Coexpression cluster:C667

Full id: C667_CD14_tenocyte_Synoviocyte_Smooth_dura_Preadipocyte_Macrophage

Phase1 CAGE Peaks

Hg19::chr2:38295461..38295480,-	p@chr2:38295461..38295480 -
Hg19::chr2:38296784..38296796,-	p@chr2:38296784..38296796 -
Hg19::chr2:38297270..38297290,-	p@chr2:38297270..38297290 -
Hg19::chr2:38297628..38297658,-	p@chr2:38297628..38297658 -
Hg19::chr2:38297677..38297731,-	p@chr2:38297677..38297731 -
Hg19::chr2:38302488..38302516,-	p5@CYP1B1
Hg19::chr2:38303286..38303301,-	p1@CYP1B1
Hg19::chr9:90342509..90342530,+	p3@CTSL1
Hg19::chr9:90342545..90342564,+	p2@CTSL1
Hg19::chr9:90344555..90344567,+	p@chr9:90344555..90344567 +
Hg19::chr9:90344568..90344585,+	p@chr9:90344568..90344585 +
Hg19::chr9:90345291..90345317,+	p@chr9:90345291..90345317 +
Hg19::chr9:90345922..90345945,+	p@chr9:90345922..90345945 +

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
5.75225560838478e-05	0.0364117780010757	2	217	IL-4 up reg. targets (Netpath):NetPath_16

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:0004217	cathepsin L activity	0.00812421811231538
GO:0008210	estrogen metabolic process	0.0243690670105399
GO:0050381	unspecific monooxygenase activity	0.0351925090884915
GO:0016712	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	0.0419380578740978
GO:0019825	oxygen binding	0.0419380578740978
GO:0010033	response to organic substance	0.0419380578740978
GO:0042445	hormone metabolic process	0.0496449157332622
GO:0004197	cysteine-type endopeptidase activity	0.0496449157332622
GO:0005792	microsome	0.0496449157332622
GO:0042598	vesicular fraction	0.0496449157332622
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0496449157332622
GO:0006725	aromatic compound metabolic process	0.0496449157332622
GO:0005764	lysosome	0.0496449157332622
GO:0000323	lytic vacuole	0.0496449157332622
GO:0007601	visual perception	0.0496449157332622
GO:0050953	sensory perception of light stimulus	0.0496449157332622
GO:0008202	steroid metabolic process	0.0496449157332622
GO:0005773	vacuole	0.0496449157332622
GO:0004497	monooxygenase activity	0.0496449157332622

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	1.82e-20	48
phagocyte	1.82e-20	48
monopoietic cell	3.76e-20	59
monocyte	3.76e-20	59
monoblast	3.76e-20	59
promonocyte	3.76e-20	59
macrophage dendritic cell progenitor	6.16e-19	61
myeloid lineage restricted progenitor cell	5.56e-17	66
granulocyte monocyte progenitor cell	1.76e-16	67
classical monocyte	1.10e-15	42
CD14-positive, CD16-negative classical monocyte	1.10e-15	42
connective tissue cell	4.05e-15	361
myeloid leukocyte	3.22e-14	72
mesenchymal cell	6.19e-14	354
multi fate stem cell	1.26e-13	427
somatic stem cell	8.68e-13	433
stuff accumulating cell	1.95e-12	87
stem cell	1.01e-11	441
fibroblast	2.20e-10	76
motile cell	7.75e-10	386
preadipocyte	1.13e-07	12
macrophage	6.42e-07	6

Uber Anatomy

Ontology term	p-value	n
skeletal system	1.14e-17	100
skeletal element	4.95e-17	90
bone marrow	1.83e-16	76
musculoskeletal system	2.64e-16	167
bone element	2.93e-16	82
connective tissue	1.53e-15	371
mesoderm	6.86e-13	315
mesoderm-derived structure	6.86e-13	315
presumptive mesoderm	6.86e-13	315
immune system	9.38e-13	93
hematopoietic system	1.58e-10	98
blood island	1.58e-10	98
hemolymphoid system	1.01e-08	108
organ	9.97e-07	503

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.