Coexpression cluster:C658

Full id: C658_Monocytederived_CD4_mycosis_Whole_Neutrophils_mucinous_lymph

Phase1 CAGE Peaks

Hg19::chr11:73685878..73685921,+	p1@CU680035
Hg19::chr11:73685925..73685959,-	p@chr11:73685925..73685959 -
Hg19::chr11:73685992..73686067,-	p@chr11:73685992..73686067 -
Hg19::chr11:73686080..73686092,-	p@chr11:73686080..73686092 -
Hg19::chr11:73686156..73686172,-	p@chr11:73686156..73686172 -
Hg19::chr11:73686574..73686614,-	p@chr11:73686574..73686614 -
Hg19::chr11:73686645..73686687,-	p@chr11:73686645..73686687 -
Hg19::chr11:73687727..73687743,-	p@chr11:73687727..73687743 -
Hg19::chr11:73687776..73687798,-	p@chr11:73687776..73687798 -
Hg19::chr11:73687914..73687931,-	p6@UCP2
Hg19::chr11:73687932..73687955,-	p4@UCP2
Hg19::chr11:73687967..73687985,-	p7@UCP2
Hg19::chr11:73687997..73688019,-	p5@UCP2

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:0000303	response to superoxide	0.00345873071941599
GO:0000305	response to oxygen radical	0.00345873071941599
GO:0000302	response to reactive oxygen species	0.0124514305898976
GO:0006839	mitochondrial transport	0.0166019074531967
GO:0007005	mitochondrion organization and biogenesis	0.0233464323560579
GO:0006979	response to oxidative stress	0.0233464323560579
GO:0015992	proton transport	0.0233464323560579
GO:0006818	hydrogen transport	0.0233464323560579
GO:0005743	mitochondrial inner membrane	0.0457935947250677
GO:0019866	organelle inner membrane	0.0457935947250677
GO:0031966	mitochondrial membrane	0.0498057223595903
GO:0005740	mitochondrial envelope	0.0498057223595903

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	8.50e-50	172
angioblastic mesenchymal cell	8.50e-50	172
hematopoietic cell	1.94e-49	182
hematopoietic oligopotent progenitor cell	8.14e-47	165
hematopoietic multipotent progenitor cell	8.14e-47	165
leukocyte	8.49e-42	140
hematopoietic lineage restricted progenitor cell	7.52e-39	124
nongranular leukocyte	3.80e-38	119
myeloid cell	4.00e-27	112
common myeloid progenitor	4.00e-27	112
myeloid lineage restricted progenitor cell	2.89e-20	70
granulocyte monocyte progenitor cell	2.80e-19	71
myeloid leukocyte	4.13e-19	76
macrophage dendritic cell progenitor	5.88e-19	65
monopoietic cell	2.98e-18	63
monocyte	2.98e-18	63
monoblast	2.98e-18	63
promonocyte	2.98e-18	63
lymphocyte	1.08e-17	53
common lymphoid progenitor	1.08e-17	53
lymphoid lineage restricted progenitor cell	4.24e-17	52
classical monocyte	4.00e-13	45
CD14-positive, CD16-negative classical monocyte	8.24e-13	42
lymphocyte of B lineage	2.97e-10	24
pro-B cell	2.97e-10	24
T cell	1.82e-07	25
pro-T cell	1.82e-07	25
B cell	7.91e-07	14

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.22e-23	102
blood island	1.22e-23	102
hemolymphoid system	3.84e-20	112
bone marrow	1.41e-15	80
bone element	3.10e-13	86
immune system	5.62e-11	115
skeletal element	4.48e-09	101
skeletal system	4.48e-09	101
blood	6.81e-07	15
haemolymphatic fluid	6.81e-07	15
organism substance	6.81e-07	15

Disease

Ontology term	p-value	n
hematologic cancer	1.16e-11	51
immune system cancer	1.16e-11	51
leukemia	4.34e-09	39
myeloid leukemia	1.96e-07	31

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
POLR2A#5430	12	1.98226447066899	0.000770364995918076	0.00604161221060959

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.