Coexpression cluster:C3998

Full id: C3998_merkel_neuroepithelioma_small_medulloblastoma_acute_Hodgkin_retinoblastoma

Phase1 CAGE Peaks

Hg19::chr1:840185..840202,+	p@chr1:840185..840202 +
Hg19::chr1:840205..840230,+	p@chr1:840205..840230 +
Hg19::chr1:840237..840249,+	p@chr1:840237..840249 +

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><br><br>disease_data<br>

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Disease

Ontology term	p-value	n
cancer	3.45e-13	235
disease of cellular proliferation	3.45e-12	239
cell type cancer	6.04e-12	143
neuroectodermal tumor	4.81e-08	10
sarcoma	1.40e-07	20

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
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000527302200247482
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.00139281165834784
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190250997768676
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660832604517603
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279766957069659
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171972953567227
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322661334717502
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321026922770007
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462847873296247
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00763098401382597
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000371461133173496
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154276052403781
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434460943246248
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108825124948799
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186764502444076
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294868661682449
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173070027394677
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066468585203979
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768485001074007
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000359109896067533
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277136887422608
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309368046693792
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109152933565484
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00543747794562211
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000647595316424877
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190524312335582
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329773754186845
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140374577101661
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389458731097257
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109537893396009

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.