Coexpression cluster:C2388

Full id: C2388_granulocyte_non_Hodgkin_Burkitt_acute_Reticulocytes_embryonic

Phase1 CAGE Peaks

Hg19::chr16:72698834..72698913,-	p@chr16:72698834..72698913 -
Hg19::chr1:93646238..93646298,+	p1@CCDC18
Hg19::chr3:121264813..121264846,-	p1@POLQ
Hg19::chr3:121264848..121264859,-	p2@POLQ

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:0003887	DNA-directed DNA polymerase activity	0.0288472860002355
GO:0003684	damaged DNA binding	0.0288472860002355

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 of B lineage	1.99e-08	24
pro-B cell	1.99e-08	24
hematopoietic stem cell	9.02e-07	172
angioblastic mesenchymal cell	9.02e-07	172

Disease

Ontology term	p-value	n
cancer	2.09e-47	235
disease of cellular proliferation	8.20e-46	239
organ system cancer	6.57e-27	137
hematologic cancer	1.29e-26	51
immune system cancer	1.29e-26	51
leukemia	2.62e-21	39
cell type cancer	9.66e-21	143
myeloid leukemia	9.97e-17	31
carcinoma	1.87e-16	106
lymphoma	7.51e-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
CEBPB#1051	3	5.97836071936861	0.00715383248472697	0.0297238666005888
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.010644704166746
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000726349558881852
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.010139476168106
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160788564772538
ELK4#2005	3	12.176761243851	0.000891263257762061	0.0066364354325832
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154472176800309
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390112997896421
GATA3#2625	2	13.618258178603	0.0076966520809334	0.0316905439259059
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.018587083163447
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.0030729973218624
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188305777222278
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123839337753342
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795687443455428
SIX5#147912	3	12.8150365165942	0.000766447113693038	0.00601540317930317
SMARCC2#6601	2	47.0776872134488	0.000666928296709587	0.00545060837155118
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00683757176786396
SP2#6668	3	19.6151478703835	0.000217100426924534	0.00248588438631415
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.032190022189709
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243946373802982
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106744308365082
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00976482771434353
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.0279682105846715

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.