Coexpression cluster:C746

Full id: C746_Neutrophils_chronic_Monocytederived_CD4_Whole_Hodgkin_lymph

Phase1 CAGE Peaks

Hg19::chr12:15095224..15095238,-	p@chr12:15095224..15095238 -
Hg19::chr12:15095377..15095412,-	p@chr12:15095377..15095412 -
Hg19::chr12:15095596..15095637,-	p@chr12:15095596..15095637 -
Hg19::chr12:15097732..15097776,-	p@chr12:15097732..15097776 -
Hg19::chr16:30198754..30198769,+	p@chr16:30198754..30198769 +
Hg19::chr22:37621663..37621687,-	p4@RAC2
Hg19::chr2:234104079..234104082,+	p4@INPP5D
Hg19::chrX:70327539..70327558,-	p@chrX:70327539..70327558 -
Hg19::chrX:70327608..70327641,-	p@chrX:70327608..70327641 -
Hg19::chrX:70327646..70327667,-	p@chrX:70327646..70327667 -
Hg19::chrX:70329181..70329194,-	p2@IL2RG

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
2.03984814542931e-05	0.0047782444038979	2	75	B cell receptor signaling pathway (KEGG):04662
2.26457080753455e-05	0.0047782444038979	2	79	Fc epsilon RI signaling pathway (KEGG):04664
3.28059829023111e-05	0.00479055337409632	2	95	Fc gamma R-mediated phagocytosis (KEGG):04666
3.78400740449947e-05	0.00479055337409632	2	102	IL-3 Signaling Pathway (Wikipathways):WP286
1.48230348787841e-05	0.0047782444038979	2	64	IL-4 signaling Pathway (Wikipathways):WP395

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:0019982	interleukin-7 binding	0.0047242008376489
GO:0004917	interleukin-7 receptor activity	0.0047242008376489
GO:0004913	interleukin-4 receptor activity	0.0047242008376489
GO:0019979	interleukin-4 binding	0.0047242008376489
GO:0019976	interleukin-2 binding	0.0047242008376489
GO:0004911	interleukin-2 receptor activity	0.0047242008376489
GO:0046030	inositol trisphosphate phosphatase activity	0.00944701104561127
GO:0004445	inositol-polyphosphate 5-phosphatase activity	0.00944701104561127
GO:0004907	interleukin receptor activity	0.0314511171465861
GO:0007165	signal transduction	0.0314511171465861
GO:0019965	interleukin binding	0.0314511171465861
GO:0006955	immune response	0.0314511171465861
GO:0007154	cell communication	0.0314511171465861
GO:0030031	cell projection biogenesis	0.0314511171465861
GO:0009897	external side of plasma membrane	0.0314511171465861
GO:0002376	immune system process	0.0316296020883855
GO:0004437	inositol or phosphatidylinositol phosphatase activity	0.0316296020883855
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.0361485493485189
GO:0019838	growth factor binding	0.0441463508053512
GO:0019955	cytokine binding	0.0466375408730237

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	6.05e-101	168
angioblastic mesenchymal cell	6.05e-101	168
hematopoietic cell	2.55e-97	177
hematopoietic oligopotent progenitor cell	1.75e-96	161
hematopoietic multipotent progenitor cell	1.75e-96	161
leukocyte	4.34e-92	136
nongranular leukocyte	3.95e-80	115
hematopoietic lineage restricted progenitor cell	3.83e-79	120
myeloid cell	2.67e-52	108
common myeloid progenitor	2.67e-52	108
myeloid leukocyte	1.96e-43	72
granulocyte monocyte progenitor cell	4.35e-39	67
lymphocyte	1.98e-38	53
common lymphoid progenitor	1.98e-38	53
lymphoid lineage restricted progenitor cell	8.12e-38	52
macrophage dendritic cell progenitor	2.46e-37	61
myeloid lineage restricted progenitor cell	5.07e-37	66
nucleate cell	2.77e-36	55
monopoietic cell	3.42e-36	59
monocyte	3.42e-36	59
monoblast	3.42e-36	59
promonocyte	3.42e-36	59
defensive cell	1.21e-33	48
phagocyte	1.21e-33	48
classical monocyte	2.90e-29	42
CD14-positive, CD16-negative classical monocyte	2.90e-29	42
mesenchymal cell	6.18e-23	354
connective tissue cell	1.31e-21	361
T cell	1.75e-19	25
pro-T cell	1.75e-19	25
motile cell	4.94e-17	386
lymphocyte of B lineage	8.59e-17	24
pro-B cell	8.59e-17	24
mature alpha-beta T cell	2.54e-16	18
alpha-beta T cell	2.54e-16	18
immature T cell	2.54e-16	18
mature T cell	2.54e-16	18
immature alpha-beta T cell	2.54e-16	18
multi fate stem cell	4.29e-12	427
stuff accumulating cell	7.40e-12	87
somatic stem cell	9.90e-12	433
stem cell	3.17e-11	441
B cell	9.88e-11	14
CD8-positive, alpha-beta T cell	2.06e-10	11
CD4-positive, alpha-beta T cell	8.55e-07	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.26e-50	98
blood island	1.26e-50	98
hemolymphoid system	7.40e-46	108
immune system	1.01e-34	93
bone marrow	1.70e-34	76
bone element	2.68e-30	82
skeletal element	1.27e-25	90
skeletal system	6.59e-21	100
connective tissue	8.08e-20	371
lateral plate mesoderm	2.00e-15	203
blood	3.36e-12	15
haemolymphatic fluid	3.36e-12	15
organism substance	3.36e-12	15

Disease

Ontology term	p-value	n
hematologic cancer	7.56e-19	51
immune system cancer	7.56e-19	51
leukemia	2.83e-15	39
myeloid leukemia	1.45e-10	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)
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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.