Coexpression cluster:C2764

Full id: C2764_Smooth_Lens_Renal_Ciliary_Mesothelial_mucinous_glioblastoma

Phase1 CAGE Peaks

Hg19::chr3:98620486..98620493,-	p4@DCBLD2
Hg19::chr3:98620500..98620547,-	p1@DCBLD2
Hg19::chr3:98620631..98620663,-	p13@DCBLD2
Hg19::chr3:98620849..98620854,-	p32@DCBLD2

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
embryonic cell	5.84e-37	248
non-terminally differentiated cell	8.50e-36	180
mesodermal cell	7.49e-21	119
muscle precursor cell	5.29e-19	57
myoblast	5.29e-19	57
multi-potent skeletal muscle stem cell	5.29e-19	57
animal cell	5.26e-18	679
eukaryotic cell	5.26e-18	679
contractile cell	8.54e-18	59
muscle cell	1.53e-17	54
epithelial cell	1.02e-16	254
electrically responsive cell	1.75e-16	60
electrically active cell	1.75e-16	60
smooth muscle cell	6.06e-16	42
smooth muscle myoblast	6.06e-16	42
vascular associated smooth muscle cell	1.02e-15	32
fibroblast	9.88e-13	75
somatic cell	7.49e-11	591
ectodermal cell	3.77e-10	71
neurectodermal cell	6.63e-08	59
native cell	1.61e-07	722

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	1.04e-24	143
cell layer	2.58e-23	312
organism subdivision	7.95e-23	365
epithelium	1.13e-22	309
epithelial tube	6.91e-21	118
multilaminar epithelium	1.43e-20	82
trunk	7.30e-20	216
somite	3.74e-19	83
paraxial mesoderm	3.74e-19	83
presomitic mesoderm	3.74e-19	83
presumptive segmental plate	3.74e-19	83
trunk paraxial mesoderm	3.74e-19	83
presumptive paraxial mesoderm	3.74e-19	83
dermomyotome	1.81e-18	70
unilaminar epithelium	1.99e-18	138
multi-tissue structure	1.79e-17	347
skeletal muscle tissue	5.76e-17	61
striated muscle tissue	5.76e-17	61
myotome	5.76e-17	61
mesenchyme	1.25e-16	238
entire embryonic mesenchyme	1.25e-16	238
vasculature	1.84e-16	79
vascular system	1.84e-16	79
muscle tissue	4.40e-16	63
musculature	4.40e-16	63
musculature of body	4.40e-16	63
artery	1.84e-15	42
arterial blood vessel	1.84e-15	42
arterial system	1.84e-15	42
multi-cellular organism	5.22e-15	659
anatomical system	7.95e-14	625
anatomical group	1.45e-13	626
splanchnic layer of lateral plate mesoderm	3.37e-13	84
blood vessel	3.96e-13	60
epithelial tube open at both ends	3.96e-13	60
blood vasculature	3.96e-13	60
vascular cord	3.96e-13	60
vessel	6.27e-13	69
systemic artery	1.08e-12	33
systemic arterial system	1.08e-12	33
anatomical cluster	3.75e-11	286
primordium	6.79e-11	168
anatomical conduit	1.52e-10	241
embryonic structure	1.67e-10	605
developing anatomical structure	1.67e-10	605
cardiovascular system	1.69e-10	110
germ layer	1.75e-10	604
embryonic tissue	1.75e-10	604
presumptive structure	1.75e-10	604
epiblast (generic)	1.75e-10	604
embryo	1.99e-10	612
circulatory system	3.58e-10	113
surface structure	6.12e-09	95
tube	2.06e-08	194
pigment epithelium of eye	1.09e-07	11
immaterial anatomical entity	1.20e-07	126
integument	1.66e-07	45
integumental system	1.66e-07	45
body cavity precursor	3.30e-07	63
ectodermal placode	4.40e-07	29
anatomical space	6.32e-07	104

Disease

Ontology term	p-value	n
ovarian cancer	4.12e-08	14
female reproductive organ cancer	3.51e-07	27
reproductive organ cancer	6.16e-07	29

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	4	6.33620157696263	0.000620310058721564	0.00513145047309477
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.00129245224462406
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106686716229489
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.0099846742300575
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101590186144939
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161171996836281
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00434868813829926
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00195202085547476
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186445516696366
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0320166043837361
MYC#4609	4	5.2222818716094	0.00134430939527274	0.0088893458865955
NFYA#4800	4	18.4255806998305	8.67100748407158e-06	0.000234974403380631
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00619229100680356
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.043515941164299
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188586411763592
RFX5#5993	4	12.0479108271951	4.74457429336527e-05	0.000827795848020006
SP1#6667	4	5.6983813781409	0.000948260606533398	0.006853185903103
SP2#6668	4	26.1535304938446	2.13562021071447e-06	7.75798397171509e-05
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322957100063927
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140375937545141
TBP#6908	4	3.70677068709639	0.00529637781478435	0.024478842439185
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00249589380959154

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.