Coexpression cluster:C1972

Full id: C1972_Fibroblast_Synoviocyte_Endothelial_osteosarcoma_mature_cerebellum_alveolar

Phase1 CAGE Peaks

Hg19::chr6:151646636..151646655,+	p5@AKAP12
Hg19::chr6:151646657..151646671,+	p8@AKAP12
Hg19::chr6:151646675..151646705,+	p4@AKAP12
Hg19::chr6:151646706..151646717,+	p11@AKAP12
Hg19::chr6:151646718..151646731,+	p10@AKAP12

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	6.00e-24	119
non-terminally differentiated cell	8.47e-22	180
endothelial cell of vascular tree	2.28e-13	24
meso-epithelial cell	2.52e-13	44
lining cell	1.12e-12	57
barrier cell	1.12e-12	57
embryonic cell	3.12e-12	248
muscle precursor cell	8.84e-12	57
myoblast	8.84e-12	57
multi-potent skeletal muscle stem cell	8.84e-12	57
endothelial cell	2.02e-11	35
contractile cell	2.82e-11	59
muscle cell	4.97e-11	54
blood vessel endothelial cell	5.91e-10	18
embryonic blood vessel endothelial progenitor cell	5.91e-10	18
fibroblast	5.55e-09	75
electrically responsive cell	6.54e-09	60
electrically active cell	6.54e-09	60
smooth muscle cell	1.31e-07	42
smooth muscle myoblast	1.31e-07	42

Uber Anatomy

Ontology term	p-value	n
cell layer	4.08e-25	312
epithelium	7.38e-24	309
vasculature	2.66e-23	79
vascular system	2.66e-23	79
anatomical cluster	3.44e-22	286
epithelial tube	1.09e-19	118
vessel	7.98e-19	69
multi-tissue structure	1.58e-18	347
unilaminar epithelium	4.36e-18	138
splanchnic layer of lateral plate mesoderm	7.05e-17	84
anatomical conduit	7.38e-17	241
blood vessel	1.66e-16	60
epithelial tube open at both ends	1.66e-16	60
blood vasculature	1.66e-16	60
vascular cord	1.66e-16	60
trunk mesenchyme	4.85e-16	143
cardiovascular system	7.36e-16	110
circulatory system	8.34e-16	113
tube	3.24e-15	194
multi-cellular organism	1.10e-14	659
organism subdivision	1.18e-14	365
trunk	7.87e-14	216
multilaminar epithelium	3.29e-13	82
anatomical system	4.47e-13	625
somite	5.63e-13	83
paraxial mesoderm	5.63e-13	83
presomitic mesoderm	5.63e-13	83
presumptive segmental plate	5.63e-13	83
trunk paraxial mesoderm	5.63e-13	83
presumptive paraxial mesoderm	5.63e-13	83
anatomical group	8.19e-13	626
mesenchyme	2.01e-12	238
entire embryonic mesenchyme	2.01e-12	238
dermomyotome	2.26e-12	70
skeletal muscle tissue	1.02e-11	61
striated muscle tissue	1.02e-11	61
myotome	1.02e-11	61
muscle tissue	1.63e-11	63
musculature	1.63e-11	63
musculature of body	1.63e-11	63
artery	7.30e-11	42
arterial blood vessel	7.30e-11	42
arterial system	7.30e-11	42
squamous epithelium	1.09e-10	25
embryo	2.09e-10	612
endothelium	5.91e-10	18
blood vessel endothelium	5.91e-10	18
cardiovascular system endothelium	5.91e-10	18
embryonic structure	6.98e-10	605
developing anatomical structure	6.98e-10	605
germ layer	1.36e-09	604
embryonic tissue	1.36e-09	604
presumptive structure	1.36e-09	604
epiblast (generic)	1.36e-09	604
simple squamous epithelium	3.80e-09	22
systemic artery	6.32e-09	33
systemic arterial system	6.32e-09	33
compound organ	5.99e-07	69
aorta	9.32e-07	21
aortic system	9.32e-07	21

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	5	22.4631745260087	1.74638470646713e-07	9.5793420356471e-06
E2F1#1869	4	3.92591137190346	0.00721498454710636	0.029882843080395
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00323254030048284
EGR1#1958	5	4.98817909481014	0.000323739800059071	0.00331123895586812
GTF2B#2959	5	31.9438299343242	3.00149609204784e-08	2.03951366530504e-06
MAX#4149	5	6.45255550900712	8.93743970843928e-05	0.00130803989028824
POLR3A#11128	5	339.132110091743	2.18870993324884e-13	3.30327567512392e-11
STAT1#6772	5	20.7065874971992	2.62418353652031e-07	1.35542583763919e-05
STAT3#6774	5	10.5194649971542	7.759040745861e-06	0.000220682586181094
TCF7L2#6934	5	10.7701765631373	6.89693748574565e-06	0.000200141498770155
USF1#7391	5	6.36149927720796	9.59569864925045e-05	0.00137076346769124
USF2#7392	5	12.9921973850696	2.69963551658264e-06	9.43914408156594e-05

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.