Coexpression cluster:C3943

Full id: C3943_neuroblastoma_hepatoblastoma_testicular_chronic_pineal_gastrointestinal_nonsmall

Phase1 CAGE Peaks

Hg19::chr1:225117350..225117409,+	p1@DNAH14
Hg19::chr1:225117410..225117417,+	p6@DNAH14
Hg19::chr1:225117419..225117430,+	p4@DNAH14

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>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	6.15e-16	254

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	4.77e-09	347
digestive system	1.14e-08	155
digestive tract	1.14e-08	155
primitive gut	1.14e-08	155
endoderm-derived structure	7.38e-08	169
endoderm	7.38e-08	169
presumptive endoderm	7.38e-08	169
anatomical space	1.65e-07	104
subdivision of digestive tract	3.50e-07	129
endodermal part of digestive tract	3.50e-07	129
primordium	6.29e-07	168
body cavity	9.06e-07	46
immaterial anatomical entity	9.40e-07	126

Disease

Ontology term	p-value	n
disease of cellular proliferation	8.85e-34	239
cell type cancer	1.45e-33	143
cancer	1.70e-33	235
carcinoma	1.49e-28	106
organ system cancer	3.14e-10	137
germ cell and embryonal cancer	7.21e-07	22
germ cell cancer	7.21e-07	22

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	0.0190162869642973
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00660693774138503
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.032559205920425
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322472592369853
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320867774312699
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462642078701786
EP300#2033	3	6.7739417262232	0.00321688050010379	0.016759005464675
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154219747275167
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00388064388510327
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00437042755313833
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000851907128508202
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00434199467311013
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186683776263978
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294726436354253
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00471359185956224
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000358947988990857
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276997301162416
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154957866056757
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00642997522164751
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054340948515511
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000647223491362815
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190408051724412
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329650446620966
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140322109030339

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.