Coexpression cluster:C3669

Full id: C3669_B_Dendritic_splenic_adult_xeroderma_hereditary_b

Phase1 CAGE Peaks

Hg19::chr17:67114473..67114480,-	p5@ABCA6
Hg19::chr19:7764314..7764346,-	p2@FCER2
Hg19::chr1:183559882..183559940,-	p9@NCF2

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:0019863	IgE binding	0.0260477980848495
GO:0019865	immunoglobulin binding	0.0312398778455792
GO:0006801	superoxide metabolic process	0.0312398778455792
GO:0001669	acrosome	0.0312398778455792
GO:0005178	integrin binding	0.0390257069868824
GO:0006800	oxygen and reactive oxygen species metabolic process	0.0390257069868824

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
nongranular leukocyte	4.48e-63	115
leukocyte	1.84e-60	136
defensive cell	1.86e-58	48
phagocyte	1.86e-58	48
classical monocyte	4.45e-58	42
CD14-positive, CD16-negative classical monocyte	4.45e-58	42
macrophage dendritic cell progenitor	1.77e-56	61
monopoietic cell	6.11e-56	59
monocyte	6.11e-56	59
monoblast	6.11e-56	59
promonocyte	6.11e-56	59
hematopoietic lineage restricted progenitor cell	1.55e-55	120
hematopoietic stem cell	6.76e-52	168
angioblastic mesenchymal cell	6.76e-52	168
hematopoietic oligopotent progenitor cell	1.50e-51	161
hematopoietic multipotent progenitor cell	1.50e-51	161
granulocyte monocyte progenitor cell	2.83e-50	67
hematopoietic cell	8.81e-50	177
myeloid lineage restricted progenitor cell	1.11e-48	66
myeloid leukocyte	3.43e-48	72
myeloid cell	2.45e-39	108
common myeloid progenitor	2.45e-39	108
stuff accumulating cell	8.08e-27	87
mesenchymal cell	2.01e-14	354
connective tissue cell	8.78e-14	361
lymphocyte of B lineage	5.50e-13	24
pro-B cell	5.50e-13	24
motile cell	1.53e-11	386
lymphocyte	5.71e-11	53
common lymphoid progenitor	5.71e-11	53
nucleate cell	2.24e-10	55
lymphoid lineage restricted progenitor cell	5.63e-10	52
multi fate stem cell	2.12e-09	427
somatic stem cell	5.07e-09	433
conventional dendritic cell	1.05e-08	8
stem cell	1.55e-08	441
dendritic cell	5.95e-07	10

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.44e-50	98
blood island	1.44e-50	98
hemolymphoid system	2.36e-46	108
immune system	1.19e-45	93
bone marrow	8.54e-43	76
bone element	1.02e-38	82
skeletal element	3.93e-34	90
skeletal system	1.95e-29	100
lateral plate mesoderm	4.06e-20	203
musculoskeletal system	1.39e-13	167
connective tissue	6.53e-13	371
hemopoietic organ	1.96e-09	7
immune organ	1.96e-09	7
mesoderm	3.34e-08	315
mesoderm-derived structure	3.34e-08	315
presumptive mesoderm	3.34e-08	315
spleen	8.22e-07	3
gastrointestinal system mesentery	8.22e-07	3
stomach region	8.22e-07	3
mesentery	8.22e-07	3
gastrointestinal system serosa	8.22e-07	3
mesentery of stomach	8.22e-07	3
gut mesentery	8.22e-07	3
dorsal mesentery	8.22e-07	3
dorsal mesogastrium	8.22e-07	3
peritoneal cavity	8.22e-07	3
spleen primordium	8.22e-07	3

Disease

Ontology term	p-value	n
lymphoma	1.29e-12	10

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.