Coexpression cluster:C678

Full id: C678_Smooth_CD14_embryonic_mesothelioma_gall_Fibroblast_meningioma

Phase1 CAGE Peaks

Hg19::chr10:91152368..91152419,+	p1@IFIT1
Hg19::chr12:113344811..113344832,+	p2@OAS1
Hg19::chr12:113405759..113405764,+	p@chr12:113405759..113405764 +
Hg19::chr17:40263911..40263923,-	p6@DHX58
Hg19::chr1:948866..948885,+	p1@ISG15
Hg19::chr22:18632907..18632918,+	p3@USP18
Hg19::chr22:18632929..18632945,+	p1@USP18
Hg19::chr2:7005572..7005619,-	p2@CMPK2
Hg19::chr4:89299964..89299986,+	p3@HERC6
Hg19::chr4:89299994..89300011,+	p2@HERC6
Hg19::chr4:89300057..89300068,+	p7@HERC6
Hg19::chr4:89300072..89300089,+	p4@HERC6

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
0.000127057221192237	0.0268090736715619	2	71	RIG-I-like receptor signaling pathway (KEGG):04622
6.27877433870237e-05	0.019872320781993	2	50	Type II interferon signaling (IFNG) (Wikipathways):WP619
3.67536037054371e-08	2.32650311455417e-05	5	511	Signaling in Immune system (Reactome):REACT_6900

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:0006512	ubiquitin cycle	0.00539557078421984
GO:0009615	response to virus	0.00539557078421984
GO:0032020	ISG15-protein conjugation	0.0105553619861631
GO:0051707	response to other organism	0.0105553619861631
GO:0043632	modification-dependent macromolecule catabolic process	0.0105553619861631
GO:0019941	modification-dependent protein catabolic process	0.0105553619861631
GO:0009607	response to biotic stimulus	0.0105553619861631
GO:0051603	proteolysis involved in cellular protein catabolic process	0.0105553619861631
GO:0044257	cellular protein catabolic process	0.0105553619861631
GO:0051704	multi-organism process	0.012320234401282
GO:0030163	protein catabolic process	0.0127801185248416
GO:0005737	cytoplasm	0.017462333649797
GO:0043285	biopolymer catabolic process	0.017462333649797
GO:0044424	intracellular part	0.0193439322321757
GO:0044265	cellular macromolecule catabolic process	0.01998048690809
GO:0009057	macromolecule catabolic process	0.0253150277329111
GO:0043687	post-translational protein modification	0.0253150277329111
GO:0005622	intracellular	0.0348662193231298
GO:0044248	cellular catabolic process	0.0368921277854879
GO:0006464	protein modification process	0.0368921277854879
GO:0043412	biopolymer modification	0.0393377907931135
GO:0009056	catabolic process	0.0439058078389735
GO:0003723	RNA binding	0.0439058078389735

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><br>

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Cell Type

Ontology term	p-value	n
defensive cell	4.86e-13	48
phagocyte	4.86e-13	48
nongranular leukocyte	4.74e-12	115
classical monocyte	5.27e-12	42
CD14-positive, CD16-negative classical monocyte	5.27e-12	42
monopoietic cell	2.41e-11	59
monocyte	2.41e-11	59
monoblast	2.41e-11	59
promonocyte	2.41e-11	59
hematopoietic lineage restricted progenitor cell	7.10e-11	120
myeloid lineage restricted progenitor cell	1.05e-10	66
macrophage dendritic cell progenitor	1.26e-10	61
granulocyte monocyte progenitor cell	2.22e-10	67
myeloid leukocyte	2.57e-10	72
leukocyte	8.99e-10	136

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.77e-13	108
hematopoietic system	2.49e-13	98
blood island	2.49e-13	98
adult organism	1.86e-12	114
immune system	4.30e-11	93
bone marrow	3.00e-09	76
bone element	1.92e-08	82
skeletal element	3.77e-07	90

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
E2F1#1869	7	2.86264370867961	0.00436076322914768	0.0206733432087587
GATA1#2623	5	5.65012839325018	0.00111039311334309	0.00771168681769114
HNF4A#3172	3	5.78307259073842	0.0132439562849054	0.0468527047774283
IRF1#3659	5	3.18215156398496	0.0137018857077083	0.0483368093709625
MEF2A#4205	4	6.24774363654802	0.00283471242741202	0.0153714709868372
NFKB1#4790	6	2.74403171209692	0.0123424720145443	0.044716253329413
PAX5#5079	7	3.89057989318707	0.000669972280701136	0.0054094499438845
POLR2A#5430	10	1.78954431379839	0.0105685965877023	0.0390508989571215
SMC3#9126	4	5.01497761497761	0.00626178397702115	0.027627664939213
STAT1#6772	6	10.3532937485996	9.08847659828404e-06	0.000242759950754012
STAT2#6773	6	32.6318855932203	1.09905339974521e-08	8.26378963398058e-07
TCF12#6938	5	4.43102704257768	0.00330250138892161	0.0170832066645658
TFAP2C#7022	7	6.3053833557518	3.01291531004594e-05	0.000619787004266079
ZNF143#7702	4	4.50029218407597	0.00918062696657501	0.0347245943706406

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.