Coexpression cluster:C277

Full id: C277_mesothelioma_epithelioid_thyroid_extraskeletal_alveolar_glioblastoma_adenocarcinoma

Phase1 CAGE Peaks

Hg19::chr11:28792916..28792929,+	p@chr11:28792916..28792929 +
Hg19::chr14:36642956..36642966,+	p@chr14:36642956..36642966 +
Hg19::chr14:36642986..36642989,+	p@chr14:36642986..36642989 +
Hg19::chr14:36643089..36643094,+	p@chr14:36643089..36643094 +
Hg19::chr19:21452679..21452684,-	p@chr19:21452679..21452684 -
Hg19::chr19:21452690..21452695,-	p@chr19:21452690..21452695 -
Hg19::chr19:21452713..21452724,-	p@chr19:21452713..21452724 -
Hg19::chr19:23015117..23015128,+	p@chr19:23015117..23015128 +
Hg19::chr19:36909811..36909826,-	p3@ZFP82
Hg19::chr19:36909838..36909849,-	p5@ZFP82
Hg19::chr19:36914887..36914892,-	p@chr19:36914887..36914892 -
Hg19::chr19:37264112..37264129,+	p2@uc002oes.1
Hg19::chr19:37264138..37264154,+	p4@uc002oes.1
Hg19::chr19:37464799..37464817,+	p@chr19:37464799..37464817 +
Hg19::chr19:38104849..38104860,+	p@chr19:38104849..38104860 +
Hg19::chr19:38145832..38145833,-	p@chr19:38145832..38145833 -
Hg19::chr19:38182936..38182940,-	p@chr19:38182936..38182940 -
Hg19::chr19:38182963..38182975,-	p@chr19:38182963..38182975 -
Hg19::chr19:38183029..38183044,-	p@chr19:38183029..38183044 -
Hg19::chr19:38210552..38210570,-	p2@ZNF607
Hg19::chr19:38281159..38281170,+	p@chr19:38281159..38281170 +
Hg19::chr19:38281171..38281178,+	p@chr19:38281171..38281178 +
Hg19::chr19:41727698..41727705,+	p@chr19:41727698..41727705 +
Hg19::chr19:44331295..44331299,-	p4@ENST00000499389 p4@uc002oxo.1
Hg19::chr19:44331304..44331307,-	p5@ENST00000499389 p5@uc002oxo.1
Hg19::chr19:44331332..44331339,-	p3@ENST00000499389 p3@uc002oxo.1
Hg19::chr19:44331593..44331618,+	p5@ZNF283
Hg19::chr19:44331766..44331774,+	p@chr19:44331766..44331774 +
Hg19::chr19:44331769..44331809,-	p2@ENST00000499389 p2@uc002oxo.1
Hg19::chr19:44331884..44331893,+	p8@ZNF283
Hg19::chr19:44331916..44331929,+	p6@ZNF283
Hg19::chr19:44405623..44405636,-	p1@uc002oxt.2
Hg19::chr19:44405761..44405769,-	p2@uc002oxt.2
Hg19::chr19:44405872..44405879,+	p@chr19:44405872..44405879 +
Hg19::chr19:52932395..52932413,+	p1@ZNF534
Hg19::chr19:52932444..52932455,+	p2@ZNF534
Hg19::chr19:56879625..56879636,+	p5@ZNF542
Hg19::chr19:56879817..56879825,+	p4@ZNF542
Hg19::chr19:9406118..9406133,-	p@chr19:9406118..9406133 -
Hg19::chr19:9420326..9420349,-	p2@ZNF699
Hg19::chr1:240926680..240926686,+	p@chr1:240926680..240926686 +
Hg19::chr21:47460896..47460904,+	p@chr21:47460896..47460904 +
Hg19::chr21:47461437..47461440,+	p@chr21:47461437..47461440 +
Hg19::chr5:1380178..1380183,-	p1@ENST00000504989 p1@uc003jcj.1
Hg19::chr5:178696464..178696469,-	p@chr5:178696464..178696469 -
Hg19::chr6:2938437..2938442,-	p@chr6:2938437..2938442 -
Hg19::chr8:90710257..90710295,+	p@chr8:90710257..90710295 +

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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p.value	FDR	nGenes	nPathway	Name
1.69712115516446e-07	0.00010742776912191	4	390	{ASH2L,391} (Static Module):NA

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:0006355	regulation of transcription, DNA-dependent	0.000694105102075861
GO:0006351	transcription, DNA-dependent	0.000694105102075861
GO:0032774	RNA biosynthetic process	0.000694105102075861
GO:0045449	regulation of transcription	0.000694105102075861
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.000694105102075861
GO:0006350	transcription	0.000694105102075861
GO:0010468	regulation of gene expression	0.000694105102075861
GO:0031323	regulation of cellular metabolic process	0.000694105102075861
GO:0019222	regulation of metabolic process	0.000694105102075861
GO:0016070	RNA metabolic process	0.000694105102075861
GO:0008270	zinc ion binding	0.000694105102075861
GO:0046914	transition metal ion binding	0.00122601820250566
GO:0010467	gene expression	0.00173584310847537
GO:0050794	regulation of cellular process	0.00192843172763104
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00198867441603267
GO:0050789	regulation of biological process	0.00226568844957581
GO:0003676	nucleic acid binding	0.00248129964629139
GO:0043169	cation binding	0.0025249278869468
GO:0065007	biological regulation	0.00275580653910112
GO:0046872	metal ion binding	0.00279506898691079
GO:0043167	ion binding	0.00284718050993229
GO:0043283	biopolymer metabolic process	0.00460895279211949
GO:0043170	macromolecule metabolic process	0.0171109407578659
GO:0044237	cellular metabolic process	0.0260519854613869
GO:0005634	nucleus	0.0260519854613869
GO:0044238	primary metabolic process	0.0260519854613869
GO:0005622	intracellular	0.0466634707599534

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><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	2.55e-15	180
fibroblast	1.24e-09	75
mesothelial cell	4.16e-08	19
preadipocyte	2.03e-07	12

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)
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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
ELF1#1997	20	1.81195657821597	0.00296219731129923	0.0157905739584922
SETDB1#9869	8	6.86298317923583	1.88787728036671e-05	0.000428253725639051
SIX5#147912	13	4.72611275789292	1.99961092276306e-06	7.3199216671031e-05
ZNF143#7702	14	4.02153769640831	4.85528166720061e-06	0.000150335239264976

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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