Coexpression cluster:C3660

Full id: C3660_breast_medulloblastoma_acute_rhabdomyosarcoma_prostate_Myoblast_neuroblastoma

Phase1 CAGE Peaks

Hg19::chr17:57233023..57233037,+	p3@PRR11
Hg19::chr17:57233046..57233064,+	p2@PRR11
Hg19::chr17:57233087..57233146,+	p1@PRR11

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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No GOStat results

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	6.84e-18	679
eukaryotic cell	6.84e-18	679
epithelial cell	7.01e-15	253
native cell	4.74e-11	722
embryonic cell	3.09e-09	250
squamous epithelial cell	2.84e-08	63

Disease

Ontology term	p-value	n
cancer	9.10e-43	235
disease of cellular proliferation	4.52e-41	239
cell type cancer	5.30e-21	143
organ system cancer	1.52e-18	137
hematologic cancer	3.60e-16	51
immune system cancer	3.60e-16	51
carcinoma	9.84e-16	106
leukemia	9.51e-13	39
myeloid leukemia	4.20e-11	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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129529091012848
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115153377194796
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324957470187304
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436648512242506
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321769901013274
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320293705588195
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00896731007269143
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387633325596125
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127944913952397
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253486488561215
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156585885887828
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186343700353238
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719646923213782
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294182507926077
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269363200786714
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199411797252812
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245589496555343
PRDM1#639	2	87.8873038516405	0.000171624884802908	0.00209103258795275
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00484190285637849
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000358463142540172
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276370899124526
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246241038657992
SP2#6668	2	17.4356869958964	0.00427356848176974	0.0203153035351638
STAT2#6773	3	65.2637711864407	3.59360517547754e-06	0.00011828318024636
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000719607582971806
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00613013752565771
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247991907154861
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00615054002547855
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00196974396892174
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328961624792206
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109308481320713

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.