Coexpression cluster:C2184

Full id: C2184_diffuse_iPS_acute_Hodgkin_nonsmall_H9_HES3GFP

Phase1 CAGE Peaks

Hg19::chr12:109535373..109535414,+	p1@UNG
Hg19::chr12:96252710..96252789,+	p1@SNRPF
Hg19::chr21:33651324..33651366,-	p1@MIS18A
Hg19::chr22:29137782..29137837,-	p1@CHEK2

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:0004844	uracil DNA N-glycosylase activity	0.0251497912781593
GO:0006974	response to DNA damage stimulus	0.0251497912781593
GO:0009719	response to endogenous stimulus	0.0251497912781593
GO:0016605	PML body	0.0256508083652422
GO:0019104	DNA N-glycosylase activity	0.0256508083652422
GO:0008630	DNA damage response, signal transduction resulting in induction of apoptosis	0.0256508083652422
GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds	0.0256508083652422
GO:0000077	DNA damage checkpoint	0.0256508083652422
GO:0030532	small nuclear ribonucleoprotein complex	0.0256508083652422
GO:0031570	DNA integrity checkpoint	0.0256508083652422
GO:0006284	base-excision repair	0.0256508083652422
GO:0044428	nuclear part	0.0256508083652422
GO:0008629	induction of apoptosis by intracellular signals	0.0256508083652422
GO:0006950	response to stress	0.0265478637208075
GO:0042770	DNA damage response, signal transduction	0.0265478637208075
GO:0000075	cell cycle checkpoint	0.0324006819574708
GO:0005634	nucleus	0.0350096761340437

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	3.05e-23	253
animal cell	6.88e-17	679
eukaryotic cell	6.88e-17	679
native cell	4.23e-10	722
embryonic cell	2.20e-08	250
squamous epithelial cell	4.14e-07	63

Disease

Ontology term	p-value	n
cancer	7.54e-57	235
disease of cellular proliferation	3.44e-55	239
cell type cancer	2.04e-29	143
organ system cancer	1.15e-27	137
hematologic cancer	5.68e-24	51
immune system cancer	5.68e-24	51
carcinoma	1.45e-23	106
leukemia	3.35e-21	39
myeloid leukemia	9.83e-18	31
germ cell and embryonal cancer	8.40e-08	22
germ cell cancer	8.40e-08	22

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
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106296222315667
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000725699407110565
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00995391875589352
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0191989102310887
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185624365292086
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319948004838115
IRF3#3661	2	23.4909761057448	0.00264110142537554	0.0145928468820652
JUNB#3726	3	22.9579744948659	0.000135977250401878	0.00177850069564455
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.0186252523942763
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00886017474017982
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794650919722665
SREBF1#6720	2	23.5029247202441	0.00263845490076824	0.0145813097354923
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321368196316063
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.000967588925626593
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243570410655334

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.