Coexpression cluster:C4169

Full id: C4169_Mast_CD14_large_migratory_Synoviocyte_immature_Mammary

Phase1 CAGE Peaks

Hg19::chr2:201676600..201676667,+	p1@BZW1
Hg19::chr2:201676675..201676692,+	p3@BZW1
Hg19::chr3:172144898..172144914,-	p1@BZW1P1

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:0006446	regulation of translational initiation	0.0351318733074296
GO:0006413	translational initiation	0.0351318733074296
GO:0003743	translation initiation factor activity	0.0351318733074296
GO:0022618	protein-RNA complex assembly	0.0351318733074296
GO:0006417	regulation of translation	0.0351318733074296
GO:0031326	regulation of cellular biosynthetic process	0.0351318733074296
GO:0008135	translation factor activity, nucleic acid binding	0.0351318733074296
GO:0009889	regulation of biosynthetic process	0.0351318733074296
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0354017033635543

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
animal cell	2.89e-39	679
eukaryotic cell	2.89e-39	679
native cell	2.32e-30	722
multi fate stem cell	4.08e-28	427
somatic stem cell	5.06e-28	433
somatic cell	9.66e-28	588
stem cell	9.81e-28	441
connective tissue cell	1.72e-20	361
mesenchymal cell	4.71e-20	354
motile cell	2.16e-14	386
classical monocyte	1.86e-12	42
CD14-positive, CD16-negative classical monocyte	1.86e-12	42
myeloid leukocyte	7.74e-12	72
defensive cell	3.29e-11	48
phagocyte	3.29e-11	48
leukocyte	5.73e-10	136
granulocyte monocyte progenitor cell	1.46e-09	67
macrophage dendritic cell progenitor	2.52e-09	61
myeloid lineage restricted progenitor cell	5.86e-09	66
fibroblast	1.52e-08	76
monopoietic cell	1.59e-08	59
monocyte	1.59e-08	59
monoblast	1.59e-08	59
promonocyte	1.59e-08	59
hematopoietic lineage restricted progenitor cell	3.81e-07	120
myeloid cell	4.52e-07	108
common myeloid progenitor	4.52e-07	108
stuff accumulating cell	6.69e-07	87

Uber Anatomy

Ontology term	p-value	n
connective tissue	6.91e-19	371
musculoskeletal system	1.04e-12	167
skeletal system	6.01e-11	100
mesoderm	7.86e-10	315
mesoderm-derived structure	7.86e-10	315
presumptive mesoderm	7.86e-10	315
skeletal element	9.58e-10	90
bone marrow	1.80e-08	76
bone element	9.05e-08	82
immune system	2.17e-07	93

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
BCL3#602	2	23.0314018691589	0.00246467476084291	0.0138562828953907
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296331884613301
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0402048415484625
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155853322253205
SIX5#147912	2	11.391143570306	0.00987382008142903	0.037083281627027
ZBTB33#10009	2	21.1098166866541	0.00292859706060324	0.0156401998574525

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.