Coexpression cluster:C1611

Full id: C1611_Renal_Hepatic_Eosinophils_Endothelial_CD14_heart_Neutrophils

Phase1 CAGE Peaks

Hg19::chr11:118481103..118481145,+	p5@PHLDB1
Hg19::chr17:1549011..1549032,-	p1@SCARF1
Hg19::chr20:23066953..23066974,-	p1@CD93
Hg19::chr20:23066988..23066999,-	p3@CD93
Hg19::chr3:119813131..119813152,-	p3@GSK3B

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:0004696	glycogen synthase kinase 3 activity	0.00409951773641881
GO:0046827	positive regulation of protein export from nucleus	0.00409951773641881
GO:0010324	membrane invagination	0.00409951773641881
GO:0006897	endocytosis	0.00409951773641881
GO:0001849	complement component C1q binding	0.00445576494695808
GO:0016044	membrane organization and biogenesis	0.00445576494695808
GO:0001846	opsonin binding	0.00445576494695808
GO:0046825	regulation of protein export from nucleus	0.00445576494695808
GO:0002039	p53 binding	0.00445576494695808
GO:0030877	beta-catenin destruction complex	0.00445576494695808
GO:0050321	tau-protein kinase activity	0.00445576494695808
GO:0006983	ER overload response	0.00445576494695808
GO:0045192	low-density lipoprotein catabolic process	0.00445576494695808
GO:0060070	Wnt receptor signaling pathway through beta-catenin	0.00517171777955849
GO:0001848	complement binding	0.00543014381110518
GO:0042159	lipoprotein catabolic process	0.00543014381110518
GO:0042116	macrophage activation	0.0069243814818691
GO:0046824	positive regulation of nucleocytoplasmic transport	0.0069243814818691
GO:0018209	peptidyl-serine modification	0.0069243814818691
GO:0018105	peptidyl-serine phosphorylation	0.0069243814818691
GO:0016043	cellular component organization and biogenesis	0.0069243814818691
GO:0016192	vesicle-mediated transport	0.0069243814818691
GO:0051222	positive regulation of protein transport	0.0069243814818691
GO:0006611	protein export from nucleus	0.00844490121160652
GO:0033554	cellular response to stress	0.00926471749863026
GO:0030169	low-density lipoprotein binding	0.00946487743275784
GO:0051059	NF-kappaB binding	0.00965017914071661
GO:0006810	transport	0.00980772946980233
GO:0051234	establishment of localization	0.0101317931421153
GO:0006984	ER-nuclear signaling pathway	0.0101317931421153
GO:0051716	cellular response to stimulus	0.0110433382966838
GO:0051179	localization	0.0110433382966838
GO:0022610	biological adhesion	0.0110433382966838
GO:0007155	cell adhesion	0.0110433382966838
GO:0002274	myeloid leukocyte activation	0.0110433382966838
GO:0051223	regulation of protein transport	0.0110433382966838
GO:0046822	regulation of nucleocytoplasmic transport	0.0110433382966838
GO:0008034	lipoprotein binding	0.0110433382966838
GO:0051050	positive regulation of transport	0.0140958045221106
GO:0006909	phagocytosis	0.0144654687403195
GO:0006898	receptor-mediated endocytosis	0.0144654687403195
GO:0006950	response to stress	0.0147825226066546
GO:0051168	nuclear export	0.0148005673400166
GO:0005977	glycogen metabolic process	0.0154266528202848
GO:0006073	glucan metabolic process	0.0154266528202848
GO:0006112	energy reserve metabolic process	0.0172885394330931
GO:0042157	lipoprotein metabolic process	0.0252825281241136
GO:0044264	cellular polysaccharide metabolic process	0.0252825281241136
GO:0005976	polysaccharide metabolic process	0.0253547441008835
GO:0007596	blood coagulation	0.0288789978975099
GO:0050817	coagulation	0.0288789978975099
GO:0007599	hemostasis	0.0291541032241128
GO:0051049	regulation of transport	0.0299617073999914
GO:0015980	energy derivation by oxidation of organic compounds	0.0312717550240248
GO:0018193	peptidyl-amino acid modification	0.0317491159829751
GO:0050878	regulation of body fluid levels	0.0322091855854129
GO:0042060	wound healing	0.0331571654041858
GO:0016055	Wnt receptor signaling pathway	0.0360530277052107
GO:0006913	nucleocytoplasmic transport	0.0374829917162732
GO:0051169	nuclear transport	0.0374829917162732
GO:0045321	leukocyte activation	0.0425105027103473
GO:0001775	cell activation	0.0484713101515121
GO:0005515	protein binding	0.0484713101515121
GO:0006605	protein targeting	0.0490166176015429

