Coexpression cluster:C3953

Full id: C3953_Smooth_CD4_Hair_acute_iPS_xeroderma_Nucleus

Phase1 CAGE Peaks

Hg19::chr1:24018278..24018303,+	p1@RPL11
Hg19::chr2:101618729..101618761,+	p1@RPL31
Hg19::chr3:197677047..197677074,+	p1@RPL35A

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
3.23952687815502e-08	1.05948726550059e-05	3	92	Ribosome (KEGG):03010
3.34751110742684e-08	1.05948726550059e-05	3	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1037505066909e-06	0.00011644567845589	3	296	Metabolism of proteins (Reactome):REACT_17015
6.2031341872007e-08	1.30886131349935e-05	3	114	Regulation of beta-cell development (Reactome):REACT_13698
3.18533613032144e-06	0.000252039721311684	3	421	Gene Expression (Reactome):REACT_71
1.29326205516739e-06	0.000116947840131565	3	312	Diabetes pathways (Reactome):REACT_15380
1.23098667822397e-07	1.55842913463155e-05	3	143	Influenza Infection (Reactome):REACT_6167
1.10547371417187e-07	1.55842913463155e-05	3	138	{RPS27A,138} (Static Module):NA

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:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	8.11246671004954e-08
GO:0005830	cytosolic ribosome (sensu Eukaryota)	2.99701452344948e-07
GO:0015934	large ribosomal subunit	5.54678852341937e-07
GO:0044445	cytosolic part	2.49698689484997e-06
GO:0033279	ribosomal subunit	3.28124645425421e-06
GO:0005829	cytosol	4.4946882578473e-05
GO:0003735	structural constituent of ribosome	9.91441963952388e-05
GO:0005840	ribosome	0.000112771658049979
GO:0003723	RNA binding	0.000152830307734731
GO:0030529	ribonucleoprotein complex	0.000217462340567173
GO:0006412	translation	0.000235913035980226
GO:0009059	macromolecule biosynthetic process	0.000470758868352947
GO:0044249	cellular biosynthetic process	0.000827081666316246
GO:0009058	biosynthetic process	0.00155979504619136
GO:0043232	intracellular non-membrane-bound organelle	0.00229977448464354
GO:0043228	non-membrane-bound organelle	0.00229977448464354
GO:0032991	macromolecular complex	0.00509120568496683
GO:0044446	intracellular organelle part	0.00548130567723766
GO:0044422	organelle part	0.00548130567723766
GO:0000049	tRNA binding	0.00588633108744147
GO:0044444	cytoplasmic part	0.00681719258441986
GO:0019843	rRNA binding	0.00837260151835178
GO:0010467	gene expression	0.0104299359727179
GO:0044267	cellular protein metabolic process	0.0107018979530247
GO:0044260	cellular macromolecule metabolic process	0.0107018979530247
GO:0019538	protein metabolic process	0.0114328712142776
GO:0003676	nucleic acid binding	0.0142031328827836
GO:0005737	cytoplasm	0.0221219764203332
GO:0005730	nucleolus	0.0290011854976768
GO:0005515	protein binding	0.0357886869663508
GO:0006605	protein targeting	0.0357886869663508

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
native cell	2.10e-19	722
animal cell	5.46e-15	679
eukaryotic cell	5.46e-15	679
CD14-positive, CD16-negative classical monocyte	1.60e-12	42
stem cell	7.87e-12	444
hematopoietic oligopotent progenitor cell	1.07e-11	165
hematopoietic multipotent progenitor cell	1.07e-11	165
hematopoietic stem cell	2.67e-11	172
angioblastic mesenchymal cell	2.67e-11	172
classical monocyte	2.74e-11	45
hematopoietic cell	6.31e-11	182
multi fate stem cell	9.59e-11	430
hematopoietic lineage restricted progenitor cell	2.73e-10	124
nongranular leukocyte	3.01e-10	119
connective tissue cell	3.47e-10	365
somatic stem cell	4.16e-10	436
mesenchymal cell	1.45e-09	358
somatic cell	9.18e-09	591
motile cell	8.54e-08	390
lymphoid lineage restricted progenitor cell	4.71e-07	52
lymphocyte	5.32e-07	53
common lymphoid progenitor	5.32e-07	53
leukocyte	5.75e-07	140

Uber Anatomy

Ontology term	p-value	n
connective tissue	4.11e-10	375

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.