Coexpression cluster:C2343

Full id: C2343_squamous_malignant_meningioma_embryonic_mesothelioma_bile_papillotubular

Phase1 CAGE Peaks

Hg19::chr15:67418047..67418093,+	p4@SMAD3
Hg19::chr15:67418099..67418118,+	p16@SMAD3
Hg19::chr15:67418119..67418162,+	p5@SMAD3
Hg19::chr15:67418177..67418204,+	p9@SMAD3

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	2.05e-19	254
mesodermal cell	6.26e-18	119
embryonic cell	1.95e-14	248
smooth muscle cell	4.07e-14	42
smooth muscle myoblast	4.07e-14	42
contractile cell	2.64e-13	59
muscle cell	9.02e-13	54
muscle precursor cell	1.14e-12	57
myoblast	1.14e-12	57
multi-potent skeletal muscle stem cell	1.14e-12	57
vascular associated smooth muscle cell	1.54e-12	32
animal cell	9.41e-12	679
eukaryotic cell	9.41e-12	679
non-terminally differentiated cell	5.38e-11	180
squamous epithelial cell	6.91e-10	62
electrically responsive cell	4.34e-09	60
electrically active cell	4.34e-09	60
mesothelial cell	4.92e-09	19

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	4.12e-20	347
mesenchyme	9.97e-19	238
entire embryonic mesenchyme	9.97e-19	238
trunk mesenchyme	1.82e-15	143
multilaminar epithelium	4.59e-14	82
anatomical cluster	4.67e-14	286
trunk	6.53e-14	216
cell layer	1.04e-13	312
epithelial tube	1.34e-13	118
somite	1.57e-13	83
paraxial mesoderm	1.57e-13	83
presomitic mesoderm	1.57e-13	83
presumptive segmental plate	1.57e-13	83
trunk paraxial mesoderm	1.57e-13	83
presumptive paraxial mesoderm	1.57e-13	83
epithelium	3.46e-13	309
unilaminar epithelium	6.61e-13	138
organism subdivision	1.11e-12	365
vasculature	2.39e-12	79
vascular system	2.39e-12	79
artery	2.41e-12	42
arterial blood vessel	2.41e-12	42
arterial system	2.41e-12	42
endoderm-derived structure	2.46e-12	169
endoderm	2.46e-12	169
presumptive endoderm	2.46e-12	169
skeletal muscle tissue	3.36e-12	61
striated muscle tissue	3.36e-12	61
myotome	3.36e-12	61
muscle tissue	1.04e-11	63
musculature	1.04e-11	63
musculature of body	1.04e-11	63
primordium	1.06e-11	168
dermomyotome	5.10e-11	70
digestive system	6.77e-11	155
digestive tract	6.77e-11	155
primitive gut	6.77e-11	155
vessel	9.15e-11	69
blood vessel	9.34e-11	60
epithelial tube open at both ends	9.34e-11	60
blood vasculature	9.34e-11	60
vascular cord	9.34e-11	60
systemic artery	9.46e-11	33
systemic arterial system	9.46e-11	33
splanchnic layer of lateral plate mesoderm	1.60e-10	84
respiratory system	2.26e-10	72
anatomical system	3.11e-09	625
anatomical group	5.05e-09	626
anatomical conduit	6.10e-09	241
respiratory tract	1.85e-08	53
segment of respiratory tract	1.87e-08	46
mesoderm	2.04e-08	448
mesoderm-derived structure	2.04e-08	448
presumptive mesoderm	2.04e-08	448
mixed endoderm/mesoderm-derived structure	3.15e-08	130
cardiovascular system	3.18e-08	110
subdivision of head	3.98e-08	48
multi-cellular organism	5.42e-08	659
circulatory system	6.59e-08	113
surface structure	1.90e-07	95
germ layer	2.04e-07	604
embryonic tissue	2.04e-07	604
presumptive structure	2.04e-07	604
epiblast (generic)	2.04e-07	604
embryonic structure	2.19e-07	605
developing anatomical structure	2.19e-07	605
foregut	2.48e-07	98
respiratory primordium	2.82e-07	38
endoderm of foregut	2.82e-07	38
endo-epithelium	4.62e-07	82

Disease

Ontology term	p-value	n
carcinoma	2.82e-08	106
squamous cell carcinoma	4.56e-07	14

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
BRCA1#672	4	20.1842306432238	6.02116732184487e-06	0.000179362434091887
CEBPB#1051	4	7.97114762582482	0.000247638578809083	0.00267789661754419
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106403008498114
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00433765761647554
ESR1#2099	4	30.7686032961545	1.11467714392546e-06	4.59959566315412e-05
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00194701016754358
FOSL1#8061	4	39.713579716373	4.01511434669553e-07	1.93688003350824e-05
FOXA1#3169	4	11.0814197493855	6.62943068949433e-05	0.00106946418254572
GATA2#2624	4	12.744931733554	3.78864877853583e-05	0.000720996154849679
GATA3#2625	4	27.236516357206	1.81561517799785e-06	6.76251902906266e-05
JUN#3725	4	12.5128291923363	4.07770316866756e-05	0.000742065239993851
JUNB#3726	4	30.6106326598211	1.13787152942193e-06	4.65120018243825e-05
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00391198296338935
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00485034024108237
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.00142206354858194
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00886800965973278
NR3C1#2908	4	14.973023331173	1.98868032687801e-05	0.000442282335304115
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00129190673302761
RFX5#5993	4	12.0479108271951	4.74457429336527e-05	0.000826001991373188
SMARCB1#6598	4	18.2527157811574	9.00423392720929e-06	0.00024106464678898
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000437237842485976
STAT1#6772	4	20.7065874971992	5.43610708103893e-06	0.000165137169120601
STAT3#6774	4	10.5194649971542	8.16377768286615e-05	0.00123014972936208
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321788721993419
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243860337079867
TCF7L2#6934	4	10.7701765631373	7.42969445082454e-05	0.00115245783268924
TFAP2A#7020	4	16.518634373045	1.34240829060362e-05	0.000326349579754077
TFAP2C#7022	4	10.8092286098602	7.32289634782688e-05	0.00114456146613393
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346198026886187

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.