Coexpression cluster:C2444

Full id: C2444_Alveolar_Endothelial_Smooth_leiomyoma_Preadipocyte_Hair_Renal

Phase1 CAGE Peaks

Hg19::chr17:79826116..79826136,-	p6@ARHGDIA
Hg19::chr17:79826202..79826231,-	p3@ARHGDIA
Hg19::chr17:79826305..79826324,-	p2@ARHGDIA
Hg19::chr17:79826336..79826347,-	p16@ARHGDIA

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
somatic cell	3.62e-22	588
animal cell	7.13e-20	679
eukaryotic cell	7.13e-20	679
native cell	3.37e-15	722
embryonic cell	2.50e-12	250
mesodermal cell	5.86e-12	121
somatic stem cell	2.63e-10	433
stem cell	1.36e-09	441
fibroblast	2.05e-09	76
multi fate stem cell	2.11e-09	427
contractile cell	2.17e-07	59
electrically responsive cell	2.68e-07	61
electrically active cell	2.68e-07	61
muscle precursor cell	8.19e-07	58
myoblast	8.19e-07	58
multi-potent skeletal muscle stem cell	8.19e-07	58

Uber Anatomy

Ontology term	p-value	n
mesoderm	1.75e-11	315
mesoderm-derived structure	1.75e-11	315
presumptive mesoderm	1.75e-11	315
epithelial vesicle	6.35e-09	78
epithelial tube open at both ends	3.99e-08	59
blood vessel	3.99e-08	59
blood vasculature	3.99e-08	59
vascular cord	3.99e-08	59
vessel	6.06e-08	68
vasculature	1.06e-07	78
vascular system	1.06e-07	78
splanchnic layer of lateral plate mesoderm	1.07e-07	83
artery	1.49e-07	42
arterial blood vessel	1.49e-07	42
arterial system	1.49e-07	42
surface structure	2.00e-07	99
lateral plate mesoderm	2.38e-07	203
epithelial tube	2.67e-07	117
dense mesenchyme tissue	5.64e-07	73
somite	5.79e-07	71
presomitic mesoderm	5.79e-07	71
presumptive segmental plate	5.79e-07	71
dermomyotome	5.79e-07	71
trunk paraxial mesoderm	5.79e-07	71
paraxial mesoderm	6.22e-07	72
presumptive paraxial mesoderm	6.22e-07	72
integument	7.19e-07	46
integumental system	7.19e-07	46

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
BCL3#602	4	34.5471028037383	7.01262157705428e-07	3.1473622040652e-05
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.0051213092666262
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101419148611895
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154533621580261
FOSL2#2355	4	16.9302006045617	1.2165416097647e-05	0.00030359471728128
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390294919645114
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000721653638120561
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.018601196362508
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00248087898306239
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.0079620671999622
TAL1#6886	4	29.8686166774402	1.25525650806991e-06	5.03834490569996e-05
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106839610110542
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342397812862595
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00248774173400224

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.