Coexpression cluster:C4393

Full id: C4393_Reticulocytes_Burkitt_Dendritic_non_lymphoma_acute_NK

Phase1 CAGE Peaks

Hg19::chr4:174254864..174254925,-	p3@HMGB2
Hg19::chr4:71859385..71859407,+	p2@DCK
Hg19::chr4:71859413..71859473,+	p3@DCK

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:0004137	deoxycytidine kinase activity	0.00571058518780172
GO:0006288	base-excision repair, DNA ligation	0.0085656256290494
GO:0051103	DNA ligation during DNA repair	0.00951708164044024
GO:0019136	deoxynucleoside kinase activity	0.00999264154436685
GO:0006266	DNA ligation	0.0102764813809805
GO:0008301	DNA bending activity	0.0102764813809805
GO:0019206	nucleoside kinase activity	0.0102764813809805
GO:0006268	DNA unwinding during replication	0.0102764813809805
GO:0032392	DNA geometric change	0.0102764813809805
GO:0032508	DNA duplex unwinding	0.0102764813809805
GO:0006284	base-excision repair	0.0181609510018751
GO:0000793	condensed chromosome	0.0247272939016887
GO:0003697	single-stranded DNA binding	0.0260813256323868
GO:0048471	perinuclear region of cytoplasm	0.0260813256323868
GO:0006220	pyrimidine nucleotide metabolic process	0.0262424007472481
GO:0019205	nucleobase, nucleoside, nucleotide kinase activity	0.0324359297091708
GO:0000228	nuclear chromosome	0.0332077924654081
GO:0003690	double-stranded DNA binding	0.0342095504590265
GO:0048015	phosphoinositide-mediated signaling	0.0386988232117492
GO:0043566	structure-specific DNA binding	0.0447605780502602
GO:0006261	DNA-dependent DNA replication	0.0447605780502602
GO:0006334	nucleosome assembly	0.0484070896480807

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
lymphocyte	8.23e-11	53
common lymphoid progenitor	8.23e-11	53
lymphocyte of B lineage	1.57e-10	24
pro-B cell	1.57e-10	24
lymphoid lineage restricted progenitor cell	2.70e-10	52
hematopoietic stem cell	9.90e-07	172
angioblastic mesenchymal cell	9.90e-07	172

Disease

Ontology term	p-value	n
cancer	2.38e-25	235
disease of cellular proliferation	1.83e-24	239
hematologic cancer	2.61e-24	51
immune system cancer	2.61e-24	51
leukemia	9.89e-20	39
organ system cancer	2.58e-17	137
myeloid leukemia	2.73e-15	31
cell type cancer	1.13e-08	143
carcinoma	2.34e-08	106
lymphoma	2.89e-07	10

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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259670221356022
BHLHE40#8553	2	29.9145423646516	0.00146748352710614	0.00939972475237281
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190710583938144
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326868701886637
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438287946881867
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323671703700491
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321837348753132
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298355926870299
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390301696918379
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140667618987271

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.