Coexpression cluster:C954

Full id: C954_heart_CD14_Neutrophils_Eosinophils_Lymphatic_renal_Monocytederived

Phase1 CAGE Peaks

Hg19::chr6:160100686..160100698,-	p4@AK093984
Hg19::chr6:160101581..160101593,-	p18@SOD2
Hg19::chr6:160101609..160101626,-	p21@SOD2
Hg19::chr6:160101648..160101695,-	p7@SOD2
Hg19::chr6:160102006..160102195,-	p1@BC041951
Hg19::chr6:160102208..160102232,-	p6@BC041951
Hg19::chr6:160102300..160102326,-	p5@BC041951
Hg19::chr6:160102610..160102627,-	p3@BC041951
Hg19::chr6:160112805..160112821,-	p@chr6:160112805..160112821 -

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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GO ID	GO name	FDR corrected p-value
GO:0008383	manganese superoxide dismutase activity	0.0027375485694101
GO:0001315	age-dependent response to reactive oxygen species	0.0027375485694101
GO:0000303	response to superoxide	0.00342193571176262
GO:0000305	response to oxygen radical	0.00342193571176262
GO:0016721	oxidoreductase activity, acting on superoxide radicals as acceptor	0.00410632285411515
GO:0004784	superoxide dismutase activity	0.00410632285411515
GO:0001836	release of cytochrome c from mitochondria	0.00508401877176161
GO:0008637	apoptotic mitochondrial changes	0.00574885199576121
GO:0042542	response to hydrogen peroxide	0.00574885199576121
GO:0006801	superoxide metabolic process	0.00574885199576121
GO:0000302	response to reactive oxygen species	0.00671943739764298
GO:0006302	double-strand break repair	0.0082126457082303
GO:0006800	oxygen and reactive oxygen species metabolic process	0.00947612966334266
GO:0008632	apoptotic program	0.0162427881784999
GO:0007005	mitochondrion organization and biogenesis	0.0162427881784999
GO:0006979	response to oxidative stress	0.0205316142705758
GO:0030145	manganese ion binding	0.0236717435119579
GO:0031980	mitochondrial lumen	0.0263669151685289
GO:0005759	mitochondrial matrix	0.0263669151685289
GO:0043066	negative regulation of apoptosis	0.0299826748078249
GO:0043069	negative regulation of programmed cell death	0.0299826748078249
GO:0005743	mitochondrial inner membrane	0.0389478501011528
GO:0019866	organelle inner membrane	0.0393968946293367
GO:0006281	DNA repair	0.0438007771105616
GO:0031966	mitochondrial membrane	0.0438007771105616
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0438007771105616
GO:0005740	mitochondrial envelope	0.0438007771105616
GO:0006974	response to DNA damage stimulus	0.0438007771105616
GO:0009719	response to endogenous stimulus	0.0486675301228462
GO:0042981	regulation of apoptosis	0.0486675301228462
GO:0043067	regulation of programmed cell death	0.0486675301228462
GO:0044429	mitochondrial part	0.0486675301228462
GO:0042221	response to chemical stimulus	0.0486675301228462
GO:0031967	organelle envelope	0.0486675301228462
GO:0031975	envelope	0.0486675301228462
GO:0006366	transcription from RNA polymerase II promoter	0.0486675301228462

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	1.16e-25	48
phagocyte	1.16e-25	48
classical monocyte	3.83e-23	42
CD14-positive, CD16-negative classical monocyte	3.83e-23	42
myeloid leukocyte	1.82e-22	72
monopoietic cell	2.13e-21	59
monocyte	2.13e-21	59
monoblast	2.13e-21	59
promonocyte	2.13e-21	59
macrophage dendritic cell progenitor	3.92e-20	61
myeloid lineage restricted progenitor cell	2.45e-17	66
granulocyte monocyte progenitor cell	7.83e-17	67
stuff accumulating cell	1.20e-12	87
myeloid cell	4.50e-09	108
common myeloid progenitor	4.50e-09	108
leukocyte	3.87e-07	136
nongranular leukocyte	3.98e-07	115

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.10e-16	108
hematopoietic system	1.67e-16	98
blood island	1.67e-16	98
bone marrow	1.12e-15	76
immune system	9.75e-14	93
bone element	2.57e-13	82
musculoskeletal system	3.46e-13	167
skeletal element	4.48e-13	90
skeletal system	4.55e-13	100
adult organism	8.53e-13	114
mesoderm	6.34e-09	315
mesoderm-derived structure	6.34e-09	315
presumptive mesoderm	6.34e-09	315
lateral plate mesoderm	4.56e-08	203
anatomical system	6.22e-07	624
germ layer	6.25e-07	560
germ layer / neural crest	6.25e-07	560
embryonic tissue	6.25e-07	560
presumptive structure	6.25e-07	560
germ layer / neural crest derived structure	6.25e-07	560
epiblast (generic)	6.25e-07	560
anatomical group	7.67e-07	625

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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No analysis results for this cluster

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.