1.85e-15	679
eukaryotic cell	1.85e-15	679
mesodermal cell	8.18e-14	121
defensive cell	2.11e-11	48
phagocyte	2.11e-11	48
stuff accumulating cell	7.22e-11	87
embryonic cell	2.40e-10	250
somatic cell	2.57e-10	588
granulocyte monocyte progenitor cell	6.64e-10	67
macrophage dendritic cell progenitor	7.07e-10	61
classical monocyte	9.09e-10	42
CD14-positive, CD16-negative classical monocyte	9.09e-10	42
monopoietic cell	9.98e-10	59
monocyte	9.98e-10	59
monoblast	9.98e-10	59
promonocyte	9.98e-10	59
myeloid lineage restricted progenitor cell	1.77e-09	66
lining cell	2.78e-09	58
barrier cell	2.78e-09	58
myeloid leukocyte	6.28e-09	72
native cell	1.27e-08	722
smooth muscle cell	1.22e-07	43
smooth muscle myoblast	1.22e-07	43
mesothelial cell	2.77e-07	19

Uber Anatomy

Ontology term	p-value	n
mesoderm	5.22e-18	315
mesoderm-derived structure	5.22e-18	315
presumptive mesoderm	5.22e-18	315
musculoskeletal system	2.00e-12	167
lateral plate mesoderm	1.85e-10	203
multi-cellular organism	3.65e-10	656
bone marrow	5.21e-09	76
anatomical group	7.63e-09	625
anatomical system	7.96e-09	624
immune system	4.71e-08	93
skeletal element	1.00e-07	90
trunk mesenchyme	1.11e-07	122
vasculature	1.24e-07	78
vascular system	1.24e-07	78
vessel	1.54e-07	68
epithelial tube	2.30e-07	117
artery	2.52e-07	42
arterial blood vessel	2.52e-07	42
arterial system	2.52e-07	42
skeletal system	3.46e-07	100
bone element	3.84e-07	82
germ layer	8.07e-07	560
germ layer / neural crest	8.07e-07	560
embryonic tissue	8.07e-07	560
presumptive structure	8.07e-07	560
germ layer / neural crest derived structure	8.07e-07	560
epiblast (generic)	8.07e-07	560
embryo	8.13e-07	592
epithelial vesicle	8.19e-07	78
mesenchyme	8.26e-07	160
entire embryonic mesenchyme	8.26e-07	160
trunk	8.54e-07	199

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223572189986459

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.