Coexpression cluster:C865

Full id: C865_CD14_Neutrophils_Dendritic_placenta_cervical_epitheloid_spinal

Phase1 CAGE Peaks

Hg19::chrX:1367460..1367489,+	p@chrX:1367460..1367489 +
Hg19::chrX:1368516..1368527,-	p@chrX:1368516..1368527 -
Hg19::chrX:1387700..1387717,+	p1@CSF2RA
Hg19::chrX:1387721..1387738,+	p2@CSF2RA
Hg19::chrX:1393727..1393755,-	p@chrX:1393727..1393755 -
Hg19::chrX:1393820..1393849,-	p@chrX:1393820..1393849 -
Hg19::chrX:1435460..1435487,-	p@chrX:1435460..1435487 -
Hg19::chrX:1435588..1435602,-	p@chrX:1435588..1435602 -
Hg19::chrX:1455478..1455515,+	p2@IL3RA
Hg19::chrX:24167737..24167762,-	p1@ZFX-AS1

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
8.58567593366187e-05	0.0135868321650199	2	265	Cytokine-cytokine receptor interaction (KEGG):04060
2.92938943019595e-05	0.00618101169771345	2	155	Jak-STAT signaling pathway (KEGG):04630
9.39564536136585e-06	0.00297372175687229	2	88	Hematopoietic cell lineage (KEGG):04640
0.000319827473566556	0.0337417984612716	2	511	Signaling in Immune system (Reactome):REACT_6900
1.91447319275479e-06	0.00121186153101378	2	40	IL-3 up reg. targets (Netpath):NetPath_15
0.000201792837874789	0.0255469732749483	2	406	{GRB2,414} (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:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.000158559827157831
GO:0004912	interleukin-3 receptor activity	0.00153064978927681
GO:0019978	interleukin-3 binding	0.00153064978927681
GO:0004907	interleukin receptor activity	0.0183575242003379
GO:0019965	interleukin binding	0.0183575242003379
GO:0004888	transmembrane receptor activity	0.0230388577844583
GO:0019838	growth factor binding	0.028372121655368
GO:0019955	cytokine binding	0.028372121655368
GO:0004872	receptor activity	0.035793698202971
GO:0005057	receptor signaling protein activity	0.0387720512564269
GO:0004871	signal transducer activity	0.0387720512564269
GO:0060089	molecular transducer activity	0.0387720512564269

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
myeloid lineage restricted progenitor cell	3.41e-36	66
granulocyte monocyte progenitor cell	1.47e-35	67
myeloid leukocyte	2.02e-35	72
monopoietic cell	3.39e-32	59
monocyte	3.39e-32	59
monoblast	3.39e-32	59
promonocyte	3.39e-32	59
macrophage dendritic cell progenitor	5.92e-31	61
classical monocyte	3.33e-30	42
CD14-positive, CD16-negative classical monocyte	3.33e-30	42
defensive cell	1.38e-28	48
phagocyte	1.38e-28	48
myeloid cell	5.87e-27	108
common myeloid progenitor	5.87e-27	108
hematopoietic lineage restricted progenitor cell	5.81e-17	120
leukocyte	5.88e-17	136
hematopoietic stem cell	6.63e-16	168
angioblastic mesenchymal cell	6.63e-16	168
hematopoietic oligopotent progenitor cell	1.28e-15	161
hematopoietic multipotent progenitor cell	1.28e-15	161
stuff accumulating cell	5.34e-15	87
hematopoietic cell	1.04e-14	177
nongranular leukocyte	1.09e-13	115
histamine secreting cell	3.77e-07	5
biogenic amine secreting cell	3.77e-07	5
granulocytopoietic cell	3.77e-07	5
mast cell	3.77e-07	5
mast cell progenitor	3.77e-07	5
basophil mast progenitor cell	3.77e-07	5

Uber Anatomy

Ontology term	p-value	n
bone marrow	1.39e-30	76
bone element	7.21e-28	82
immune system	1.02e-25	93
skeletal element	8.27e-25	90
hematopoietic system	4.64e-24	98
blood island	4.64e-24	98
skeletal system	1.64e-23	100
hemolymphoid system	3.35e-21	108
neural tube	3.05e-14	56
neural rod	3.05e-14	56
future spinal cord	3.05e-14	56
neural keel	3.05e-14	56
spinal cord	8.34e-12	3
dorsal region element	8.34e-12	3
dorsum	8.34e-12	3
musculoskeletal system	2.25e-11	167
regional part of nervous system	6.71e-10	53
regional part of brain	6.71e-10	53
central nervous system	8.59e-10	81
regional part of telencephalon	5.43e-09	32
lateral plate mesoderm	5.84e-09	203
regional part of cerebral cortex	1.01e-08	22
neural plate	1.36e-08	82
presumptive neural plate	1.36e-08	82
nervous system	1.89e-08	89
brain grey matter	2.25e-08	34
gray matter	2.25e-08	34
telencephalon	2.25e-08	34
posterior neural tube	2.90e-08	15
chordal neural plate	2.90e-08	15
regional part of forebrain	3.89e-08	41
forebrain	3.89e-08	41
anterior neural tube	3.89e-08	41
future forebrain	3.89e-08	41
neurectoderm	4.97e-08	86
middle temporal gyrus	5.26e-08	2
cerebral cortex	1.42e-07	25
pallium	1.42e-07	25
neocortex	2.10e-07	20
cerebral hemisphere	2.98e-07	32
brain	5.57e-07	68
future brain	5.57e-07	68

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.