Coexpression cluster:C3888

Full id: C3888_Alveolar_Whole_Neutrophils_Eosinophils_mesothelioma_Renal_Bronchial

Phase1 CAGE Peaks

Hg19::chr1:159895266..159895275,-	p2@TAGLN2
Hg19::chr1:159895286..159895305,-	p1@CCDC19 p1@TAGLN2
Hg19::chr8:107710288..107710306,-	p1@TAGLN2P1

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	8.97e-39	679
eukaryotic cell	8.97e-39	679
native cell	5.07e-38	722
somatic cell	5.05e-35	588
mesodermal cell	1.79e-14	121
somatic stem cell	1.81e-10	433
embryonic cell	4.23e-10	250
stem cell	9.09e-10	441
squamous epithelial cell	9.86e-10	63
multi fate stem cell	1.04e-09	427
lining cell	2.35e-09	58
barrier cell	2.35e-09	58
epithelial cell	6.36e-09	253
classical monocyte	8.47e-08	42
CD14-positive, CD16-negative classical monocyte	8.47e-08	42
epithelial cell of nephron	2.07e-07	15
kidney cell	3.25e-07	17
kidney epithelial cell	3.25e-07	17
vascular associated smooth muscle cell	4.21e-07	32
leukocyte	6.37e-07	136
smooth muscle cell	7.35e-07	43
smooth muscle myoblast	7.35e-07	43

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	4.02e-20	203
cardiovascular system	2.72e-14	109
mesoderm	1.43e-13	315
mesoderm-derived structure	1.43e-13	315
presumptive mesoderm	1.43e-13	315
circulatory system	2.38e-13	112
vessel	4.70e-12	68
splanchnic layer of lateral plate mesoderm	9.46e-12	83
epithelial tube open at both ends	1.79e-11	59
blood vessel	1.79e-11	59
blood vasculature	1.79e-11	59
vascular cord	1.79e-11	59
artery	5.76e-11	42
arterial blood vessel	5.76e-11	42
arterial system	5.76e-11	42
epithelial tube	7.35e-11	117
vasculature	1.26e-10	78
vascular system	1.26e-10	78
nephron epithelium	2.07e-07	15
renal tubule	2.07e-07	15
nephron tubule	2.07e-07	15
nephron	2.07e-07	15
uriniferous tubule	2.07e-07	15
nephrogenic mesenchyme	2.07e-07	15
systemic artery	4.64e-07	33
systemic arterial system	4.64e-07	33

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
ESR1#2099	2	20.5124021974363	0.00309974157709518	0.0163106565180493
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155821005976755
IRF4#3662	2	14.6096751244961	0.00605612247321789	0.0268381794450038
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329901524616861
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329121254955535

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.