Coexpression cluster:C3811

Full id: C3811_Neutrophils_CD19_CD14CD16_CD14_migratory_Eosinophils_Peripheral

Phase1 CAGE Peaks

Hg19::chr19:49842010..49842054,+	p@chr19:49842010..49842054 +
Hg19::chr2:158300517..158300544,-	p2@CYTIP
Hg19::chr7:135662021..135662051,-	p2@MTPN

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:0021697	cerebellar cortex formation	0.000863456179598885
GO:0021533	cell differentiation in hindbrain	0.000863456179598885
GO:0021684	cerebellar granular layer formation	0.000863456179598885
GO:0021683	cerebellar granular layer morphogenesis	0.000863456179598885
GO:0021681	cerebellar granular layer development	0.000863456179598885
GO:0021707	cerebellar granule cell differentiation	0.000863456179598885
GO:0043403	skeletal muscle regeneration	0.00129518426939833
GO:0021575	hindbrain morphogenesis	0.00129518426939833
GO:0021587	cerebellum morphogenesis	0.00129518426939833
GO:0021696	cerebellar cortex morphogenesis	0.00129518426939833
GO:0021695	cerebellar cortex development	0.00141292829388908
GO:0022037	metencephalon development	0.00159407294695179
GO:0021549	cerebellum development	0.00159407294695179
GO:0016202	regulation of striated muscle development	0.00240534221459689
GO:0051146	striated muscle cell differentiation	0.00259036853879666
GO:0042246	tissue regeneration	0.00259036853879666
GO:0031099	regeneration	0.00274274315872587
GO:0030902	hindbrain development	0.00330991535512906
GO:0006584	catecholamine metabolic process	0.00349699752737549
GO:0018958	phenol metabolic process	0.00349699752737549
GO:0030424	axon	0.00419393001519459
GO:0048589	developmental growth	0.00435652890615801
GO:0042692	muscle cell differentiation	0.00518073707759331
GO:0006576	biogenic amine metabolic process	0.00798696966128969
GO:0043005	neuron projection	0.00839279406570117
GO:0014706	striated muscle development	0.00863456179598885
GO:0006575	amino acid derivative metabolic process	0.00863456179598885
GO:0042060	wound healing	0.0121192242350843
GO:0007420	brain development	0.0124159043756116
GO:0048646	anatomical structure formation	0.0132108795478629
GO:0007517	muscle development	0.0143723673765492
GO:0006725	aromatic compound metabolic process	0.0144432670041995
GO:0006417	regulation of translation	0.0144432670041995
GO:0031326	regulation of cellular biosynthetic process	0.0147020917066837
GO:0016049	cell growth	0.0147020917066837
GO:0008361	regulation of cell size	0.0147020917066837
GO:0030182	neuron differentiation	0.0147020917066837
GO:0009889	regulation of biosynthetic process	0.0147923677083914
GO:0007417	central nervous system development	0.0156086309389029
GO:0048699	generation of neurons	0.0156717296597198
GO:0022008	neurogenesis	0.0165530867601152
GO:0009888	tissue development	0.0188110096269757
GO:0042995	cell projection	0.0188554733172873
GO:0051246	regulation of protein metabolic process	0.0243494642646886
GO:0009611	response to wounding	0.0243494642646886
GO:0006066	alcohol metabolic process	0.0250589999948807
GO:0000902	cell morphogenesis	0.0257957533655167
GO:0032989	cellular structure morphogenesis	0.0257957533655167
GO:0006519	amino acid and derivative metabolic process	0.0289698359032769
GO:0009605	response to external stimulus	0.0323034194249936
GO:0009308	amine metabolic process	0.0323034194249936
GO:0006807	nitrogen compound metabolic process	0.033774420563541
GO:0007399	nervous system development	0.0349944127128001
GO:0065008	regulation of biological quality	0.0457152077309854
GO:0009653	anatomical structure morphogenesis	0.0493111974567291

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	2.54e-92	168
angioblastic mesenchymal cell	2.54e-92	168
leukocyte	7.05e-89	136
hematopoietic oligopotent progenitor cell	2.71e-88	161
hematopoietic multipotent progenitor cell	2.71e-88	161
hematopoietic cell	1.55e-84	177
nongranular leukocyte	1.79e-75	115
hematopoietic lineage restricted progenitor cell	6.33e-75	120
myeloid cell	2.84e-53	108
common myeloid progenitor	2.84e-53	108
myeloid leukocyte	3.92e-50	72
granulocyte monocyte progenitor cell	9.63e-45	67
myeloid lineage restricted progenitor cell	3.85e-42	66
macrophage dendritic cell progenitor	6.30e-42	61
monopoietic cell	7.65e-41	59
monocyte	7.65e-41	59
monoblast	7.65e-41	59
promonocyte	7.65e-41	59
defensive cell	7.47e-39	48
phagocyte	7.47e-39	48
classical monocyte	2.91e-35	42
CD14-positive, CD16-negative classical monocyte	2.91e-35	42
lymphocyte	2.05e-29	53
common lymphoid progenitor	2.05e-29	53
lymphoid lineage restricted progenitor cell	1.19e-28	52
nucleate cell	1.47e-28	55
mesenchymal cell	4.69e-18	354
lymphocyte of B lineage	4.10e-17	24
pro-B cell	4.10e-17	24
connective tissue cell	8.93e-17	361
stuff accumulating cell	5.67e-13	87
motile cell	9.08e-13	386
B cell	3.86e-12	14
T cell	3.07e-11	25
pro-T cell	3.07e-11	25
mature alpha-beta T cell	2.16e-10	18
alpha-beta T cell	2.16e-10	18
immature T cell	2.16e-10	18
mature T cell	2.16e-10	18
immature alpha-beta T cell	2.16e-10	18
intermediate monocyte	3.31e-09	9
CD14-positive, CD16-positive monocyte	3.31e-09	9
granulocyte	5.63e-08	8
multi fate stem cell	7.31e-08	427
stem cell	2.13e-07	441
somatic stem cell	3.07e-07	433

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.71e-50	98
blood island	2.71e-50	98
hemolymphoid system	3.33e-45	108
bone marrow	6.78e-39	76
immune system	1.41e-37	93
bone element	5.34e-34	82
skeletal element	1.48e-28	90
skeletal system	8.64e-24	100
connective tissue	1.61e-15	371
lateral plate mesoderm	8.01e-13	203
adult organism	4.18e-10	114
blood	4.51e-08	15
haemolymphatic fluid	4.51e-08	15
organism substance	4.51e-08	15

Disease

Ontology term	p-value	n
hematologic cancer	1.36e-09	51
immune system cancer	1.36e-09	51
leukemia	3.29e-07	39

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
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294489698785391

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.