Coexpression cluster:C531

Full id: C531_Neutrophils_Eosinophils_large_CD14_rectal_epitheloid_Hep2

Phase1 CAGE Peaks

Hg19::chr11:3818756..3818793,-	p1@NUP98
Hg19::chr1:207495013..207495037,+	p1@CD55
Hg19::chr1:207495772..207495786,+	p7@CD55
Hg19::chr1:207495790..207495803,+	p17@CD55
Hg19::chr1:207495844..207495859,+	p14@CD55
Hg19::chr1:207497905..207497939,+	p3@CD55
Hg19::chr1:207497946..207497958,+	p11@CD55
Hg19::chr1:207497988..207498028,+	p4@CD55
Hg19::chr1:207498974..207498994,+	p9@CD55
Hg19::chr1:207498999..207499011,+	p13@CD55
Hg19::chr1:207499012..207499044,+	p5@CD55
Hg19::chr1:207500090..207500105,+	p6@CD55
Hg19::chr1:207504446..207504457,+	p@chr1:207504446..207504457 +
Hg19::chr1:207504490..207504510,+	p@chr1:207504490..207504510 +
Hg19::chr1:207504564..207504579,+	p@chr1:207504564..207504579 +
Hg19::chr1:207504605..207504622,+	p@chr1:207504605..207504622 +
Hg19::chr1:207510129..207510165,-	p@chr1:207510129..207510165 -

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:0006999	nuclear pore organization and biogenesis	0.0122744532210089
GO:0045730	respiratory burst	0.0122744532210089
GO:0017056	structural constituent of nuclear pore	0.0190924697548727
GO:0000059	protein import into nucleus, docking	0.0218419002159206
GO:0006958	complement activation, classical pathway	0.0218419002159206
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0218419002159206
GO:0006997	nuclear organization and biogenesis	0.0218419002159206
GO:0006956	complement activation	0.0218419002159206
GO:0002541	activation of plasma proteins during acute inflammatory response	0.0218419002159206
GO:0045121	lipid raft	0.0218419002159206
GO:0016064	immunoglobulin mediated immune response	0.0218419002159206
GO:0019724	B cell mediated immunity	0.0218419002159206
GO:0043623	cellular protein complex assembly	0.0218419002159206
GO:0065002	intracellular protein transport across a membrane	0.0218419002159206
GO:0051480	cytosolic calcium ion homeostasis	0.0218419002159206
GO:0007204	elevation of cytosolic calcium ion concentration	0.0218419002159206
GO:0002253	activation of immune response	0.0218419002159206
GO:0002449	lymphocyte mediated immunity	0.0218419002159206
GO:0006959	humoral immune response	0.0218419002159206
GO:0002250	adaptive immune response	0.0218419002159206
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0218419002159206
GO:0002443	leukocyte mediated immunity	0.0218419002159206
GO:0002526	acute inflammatory response	0.0218419002159206
GO:0051028	mRNA transport	0.0218419002159206
GO:0050778	positive regulation of immune response	0.0218419002159206
GO:0002684	positive regulation of immune system process	0.0218419002159206
GO:0005643	nuclear pore	0.0218419002159206
GO:0050658	RNA transport	0.0218419002159206
GO:0051236	establishment of RNA localization	0.0218419002159206
GO:0050657	nucleic acid transport	0.0218419002159206
GO:0006403	RNA localization	0.0218419002159206
GO:0006606	protein import into nucleus	0.0218419002159206
GO:0046930	pore complex	0.0218419002159206
GO:0050776	regulation of immune response	0.0218419002159206
GO:0051170	nuclear import	0.0218419002159206
GO:0002682	regulation of immune system process	0.0218419002159206
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0218419002159206
GO:0051240	positive regulation of multicellular organismal process	0.0218419002159206
GO:0002252	immune effector process	0.0218419002159206
GO:0044453	nuclear membrane part	0.0218419002159206
GO:0045087	innate immune response	0.0218419002159206
GO:0006874	cellular calcium ion homeostasis	0.0218419002159206
GO:0055074	calcium ion homeostasis	0.0218419002159206
GO:0017038	protein import	0.0218419002159206
GO:0006875	cellular metal ion homeostasis	0.0218419002159206
GO:0055065	metal ion homeostasis	0.0218419002159206
GO:0048503	GPI anchor binding	0.0218976048652095
GO:0031965	nuclear membrane	0.02547336752759
GO:0006913	nucleocytoplasmic transport	0.02547336752759
GO:0051169	nuclear transport	0.02547336752759
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0287214589601625
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0287214589601625
GO:0005635	nuclear envelope	0.0298685474727805
GO:0030003	cellular cation homeostasis	0.0301136843778026
GO:0055080	cation homeostasis	0.0301136843778026
GO:0006605	protein targeting	0.0317543212284013
GO:0005625	soluble fraction	0.0327573563177623
GO:0055082	cellular chemical homeostasis	0.0327573563177623
GO:0006873	cellular ion homeostasis	0.0327573563177623
GO:0035091	phosphoinositide binding	0.0341071295173144
GO:0050801	ion homeostasis	0.0356780789030172
GO:0051239	regulation of multicellular organismal process	0.0364119499824043
GO:0006954	inflammatory response	0.0376372976168732
GO:0048878	chemical homeostasis	0.0384434488269865
GO:0005543	phospholipid binding	0.041843015573562
GO:0006461	protein complex assembly	0.0419455896578316
GO:0006260	DNA replication	0.0431328841847652
GO:0019725	cellular homeostasis	0.0448795788258851
GO:0009893	positive regulation of metabolic process	0.0461053402929223
GO:0009611	response to wounding	0.0491428245464635

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
classical monocyte	5.30e-24	42
CD14-positive, CD16-negative classical monocyte	5.30e-24	42
defensive cell	5.79e-20	48
phagocyte	5.79e-20	48
myeloid leukocyte	3.74e-18	72
granulocyte monocyte progenitor cell	1.33e-15	67
leukocyte	1.69e-15	136
myeloid lineage restricted progenitor cell	1.78e-15	66
myeloid cell	2.84e-15	108
common myeloid progenitor	2.84e-15	108
macrophage dendritic cell progenitor	5.64e-15	61
monopoietic cell	6.60e-14	59
monocyte	6.60e-14	59
monoblast	6.60e-14	59
promonocyte	6.60e-14	59
hematopoietic stem cell	3.04e-13	168
angioblastic mesenchymal cell	3.04e-13	168
hematopoietic oligopotent progenitor cell	3.06e-13	161
hematopoietic multipotent progenitor cell	3.06e-13	161
hematopoietic lineage restricted progenitor cell	7.77e-13	120
hematopoietic cell	1.03e-11	177
nongranular leukocyte	3.16e-11	115
stuff accumulating cell	1.52e-07	87

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	7.30e-14	98
blood island	7.30e-14	98
hemolymphoid system	1.12e-12	108
bone marrow	2.67e-11	76
bone element	5.72e-11	82
immune system	1.13e-09	93
skeletal element	1.56e-08	90
larynx	5.35e-08	9
skeletal system	1.12e-07	100

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
POLR2A#5430	17	2.14745317655807	2.27473247069268e-06	8.12763546037197e-05

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.