Coexpression cluster:C2568

Full id: C2568_CD4_Smooth_Aortic_acute_CD34_Fibroblast_CD8

Phase1 CAGE Peaks

Hg19::chr1:22234543..22234549,+	p1@ENST00000423231
Hg19::chr1:53238346..53238348,-	p1@ENST00000437890
Hg19::chr4:109541723..109541738,+	p1@RPL34
Hg19::chr9:136215044..136215086,+	p1@RPL7A

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
1.02743394677841e-05	0.00315487951907255	2	92	Ribosome (KEGG):03010
1.05001491264167e-05	0.00315487951907255	2	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
0.000107161409738044	0.0107682553184368	2	296	Metabolism of proteins (Reactome):REACT_17015
1.58091305570944e-05	0.00315487951907255	2	114	Regulation of beta-cell development (Reactome):REACT_13698
0.000216998173040322	0.0171699804418155	2	421	Gene Expression (Reactome):REACT_71
0.000119080232589348	0.0107682553184368	2	312	Diabetes pathways (Reactome):REACT_15380
2.49200593923582e-05	0.00315487951907255	2	143	Influenza Infection (Reactome):REACT_6167
2.32019424245013e-05	0.00315487951907255	2	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)	5.52188315379147e-05
GO:0005830	cytosolic ribosome (sensu Eukaryota)	0.000103395585369577
GO:0015934	large ribosomal subunit	0.000135625200268563
GO:0044445	cytosolic part	0.000334498691046984
GO:0033279	ribosomal subunit	0.000372239011198639
GO:0042788	polysomal ribosome	0.00168758983169338
GO:0005829	cytosol	0.00171424291592199
GO:0003735	structural constituent of ribosome	0.00253119844918806
GO:0005844	polysome	0.00253119844918806
GO:0005840	ribosome	0.00268251742263055
GO:0003723	RNA binding	0.00322991211205015
GO:0030529	ribonucleoprotein complex	0.00401754259108733
GO:0006412	translation	0.0041720570111862
GO:0009059	macromolecule biosynthetic process	0.00650588975790638
GO:0044249	cellular biosynthetic process	0.00932462001903585
GO:0009058	biosynthetic process	0.0140181638787613
GO:0042254	ribosome biogenesis and assembly	0.0165024219924451
GO:0043232	intracellular non-membrane-bound organelle	0.016714845025811
GO:0043228	non-membrane-bound organelle	0.016714845025811
GO:0032991	macromolecular complex	0.0276252430289505
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0276252430289505
GO:0044446	intracellular organelle part	0.0276252430289505
GO:0044422	organelle part	0.0276252430289505
GO:0044444	cytoplasmic part	0.0327293167586561
GO:0010467	gene expression	0.0441384679540688
GO:0044267	cellular protein metabolic process	0.0441384679540688
GO:0044260	cellular macromolecule metabolic process	0.0441384679540688
GO:0019538	protein metabolic process	0.0456568104643413

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	2.47e-24	722
hematopoietic cell	2.64e-19	182
hematopoietic lineage restricted progenitor cell	4.25e-19	124
somatic cell	1.39e-18	591
hematopoietic stem cell	2.01e-18	172
angioblastic mesenchymal cell	2.01e-18	172
stem cell	3.89e-18	444
CD14-positive, CD16-negative classical monocyte	4.11e-18	42
nongranular leukocyte	8.13e-18	119
multi fate stem cell	9.24e-18	430
hematopoietic oligopotent progenitor cell	1.88e-17	165
hematopoietic multipotent progenitor cell	1.88e-17	165
somatic stem cell	5.00e-17	436
animal cell	9.81e-17	679
eukaryotic cell	9.81e-17	679
connective tissue cell	1.01e-16	365
leukocyte	2.92e-16	140
classical monocyte	8.69e-16	45
mesenchymal cell	2.67e-15	358
motile cell	3.50e-13	390
lymphoid lineage restricted progenitor cell	4.92e-11	52
lymphocyte	1.04e-10	53
common lymphoid progenitor	1.04e-10	53
macrophage dendritic cell progenitor	1.03e-08	65
myeloid lineage restricted progenitor cell	3.11e-08	70
mature alpha-beta T cell	3.16e-08	18
alpha-beta T cell	3.16e-08	18
immature T cell	3.16e-08	18
mature T cell	3.16e-08	18
immature alpha-beta T cell	3.16e-08	18
myeloid cell	4.83e-08	112
common myeloid progenitor	4.83e-08	112
monopoietic cell	4.90e-08	63
monocyte	4.90e-08	63
monoblast	4.90e-08	63
promonocyte	4.90e-08	63
granulocyte monocyte progenitor cell	5.50e-08	71
B cell	1.48e-07	14
T cell	4.41e-07	25
pro-T cell	4.41e-07	25

Uber Anatomy

Ontology term	p-value	n
connective tissue	2.30e-16	375
bone marrow	4.89e-09	80
hemolymphoid system	3.00e-08	112
hematopoietic system	3.69e-08	102
blood island	3.69e-08	102
bone element	4.14e-08	86
skeletal element	6.02e-07	101
skeletal system	6.02e-07	101

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
BRCA1#672	2	10.0921153216119	0.013771396990026	0.0484739621260263
KAT2A#2648	1	154.0225	0.00647681994931104	0.0281249261438649
ZZZ3#26009	2	119.706606217617	0.000103963068385957	0.00145254834771385

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.