Coexpression cluster:C433

Full id: C433_Macrophage_Monocytederived_Dendritic_Neutrophils_Urothelial_Eosinophils_immature

Phase1 CAGE Peaks

Hg19::chr13:49110026..49110037,-	p15@RCBTB2
Hg19::chr13:77338767..77338773,+	p@chr13:77338767..77338773 +
Hg19::chr1:161059154..161059172,-	p6@PVRL4
Hg19::chr20:44637526..44637554,+	p1@MMP9
Hg19::chr20:44638538..44638547,-	p@chr20:44638538..44638547 -
Hg19::chr20:44638625..44638633,-	p@chr20:44638625..44638633 -
Hg19::chr20:44638633..44638646,+	p@chr20:44638633..44638646 +
Hg19::chr20:44640866..44640875,-	p@chr20:44640866..44640875 -
Hg19::chr20:48914162..48914165,+	p@chr20:48914162..48914165 +
Hg19::chr2:119699764..119699777,+	p2@MARCO
Hg19::chr2:119699790..119699805,+	p3@MARCO
Hg19::chr2:119699824..119699835,+	p4@MARCO
Hg19::chr2:119699884..119699905,+	p1@MARCO
Hg19::chr2:119731986..119731993,+	p@chr2:119731986..119731993 +
Hg19::chr2:119735453..119735460,-	p@chr2:119735453..119735460 -
Hg19::chr2:119735483..119735502,-	p@chr2:119735483..119735502 -
Hg19::chr2:119739008..119739032,-	p@chr2:119739008..119739032 -
Hg19::chr2:119748190..119748210,-	p@chr2:119748190..119748210 -
Hg19::chr2:119750034..119750055,-	p@chr2:119750034..119750055 -
Hg19::chr2:38368798..38368805,-	p@chr2:38368798..38368805 -
Hg19::chr7:75443066..75443080,-	p2@CCL24
Hg19::chr7:75443118..75443130,-	p1@CCL24
Hg19::chr9:86983573..86983587,-	p6@SLC28A3

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:0004229	gelatinase B activity	0.024895531419419
GO:0005087	Ran guanyl-nucleotide exchange factor activity	0.024895531419419
GO:0001882	nucleoside binding	0.024895531419419
GO:0008133	collagenase activity	0.024895531419419
GO:0005415	nucleoside:sodium symporter activity	0.024895531419419
GO:0030225	macrophage differentiation	0.0290106079498542
GO:0008329	pattern recognition receptor activity	0.0290106079498542
GO:0005337	nucleoside transmembrane transporter activity	0.0290106079498542
GO:0005518	collagen binding	0.0290106079498542
GO:0005615	extracellular space	0.0290106079498542
GO:0030574	collagen catabolic process	0.0290106079498542
GO:0044259	multicellular organismal macromolecule metabolic process	0.0290106079498542
GO:0044268	multicellular organismal protein metabolic process	0.0290106079498542
GO:0044256	protein digestion	0.0290106079498542
GO:0044254	multicellular organismal protein catabolic process	0.0290106079498542
GO:0044266	multicellular organismal macromolecule catabolic process	0.0290106079498542
GO:0044243	multicellular organismal catabolic process	0.0290106079498542
GO:0032963	collagen metabolic process	0.0290106079498542
GO:0044236	multicellular organismal metabolic process	0.0300968024881436
GO:0015932	nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity	0.031073646407503
GO:0002573	myeloid leukocyte differentiation	0.0354996750478198

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
myeloid leukocyte	1.16e-25	76
macrophage dendritic cell progenitor	4.31e-24	65
monopoietic cell	3.74e-23	63
monocyte	3.74e-23	63
monoblast	3.74e-23	63
promonocyte	3.74e-23	63
granulocyte monocyte progenitor cell	4.45e-22	71
CD14-positive, CD16-negative classical monocyte	1.05e-21	42
myeloid lineage restricted progenitor cell	2.14e-21	70
classical monocyte	2.15e-19	45
myeloid cell	4.83e-18	112
common myeloid progenitor	4.83e-18	112
leukocyte	5.40e-12	140
nongranular leukocyte	6.43e-09	119
hematopoietic lineage restricted progenitor cell	7.83e-09	124
hematopoietic stem cell	9.37e-09	172
angioblastic mesenchymal cell	9.37e-09	172
hematopoietic oligopotent progenitor cell	2.04e-08	165
hematopoietic multipotent progenitor cell	2.04e-08	165

Uber Anatomy

Ontology term	p-value	n
adult organism	7.84e-25	115
hematopoietic system	4.27e-20	102
blood island	4.27e-20	102
hemolymphoid system	1.67e-19	112
bone marrow	1.25e-16	80
immune system	2.84e-14	115
bone element	6.27e-14	86
skeletal element	1.54e-10	101
skeletal system	1.54e-10	101
tissue	1.84e-08	787
embryo	8.25e-07	612

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
SIRT6#51548	2	13.3598612165239	0.00978099051106676	0.0367782850759784

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.