Coexpression cluster:C928

Full id: C928_Retinal_Cardiac_mesothelioma_Renal_Meningeal_Smooth_Astrocyte

Phase1 CAGE Peaks

Hg19::chr1:12677510..12677525,-	p3@DHRS3
Hg19::chr1:12677714..12677729,-	p4@DHRS3
Hg19::chr1:12677781..12677800,-	p2@DHRS3
Hg19::chr1:12678119..12678130,-	p14@DHRS3
Hg19::chr1:12678194..12678203,-	p13@DHRS3
Hg19::chr1:12678204..12678238,-	p1@DHRS3
Hg19::chr1:12678241..12678252,-	p11@DHRS3
Hg19::chr1:12678258..12678280,-	p8@DHRS3
Hg19::chr1:12679956..12679993,-	p@chr1:12679956..12679993 -

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	7.30e-16	119
contractile cell	2.57e-14	59
muscle cell	2.93e-14	54
smooth muscle cell	2.02e-13	42
smooth muscle myoblast	2.02e-13	42
muscle precursor cell	6.77e-13	57
myoblast	6.77e-13	57
multi-potent skeletal muscle stem cell	6.77e-13	57
vascular associated smooth muscle cell	1.02e-12	32
electrically responsive cell	7.72e-12	60
electrically active cell	7.72e-12	60
embryonic cell	1.98e-08	248
fat cell	2.60e-07	15
non-terminally differentiated cell	6.54e-07	180

Uber Anatomy

Ontology term	p-value	n
anatomical conduit	8.53e-20	241
epithelial tube	1.79e-19	118
epithelium	3.34e-18	309
unilaminar epithelium	4.93e-18	138
cell layer	4.94e-18	312
anatomical cluster	5.18e-18	286
multi-tissue structure	1.74e-17	347
organism subdivision	8.26e-17	365
trunk	9.90e-17	216
tube	4.38e-16	194
trunk mesenchyme	6.41e-16	143
muscle tissue	9.04e-14	63
musculature	9.04e-14	63
musculature of body	9.04e-14	63
skeletal muscle tissue	1.94e-13	61
striated muscle tissue	1.94e-13	61
myotome	1.94e-13	61
mesenchyme	8.82e-13	238
entire embryonic mesenchyme	8.82e-13	238
multi-cellular organism	6.16e-12	659
artery	6.79e-12	42
arterial blood vessel	6.79e-12	42
arterial system	6.79e-12	42
vasculature	1.79e-11	79
vascular system	1.79e-11	79
blood vessel	2.00e-11	60
epithelial tube open at both ends	2.00e-11	60
blood vasculature	2.00e-11	60
vascular cord	2.00e-11	60
vessel	1.73e-10	69
systemic artery	3.38e-10	33
systemic arterial system	3.38e-10	33
splanchnic layer of lateral plate mesoderm	4.08e-10	84
intermediate mesoderm	1.27e-09	37
anatomical system	3.51e-09	625
circulatory system	3.71e-09	113
dermomyotome	5.08e-09	70
anatomical group	6.56e-09	626
cardiovascular system	8.31e-09	110
immaterial anatomical entity	1.44e-08	126
compound organ	3.79e-08	69
multilaminar epithelium	3.98e-08	82
embryo	5.75e-08	612
subdivision of trunk	6.05e-08	113
embryonic structure	1.84e-07	605
developing anatomical structure	1.84e-07	605
pigment epithelium of eye	2.43e-07	11
germ layer	3.10e-07	604
embryonic tissue	3.10e-07	604
presumptive structure	3.10e-07	604
epiblast (generic)	3.10e-07	604
body cavity precursor	4.60e-07	63
duct	6.12e-07	26
abdominal segment of trunk	9.81e-07	61
abdomen	9.81e-07	61

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	5	3.52011198720146	0.00704556022641387	0.0293967985492565
CEBPB#1051	5	4.42841534768045	0.0025225868523706	0.0139876001207716
CHD2#1106	5	5.74667935228714	0.000761042370922	0.00597657750031752
CTBP2#1488	6	41.8113335595521	1.31796279068549e-09	1.1876334417291e-07
E2F6#1876	8	4.45969398373101	1.843503537119e-05	0.000419098097329498
EBF1#1879	5	4.94803713698278	0.00152000342508516	0.00968977828923088
GTF2B#2959	7	24.84520106003	9.99944740019878e-10	9.2829536624832e-08
HEY1#23462	6	2.69340736207047	0.00948764347376227	0.0357447421361516
HMGN3#9324	5	4.54363762408366	0.00224461831902441	0.012891866070204
MAX#4149	5	3.58475306055951	0.00650226248509667	0.0278441015080984
MXI1#4601	5	5.53420646042183	0.00090661270204698	0.00660244920082871
PBX3#5090	5	12.1747292704134	2.1331797509613e-05	0.000470213507831675
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00728788320845237
REST#5978	4	4.28890165161245	0.00945702594596283	0.0356679907829407
SIN3A#25942	8	4.80789753494679	1.02597602607548e-05	0.000268013782359423
SMARCC1#6599	7	33.9603905819356	1.13716814408286e-10	1.22564193807915e-08
TAF1#6872	8	2.97159669844026	0.000423374995123481	0.00395960070884761
TBP#6908	8	3.29490727741901	0.000191885322027247	0.00231572811962141
TCF7L2#6934	5	5.98343142396519	0.000630515439732144	0.00518466278326001
TFAP2C#7022	4	4.80410160438232	0.00629930343474712	0.0277873353362711
YY1#7528	6	3.2741138332359	0.00337595890254982	0.0172428487785309
ZNF263#10127	5	4.56768979833926	0.00219130580900913	0.0126336068113224

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.