Coexpression cluster:C4551

Full id: C4551_osteoclastoma_Mesothelial_Preadipocyte_Mallassezderived_hepatic_rectal_Smooth

Phase1 CAGE Peaks

Hg19::chr6:117803797..117803844,+	p1@DCBLD1
Hg19::chr6:117803847..117803869,+	p2@DCBLD1
Hg19::chr6:117803876..117803888,+	p3@DCBLD1

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
embryonic cell	1.12e-19	250
mesodermal cell	1.81e-19	121
muscle precursor cell	1.02e-14	58
myoblast	1.02e-14	58
multi-potent skeletal muscle stem cell	1.02e-14	58
muscle cell	3.42e-13	55
smooth muscle cell	1.66e-12	43
smooth muscle myoblast	1.66e-12	43
contractile cell	2.60e-12	59
fibroblast	5.28e-12	76
electrically responsive cell	2.45e-10	61
electrically active cell	2.45e-10	61
non-terminally differentiated cell	6.43e-10	106
vascular associated smooth muscle cell	5.91e-09	32
animal cell	3.35e-08	679
eukaryotic cell	3.35e-08	679
somatic cell	8.53e-07	588
epithelial cell	8.84e-07	253

Uber Anatomy

Ontology term	p-value	n
unilaminar epithelium	2.61e-24	148
trunk mesenchyme	9.07e-21	122
trunk	6.28e-17	199
multi-cellular organism	3.00e-16	656
organism subdivision	5.20e-16	264
mesenchyme	6.78e-16	160
entire embryonic mesenchyme	6.78e-16	160
epithelial vesicle	9.84e-16	78
anatomical group	9.92e-16	625
multilaminar epithelium	1.68e-15	83
anatomical system	1.97e-15	624
epithelial tube	5.49e-15	117
somite	1.32e-14	71
presomitic mesoderm	1.32e-14	71
presumptive segmental plate	1.32e-14	71
dermomyotome	1.32e-14	71
trunk paraxial mesoderm	1.32e-14	71
paraxial mesoderm	5.50e-14	72
presumptive paraxial mesoderm	5.50e-14	72
skeletal muscle tissue	5.62e-14	62
striated muscle tissue	5.62e-14	62
myotome	5.62e-14	62
cell layer	5.67e-14	309
muscle tissue	8.79e-14	64
musculature	8.79e-14	64
musculature of body	8.79e-14	64
dense mesenchyme tissue	9.13e-14	73
epithelium	1.04e-13	306
vasculature	2.61e-13	78
vascular system	2.61e-13	78
epithelial tube open at both ends	3.48e-13	59
blood vessel	3.48e-13	59
blood vasculature	3.48e-13	59
vascular cord	3.48e-13	59
vessel	6.12e-13	68
embryonic structure	3.47e-12	564
splanchnic layer of lateral plate mesoderm	8.20e-12	83
multi-tissue structure	1.23e-11	342
germ layer	2.96e-11	560
germ layer / neural crest	2.96e-11	560
embryonic tissue	2.96e-11	560
presumptive structure	2.96e-11	560
germ layer / neural crest derived structure	2.96e-11	560
epiblast (generic)	2.96e-11	560
artery	6.89e-11	42
arterial blood vessel	6.89e-11	42
arterial system	6.89e-11	42
developing anatomical structure	1.12e-10	581
anatomical cluster	2.48e-10	373
embryo	1.14e-09	592
anatomical conduit	1.66e-09	240
endoderm-derived structure	1.95e-09	160
endoderm	1.95e-09	160
presumptive endoderm	1.95e-09	160
systemic artery	4.59e-09	33
systemic arterial system	4.59e-09	33
surface structure	1.43e-07	99
digestive system	2.19e-07	145
digestive tract	2.19e-07	145
primitive gut	2.19e-07	145
simple squamous epithelium	2.82e-07	22
mesoderm	3.78e-07	315
mesoderm-derived structure	3.78e-07	315
presumptive mesoderm	3.78e-07	315
tube	6.47e-07	192

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	0.0190950092090446
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281007531641
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.0017223507416202
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327328807482714
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324001437432025
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00918560077796609
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322170067228315
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464580611934429
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000678984869582728
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00764745117199189
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154719884545334
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128639961498561
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295808415768011
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173582119398014
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278035924342541
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109361252737751
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000648713359365185
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191017759179548
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330974642205621
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243689463922175
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109993179102081

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.