Coexpression cluster:C3854

Full id: C3854_anaplastic_Cardiac_Mesothelial_mesothelioma_mesenchymal_Smooth_squamous

Phase1 CAGE Peaks

Hg19::chr1:12679045..12679065,-	p@chr1:12679045..12679065 -
Hg19::chr1:12679075..12679086,-	p@chr1:12679075..12679086 -
Hg19::chr1:12679100..12679121,-	p@chr1:12679100..12679121 -

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
vascular associated smooth muscle cell	1.27e-11	32
mesodermal cell	3.06e-11	119
muscle cell	4.65e-10	54
contractile cell	8.25e-10	59
smooth muscle cell	1.95e-09	42
smooth muscle myoblast	1.95e-09	42
muscle precursor cell	3.97e-09	57
myoblast	3.97e-09	57
multi-potent skeletal muscle stem cell	3.97e-09	57
electrically responsive cell	3.67e-08	60
electrically active cell	3.67e-08	60
non-terminally differentiated cell	4.65e-07	180

Uber Anatomy

Ontology term	p-value	n
epithelial tube	1.47e-19	118
artery	3.26e-14	42
arterial blood vessel	3.26e-14	42
arterial system	3.26e-14	42
unilaminar epithelium	2.34e-13	138
splanchnic layer of lateral plate mesoderm	4.73e-13	84
systemic artery	2.95e-12	33
systemic arterial system	2.95e-12	33
blood vessel	3.75e-12	60
epithelial tube open at both ends	3.75e-12	60
blood vasculature	3.75e-12	60
vascular cord	3.75e-12	60
mesoderm	4.74e-12	448
mesoderm-derived structure	4.74e-12	448
presumptive mesoderm	4.74e-12	448
circulatory system	1.67e-11	113
vessel	2.02e-11	69
vasculature	4.94e-11	79
vascular system	4.94e-11	79
cardiovascular system	1.36e-10	110
anatomical conduit	1.47e-10	241
trunk mesenchyme	2.01e-10	143
trunk	2.54e-10	216
muscle tissue	1.46e-09	63
musculature	1.46e-09	63
musculature of body	1.46e-09	63
skeletal muscle tissue	3.52e-09	61
striated muscle tissue	3.52e-09	61
myotome	3.52e-09	61
multi-cellular organism	1.11e-08	659
anatomical system	1.89e-08	625
anatomical group	3.15e-08	626
intermediate mesoderm	3.98e-08	37
anatomical cluster	4.42e-08	286
compound organ	7.30e-08	69
mesenchyme	7.71e-08	238
entire embryonic mesenchyme	7.71e-08	238
tube	1.51e-07	194
lateral plate mesoderm	2.74e-07	216

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
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000284585953737729
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115230605190455
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322271510430654
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320696560041235
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462404850684813
EP300#2033	3	6.7739417262232	0.00321688050010379	0.016746475054847
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000676549394309541
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00897629479065518
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.00037113021011499
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.0024306514309895
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00581253645195374
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107225299247973
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154155448860627
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00391328368328375
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00122806253151962
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000756868926858333
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00444228213107465
JUNB#3726	3	30.6106326598211	3.4847716247536e-05	0.00068052741906814
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156803131605878
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.000857567070313067
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186540435232198
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309045138242139
REST#5978	3	9.65002871612802	0.00111263624711459	0.00767672702731061
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165247684839838
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276823015947759
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309056215178124
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246563766100532
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00613914250182467
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197069945956881
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140224772313121
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109429440036211

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.