Coexpression cluster:C2221

Full id: C2221_Mesenchymal_Fibroblast_Keratocytes_Keratinocyte_Osteoblast_mesenchymal_Hepatocyte

Phase1 CAGE Peaks

Hg19::chr12:57623876..57623891,+	p5@SHMT2
Hg19::chr12:57623907..57623961,+	p2@SHMT2
Hg19::chr12:57623963..57623989,+	p4@SHMT2
Hg19::chr12:57623992..57624003,+	p9@SHMT2

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	6.93e-34	679
eukaryotic cell	6.93e-34	679
non-terminally differentiated cell	1.26e-22	180
somatic cell	5.15e-22	591
native cell	1.80e-18	722
embryonic cell	1.51e-15	248
fibroblast	3.07e-14	75
mesodermal cell	1.21e-12	119
epithelial cell	7.55e-12	254
vascular associated smooth muscle cell	3.93e-09	32
smooth muscle cell	4.89e-09	42
smooth muscle myoblast	4.89e-09	42
contractile cell	1.14e-08	59
muscle precursor cell	1.15e-08	57
myoblast	1.15e-08	57
multi-potent skeletal muscle stem cell	1.15e-08	57
muscle cell	1.30e-08	54
multi fate stem cell	3.94e-07	430
somatic stem cell	4.94e-07	436

Uber Anatomy

Ontology term	p-value	n
epithelial tube	6.34e-14	118
splanchnic layer of lateral plate mesoderm	2.45e-12	84
blood vessel	1.31e-11	60
epithelial tube open at both ends	1.31e-11	60
blood vasculature	1.31e-11	60
vascular cord	1.31e-11	60
trunk	1.36e-11	216
vessel	1.84e-11	69
artery	1.99e-11	42
arterial blood vessel	1.99e-11	42
arterial system	1.99e-11	42
unilaminar epithelium	2.11e-11	138
vasculature	2.87e-11	79
vascular system	2.87e-11	79
trunk mesenchyme	4.13e-09	143
systemic artery	9.37e-09	33
systemic arterial system	9.37e-09	33
mesenchyme	6.34e-08	238
entire embryonic mesenchyme	6.34e-08	238
mesoderm	8.70e-08	448
mesoderm-derived structure	8.70e-08	448
presumptive mesoderm	8.70e-08	448
multilaminar epithelium	1.56e-07	82
somite	2.96e-07	83
paraxial mesoderm	2.96e-07	83
presomitic mesoderm	2.96e-07	83
presumptive segmental plate	2.96e-07	83
trunk paraxial mesoderm	2.96e-07	83
presumptive paraxial mesoderm	2.96e-07	83
dermomyotome	3.71e-07	70
cardiovascular system	4.88e-07	110
skeletal muscle tissue	9.79e-07	61
striated muscle tissue	9.79e-07	61
myotome	9.79e-07	61

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
ATF3#467	4	22.4631745260087	3.92475754624726e-06	0.000127178949231312
CEBPB#1051	4	7.97114762582482	0.000247638578809083	0.00267651097301478
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106315051358354
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00995512128307635
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185650741131421
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00391058019047554
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00484721778820326
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.00142168219606154
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00886185248582272
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00766957295656022
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.0079480622609134
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321454685257786
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243634779157092
TFAP2A#7020	4	16.518634373045	1.34240829060362e-05	0.000326121841038268
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114404782598458
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00507159788032826
USF2#7392	4	12.9921973850696	3.50833029870167e-05	0.000680294296446535
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346097456141473

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.