Coexpression cluster:C1332

Full id: C1332_lymphoma_Reticulocytes_chronic_embryonic_Renal_Hodgkin_Alveolar

Phase1 CAGE Peaks

Hg19::chr11:118966167..118966182,-	p1@H2AFX
Hg19::chr16:29802036..29802086,+	p1@KIF22
Hg19::chr19:36545781..36545828,+	p1@WDR62
Hg19::chr22:35796108..35796172,+	p1@MCM5
Hg19::chr22:42343092..42343107,-	p2@CENPM
Hg19::chr22:42343117..42343181,-	p1@CENPM

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:0044427	chromosomal part	0.000875186642580658
GO:0005694	chromosome	0.000875186642580658
GO:0000775	chromosome, pericentric region	0.00112284037717332
GO:0000279	M phase	0.0136644533982684
GO:0022403	cell cycle phase	0.015865546315125
GO:0005634	nucleus	0.019196970695774
GO:0000724	double-strand break repair via homologous recombination	0.0201244507432831
GO:0000725	recombinational repair	0.0201244507432831
GO:0022402	cell cycle process	0.0246058068434886
GO:0043232	intracellular non-membrane-bound organelle	0.0246058068434886
GO:0043228	non-membrane-bound organelle	0.0246058068434886
GO:0007049	cell cycle	0.0273338469233302
GO:0000776	kinetochore	0.0273338469233302
GO:0005657	replication fork	0.0273338469233302
GO:0003677	DNA binding	0.0273338469233302
GO:0006302	double-strand break repair	0.0273338469233302
GO:0006270	DNA replication initiation	0.0273338469233302
GO:0043231	intracellular membrane-bound organelle	0.0273338469233302
GO:0043227	membrane-bound organelle	0.0273338469233302
GO:0003684	damaged DNA binding	0.0328162701163738
GO:0044446	intracellular organelle part	0.0338266050298457
GO:0044422	organelle part	0.0338266050298457
GO:0006259	DNA metabolic process	0.0365414791603242
GO:0051327	M phase of meiotic cell cycle	0.0365414791603242
GO:0007126	meiosis	0.0365414791603242
GO:0051321	meiotic cell cycle	0.0365414791603242
GO:0008094	DNA-dependent ATPase activity	0.039664069222455
GO:0043229	intracellular organelle	0.039664069222455
GO:0043226	organelle	0.039664069222455
GO:0006996	organelle organization and biogenesis	0.0432719300434897

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
animal cell	8.38e-18	679
eukaryotic cell	8.38e-18	679
epithelial cell	4.16e-15	254
native cell	2.47e-13	722
embryonic cell	1.80e-08	248
migratory neural crest cell	2.91e-08	41

Disease

Ontology term	p-value	n
cancer	9.20e-33	235
disease of cellular proliferation	4.45e-31	239
hematologic cancer	8.83e-22	51
immune system cancer	8.83e-22	51
organ system cancer	2.89e-19	137
leukemia	2.91e-17	39
cell type cancer	1.05e-13	143
myeloid leukemia	6.94e-13	31
carcinoma	7.64e-12	106

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)
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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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No analysis results for this cluster

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.