Coexpression cluster:C4353

Full id: C4353_heart_penis_aorta_smooth_sacrococcigeal_Mast_mesodermal

Phase1 CAGE Peaks

Hg19::chr3:99594980..99594993,-	p3@FILIP1L
Hg19::chr3:99594998..99595024,-	p1@FILIP1L
Hg19::chr3:99595037..99595051,-	p2@FILIP1L

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
mesodermal cell	1.12e-09	119
muscle precursor cell	6.13e-07	57
myoblast	6.13e-07	57
multi-potent skeletal muscle stem cell	6.13e-07	57
non-terminally differentiated cell	7.13e-07	180
fibroblast	7.67e-07	75

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	4.35e-16	659
anatomical system	3.99e-14	625
anatomical group	5.05e-14	626
trunk mesenchyme	2.87e-13	143
epithelium	3.36e-11	309
organism subdivision	4.76e-11	365
cell layer	5.03e-11	312
unilaminar epithelium	2.75e-10	138
epithelial tube	4.03e-10	118
anatomical conduit	8.21e-10	241
trunk	8.49e-10	216
somite	1.92e-09	83
paraxial mesoderm	1.92e-09	83
presomitic mesoderm	1.92e-09	83
presumptive segmental plate	1.92e-09	83
trunk paraxial mesoderm	1.92e-09	83
presumptive paraxial mesoderm	1.92e-09	83
multilaminar epithelium	2.89e-09	82
muscle tissue	5.79e-09	63
musculature	5.79e-09	63
musculature of body	5.79e-09	63
splanchnic layer of lateral plate mesoderm	8.06e-09	84
multi-tissue structure	1.18e-08	347
vasculature	1.86e-08	79
vascular system	1.86e-08	79
anatomical cluster	2.37e-08	286
dermomyotome	2.75e-08	70
skeletal muscle tissue	3.54e-08	61
striated muscle tissue	3.54e-08	61
myotome	3.54e-08	61
organ	4.57e-08	511
embryonic structure	6.42e-08	605
developing anatomical structure	6.42e-08	605
germ layer	1.25e-07	604
embryonic tissue	1.25e-07	604
presumptive structure	1.25e-07	604
epiblast (generic)	1.25e-07	604
vessel	1.50e-07	69
embryo	1.92e-07	612
mesoderm	7.33e-07	448
mesoderm-derived structure	7.33e-07	448
presumptive mesoderm	7.33e-07	448

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	0.0190692866492591
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115559983111356
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280600527146589
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326784086638931
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323583043871655
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321775809621855
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464006898225948
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00582975812798703
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00445490647012986
JUND#3727	3	6.99466394187103	0.00292184504273499	0.015727995795186
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270377621194521
POU5F1#5460	3	335.439201451906	2.63510205045339e-08	1.82256571554505e-06
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00666664784894803
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00375871293069439
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140645033873171
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243333832688342

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.