Coexpression cluster:C3922

Full id: C3922_Fibroblast_uterus_basal_mesenchymal_smooth_mature_amniotic

Phase1 CAGE Peaks

Hg19::chr1:203595903..203595934,+	p2@ATP2B4
Hg19::chr1:203595941..203595970,+	p1@ATP2B4
Hg19::chr1:203595980..203595991,+	p4@ATP2B4

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
non-terminally differentiated cell	1.31e-10	180
fibroblast	2.58e-10	75
skin fibroblast	3.20e-10	23
muscle precursor cell	3.41e-07	57
myoblast	3.41e-07	57
multi-potent skeletal muscle stem cell	3.41e-07	57
muscle cell	6.48e-07	54

Uber Anatomy

Ontology term	p-value	n
adult organism	1.86e-11	115
splanchnic layer of lateral plate mesoderm	3.16e-11	84
somite	4.77e-10	83
paraxial mesoderm	4.77e-10	83
presomitic mesoderm	4.77e-10	83
presumptive segmental plate	4.77e-10	83
trunk paraxial mesoderm	4.77e-10	83
presumptive paraxial mesoderm	4.77e-10	83
blood vessel	2.14e-09	60
epithelial tube open at both ends	2.14e-09	60
blood vasculature	2.14e-09	60
vascular cord	2.14e-09	60
circulatory system	5.15e-09	113
organism subdivision	9.15e-09	365
vessel	1.54e-08	69
cardiovascular system	2.56e-08	110
dermomyotome	4.13e-08	70
vasculature	4.99e-08	79
vascular system	4.99e-08	79
artery	9.11e-08	42
arterial blood vessel	9.11e-08	42
arterial system	9.11e-08	42
skin of body	1.40e-07	40
integument	2.53e-07	45
integumental system	2.53e-07	45
multilaminar epithelium	3.25e-07	82
muscle tissue	3.81e-07	63
musculature	3.81e-07	63
musculature of body	3.81e-07	63
systemic artery	5.01e-07	33
systemic arterial system	5.01e-07	33
surface structure	5.54e-07	95

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190136447123917
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115256370880028
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322434870394609
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032083107015183
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462562975655125
EP300#2033	3	6.7739417262232	0.00321688050010379	0.01675649788281
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154203667643504
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434124817699165
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128154739974294
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00444413416231416
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156859553006168
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.000857847596014837
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186656883042908
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720579617043322
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294690901457176
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00664310243731792
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768027871859885
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00484858676612745
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203165752309159
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309212052317686
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246703877520705
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00642905355960757
WRNIP1#56897	3	109.819964349376	7.53682839543883e-07	3.32266281465275e-05
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140292144881497
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109474071282511

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.