Coexpression cluster:C2586

Full id: C2586_Alveolar_acute_Renal_Mesenchymal_Bronchial_Trabecular_Corneal

Phase1 CAGE Peaks

Hg19::chr1:43824577..43824636,+	p2@CDC20
Hg19::chr1:43824639..43824659,+	p1@CDC20
Hg19::chr1:43824669..43824680,+	p3@CDC20
Hg19::chr9:89626496..89626506,+	p1@CDC20P1

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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GO ID	GO name	FDR corrected p-value
GO:0005819	spindle	0.0375988370513273
GO:0007067	mitosis	0.0375988370513273
GO:0000087	M phase of mitotic cell cycle	0.0375988370513273
GO:0051301	cell division	0.0375988370513273
GO:0006511	ubiquitin-dependent protein catabolic process	0.0375988370513273
GO:0043632	modification-dependent macromolecule catabolic process	0.0375988370513273
GO:0019941	modification-dependent protein catabolic process	0.0375988370513273
GO:0051603	proteolysis involved in cellular protein catabolic process	0.0375988370513273
GO:0044257	cellular protein catabolic process	0.0375988370513273
GO:0000279	M phase	0.0375988370513273
GO:0000278	mitotic cell cycle	0.0375988370513273
GO:0030163	protein catabolic process	0.0375988370513273
GO:0022403	cell cycle phase	0.0375988370513273
GO:0043285	biopolymer catabolic process	0.0427774430153552
GO:0015630	microtubule cytoskeleton	0.0427774430153552
GO:0044265	cellular macromolecule catabolic process	0.0427774430153552
GO:0006512	ubiquitin cycle	0.0427774430153552
GO:0022402	cell cycle process	0.0435730353789808
GO:0009057	macromolecule catabolic process	0.0435730353789808

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
animal cell	9.69e-24	679
eukaryotic cell	9.69e-24	679
epithelial cell	1.53e-23	254
embryonic cell	3.70e-17	248
native cell	2.89e-12	722
non-terminally differentiated cell	1.52e-10	180
squamous epithelial cell	1.31e-09	62
mesodermal cell	5.13e-08	119
somatic cell	2.21e-07	591
lining cell	9.17e-07	57
barrier cell	9.17e-07	57

Uber Anatomy

Ontology term	p-value	n
mesenchyme	1.45e-07	238
entire embryonic mesenchyme	1.45e-07	238
simple squamous epithelium	5.53e-07	22
segment of respiratory tract	6.93e-07	46

Disease

Ontology term	p-value	n
cancer	1.58e-31	235
disease of cellular proliferation	3.14e-30	239
organ system cancer	7.05e-16	137
hematologic cancer	1.01e-14	51
immune system cancer	1.01e-14	51
cell type cancer	1.64e-14	143
leukemia	2.45e-12	39
carcinoma	1.59e-11	106
myeloid leukemia	1.34e-09	31

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	3	15.1381729824178	0.000468218442143119	0.00430232851301999
CHD2#1106	3	7.75801712558764	0.00335152246453634	0.017300793528752
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.0109296345669203
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418993027246035
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0192068374775942
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234709210693462
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.037864515152586
HDAC2#3066	3	10.0617151774697	0.0015637275447474	0.00992489462448336
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0320117565048121
IRF3#3661	3	35.2364641586172	3.79279212646878e-05	0.000720078925461322
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466301099251896
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.018635912146684
NFYA#4800	3	13.8191855248729	0.000613241180673451	0.00508828916090844
NFYB#4801	3	12.5698449401523	0.00081145639769735	0.00619002956096075
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0435038218421297
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227643849772861
SP2#6668	3	19.6151478703835	0.000217100426924534	0.00248642959618065
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140360848225831
ZBTB33#10009	3	23.7485437724859	0.000122945190881838	0.00165574117221255

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.