Coexpression cluster:C2220

Full id: C2220_CD14_mature_chorionic_adipose_breast_Cardiac_choriocarcinoma

Phase1 CAGE Peaks

Hg19::chr12:56236690..56236701,-	p3@MMP19
Hg19::chr12:56236711..56236730,-	p1@MMP19
Hg19::chr3:12329397..12329433,+	p2@PPARG
Hg19::chr3:12329464..12329472,+	p6@PPARG

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:0050872	white fat cell differentiation	0.00816322523237728
GO:0045600	positive regulation of fat cell differentiation	0.00816322523237728
GO:0045598	regulation of fat cell differentiation	0.00816322523237728
GO:0045444	fat cell differentiation	0.0107115521542341
GO:0030574	collagen catabolic process	0.0107115521542341
GO:0044256	protein digestion	0.0107115521542341
GO:0044254	multicellular organismal protein catabolic process	0.0107115521542341
GO:0044266	multicellular organismal macromolecule catabolic process	0.0107115521542341
GO:0044259	multicellular organismal macromolecule metabolic process	0.0107115521542341
GO:0044268	multicellular organismal protein metabolic process	0.0107115521542341
GO:0044243	multicellular organismal catabolic process	0.0107115521542341
GO:0032963	collagen metabolic process	0.0107115521542341
GO:0044236	multicellular organismal metabolic process	0.010828942645108
GO:0007584	response to nutrient	0.0173568980647782
GO:0045597	positive regulation of cell differentiation	0.0173568980647782
GO:0048869	cellular developmental process	0.0173568980647782
GO:0030154	cell differentiation	0.0173568980647782
GO:0031667	response to nutrient levels	0.0203912413506773
GO:0009991	response to extracellular stimulus	0.0207966150112808
GO:0051094	positive regulation of developmental process	0.0207966150112808
GO:0007586	digestion	0.0276595591154259
GO:0003707	steroid hormone receptor activity	0.0325059811389192
GO:0001525	angiogenesis	0.0337966043625247
GO:0045595	regulation of cell differentiation	0.0337966043625247
GO:0048514	blood vessel morphogenesis	0.0337966043625247
GO:0004879	ligand-dependent nuclear receptor activity	0.0337966043625247
GO:0048646	anatomical structure formation	0.0337966043625247
GO:0001568	blood vessel development	0.0337966043625247
GO:0032502	developmental process	0.0337966043625247
GO:0001944	vasculature development	0.0337966043625247
GO:0004222	metalloendopeptidase activity	0.0389928192059665
GO:0050793	regulation of developmental process	0.0449986503854178
GO:0008270	zinc ion binding	0.0472467787160881

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	3.51e-14	48
phagocyte	3.51e-14	48
monopoietic cell	1.04e-12	59
monocyte	1.04e-12	59
monoblast	1.04e-12	59
promonocyte	1.04e-12	59
stuff accumulating cell	3.34e-12	87
classical monocyte	6.47e-12	42
CD14-positive, CD16-negative classical monocyte	6.47e-12	42
macrophage dendritic cell progenitor	1.42e-11	61
myeloid lineage restricted progenitor cell	1.56e-09	66
granulocyte monocyte progenitor cell	3.42e-09	67
myeloid leukocyte	7.22e-08	72
fibroblast	8.71e-08	76
fat cell	3.88e-07	15

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	3.16e-16	656
mesoderm	1.12e-15	315
mesoderm-derived structure	1.12e-15	315
presumptive mesoderm	1.12e-15	315
anatomical system	1.58e-15	624
anatomical group	3.20e-15	625
musculoskeletal system	2.49e-14	167
organ	4.13e-14	503
immune system	1.29e-10	93
developing anatomical structure	5.27e-10	581
skeletal system	6.05e-10	100
skeletal element	7.02e-10	90
embryonic structure	8.44e-10	564
embryo	8.61e-10	592
bone marrow	1.19e-09	76
mesenchyme	1.24e-09	160
entire embryonic mesenchyme	1.24e-09	160
germ layer	1.32e-09	560
germ layer / neural crest	1.32e-09	560
embryonic tissue	1.32e-09	560
presumptive structure	1.32e-09	560
germ layer / neural crest derived structure	1.32e-09	560
epiblast (generic)	1.32e-09	560
organism subdivision	1.45e-08	264
bone element	2.26e-08	82
trunk mesenchyme	5.13e-08	122
trunk	4.58e-07	199

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
ATF3#467	2	11.2315872630044	0.0111955903992222	0.0411232112581988
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00816069758151473
FOSL1#8061	2	19.8567898581865	0.00367705000923323	0.0185565318151394
JUNB#3726	2	15.3053163299106	0.00612694714847562	0.0270945604115529
SMARCC1#6599	2	21.8316796598157	0.00305120745616205	0.0160917565779987
SUZ12#23512	2	25.0578904555315	0.00232525671652061	0.0131846183949561

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.