Coexpression cluster:C4120

Full id: C4120_giant_peripheral_Mast_embryonic_acute_chronic_Mammary

Phase1 CAGE Peaks

Hg19::chr2:122494439..122494459,-	p1@MKI67IP
Hg19::chr2:122494462..122494477,-	p2@MKI67IP
Hg19::chr6:111303231..111303301,+	p1@RPF2

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:0009303	rRNA transcription	0.0168373955021783
GO:0000794	condensed nuclear chromosome	0.0200753561756741
GO:0000793	condensed chromosome	0.022449860669571
GO:0016072	rRNA metabolic process	0.0239609089838691
GO:0000228	nuclear chromosome	0.0256446485340869
GO:0005730	nucleolus	0.035617567408454

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	9.45e-14	679
eukaryotic cell	9.45e-14	679
native cell	1.43e-10	722
epithelial cell	4.57e-08	253

Disease

Ontology term	p-value	n
disease of cellular proliferation	6.52e-48	239
cancer	1.64e-46	235
cell type cancer	1.07e-23	143
organ system cancer	1.04e-21	137
carcinoma	6.94e-19	106
hematologic cancer	4.07e-16	51
immune system cancer	4.07e-16	51
leukemia	1.76e-13	39
myeloid leukemia	1.96e-10	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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190409834408743
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115430591124892
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326072637889422
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323001628301244
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463323483373277
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763612237758183
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154404904355468
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128351199471654
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186917175868847
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721268413618401
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295082257236004
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270065567002324
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173214813107275
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277369844079963
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00544171274152991
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190694487304291
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330008292885313

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.