Coexpression cluster:C3884

Full id: C3884_large_Sebocyte_anaplastic_Keratinocyte_retinoblastoma_papillotubular_carcinoid

Phase1 CAGE Peaks

Hg19::chr1:156783780..156783794,-	p7@SH2D2A
Hg19::chr1:156783824..156783836,-	p9@SH2D2A
Hg19::chr1:156783894..156783917,-	p2@SH2D2A

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	1.32e-17	253

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	5.77e-11	160
endoderm	5.77e-11	160
presumptive endoderm	5.77e-11	160
respiratory primordium	2.12e-09	38
endoderm of foregut	2.12e-09	38
endo-epithelium	5.22e-09	82
digestive system	6.28e-09	145
digestive tract	6.28e-09	145
primitive gut	6.28e-09	145
respiratory tract	7.55e-09	54
larynx	1.22e-08	9
segment of respiratory tract	1.09e-07	47
subdivision of digestive tract	1.31e-07	118
respiratory system	2.99e-07	74
epithelium of mucosa	9.19e-07	8

Disease

Ontology term	p-value	n
carcinoma	1.06e-21	106
cell type cancer	3.92e-17	143
cancer	2.14e-15	235
disease of cellular proliferation	4.87e-15	239
chronic leukemia	1.42e-07	8

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	0.0190110031946489
CTCF#10664	3	5.36025637307503	0.006492509252767	0.027954781243805
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171820418002735
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325484124159392
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322372020043668
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320782144330991
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046248389965409
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00762636539539124
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154187591364559
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108756923241049
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186603119839112
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00720481324911683
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294631695666712
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000358786227842146
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276904321746929
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203117682806661
SMARCC1#6599	3	43.6633593196315	1.20046018043203e-05	0.000301889864637951
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309149698606793
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154917039323505
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190354440822941
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421769199105508
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140269680166544

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.