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 leukocyte	1.94e-28	72
classical monocyte	8.66e-28	42
CD14-positive, CD16-negative classical monocyte	8.66e-28	42
defensive cell	2.95e-25	48
phagocyte	2.95e-25	48
monopoietic cell	2.69e-24	59
monocyte	2.69e-24	59
monoblast	2.69e-24	59
promonocyte	2.69e-24	59
macrophage dendritic cell progenitor	9.51e-24	61
endothelial cell	1.26e-23	36
granulocyte monocyte progenitor cell	2.21e-23	67
endothelial cell of vascular tree	5.35e-22	24
myeloid lineage restricted progenitor cell	7.48e-22	66
myeloid cell	8.78e-21	108
common myeloid progenitor	8.78e-21	108
blood vessel endothelial cell	5.63e-17	18
embryonic blood vessel endothelial progenitor cell	5.63e-17	18
meso-epithelial cell	7.27e-17	45
leukocyte	5.13e-12	136
hematopoietic stem cell	2.75e-11	168
angioblastic mesenchymal cell	2.75e-11	168
hematopoietic oligopotent progenitor cell	4.51e-10	161
hematopoietic multipotent progenitor cell	4.51e-10	161
stuff accumulating cell	8.49e-10	87
nongranular leukocyte	1.55e-09	115
hematopoietic cell	1.77e-09	177
endothelial cell of artery	2.18e-09	9
lining cell	2.24e-09	58
barrier cell	2.24e-09	58
hematopoietic lineage restricted progenitor cell	2.48e-08	120
vein endothelial cell	6.62e-07	6
granulocyte	6.96e-07	8
aortic endothelial cell	8.63e-07	6

Uber Anatomy

Ontology term	p-value	n
adult organism	1.13e-41	114
hemolymphoid system	3.21e-28	108
lateral plate mesoderm	2.17e-27	203
hematopoietic system	3.40e-24	98
blood island	3.40e-24	98
immune system	8.89e-24	93
bone marrow	7.15e-19	76
blood vessel endothelium	5.63e-17	18
endothelium	5.63e-17	18
cardiovascular system endothelium	5.63e-17	18
bone element	5.21e-16	82
skeletal element	7.00e-13	90
simple squamous epithelium	2.32e-12	22
mesoderm	2.72e-11	315
mesoderm-derived structure	2.72e-11	315
presumptive mesoderm	2.72e-11	315
circulatory system	1.84e-10	112
neural tube	2.06e-10	56
neural rod	2.06e-10	56
future spinal cord	2.06e-10	56
neural keel	2.06e-10	56
skeletal system	2.42e-10	100
squamous epithelium	6.16e-10	25
tube	1.97e-09	192
endothelial tube	2.18e-09	9
arterial system endothelium	2.18e-09	9
endothelium of artery	2.18e-09	9
regional part of nervous system	2.50e-09	53
regional part of brain	2.50e-09	53
cardiovascular system	2.58e-09	109
anatomical conduit	4.23e-09	240
regional part of forebrain	1.34e-08	41
forebrain	1.34e-08	41
anterior neural tube	1.34e-08	41
future forebrain	1.34e-08	41
germ layer	5.84e-08	560
germ layer / neural crest	5.84e-08	560
embryonic tissue	5.84e-08	560
presumptive structure	5.84e-08	560
germ layer / neural crest derived structure	5.84e-08	560
epiblast (generic)	5.84e-08	560
embryonic structure	6.01e-08	564
brain grey matter	2.63e-07	34
gray matter	2.63e-07	34
vessel	2.71e-07	68
telencephalon	3.07e-07	34
anatomical system	3.08e-07	624
developing anatomical structure	3.77e-07	581
anatomical group	3.89e-07	625
embryo	5.17e-07	592
regional part of cerebral cortex	6.00e-07	22
cerebral hemisphere	9.26e-07	32

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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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.