Coexpression cluster:C4271

Full id: C4271_cord_migratory_CD14_immature_b_xeroderma_Dendritic

Phase1 CAGE Peaks

Hg19::chr3:119278376..119278390,-	p2@CD80
Hg19::chr9:114246503..114246515,-	p12@KIAA0368
Hg19::chr9:114246521..114246540,-	p5@KIAA0368

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:0045627	positive regulation of T-helper 1 cell differentiation	0.00585830455523893
GO:0045425	positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process	0.00585830455523893
GO:0045625	regulation of T-helper 1 cell differentiation	0.00585830455523893
GO:0045624	positive regulation of T-helper cell differentiation	0.00585830455523893
GO:0045423	regulation of granulocyte macrophage colony-stimulating factor biosynthetic process	0.00585830455523893
GO:0045063	T-helper 1 cell differentiation	0.00585830455523893
GO:0032604	granulocyte macrophage colony-stimulating factor production	0.00585830455523893
GO:0042253	granulocyte macrophage colony-stimulating factor biosynthetic process	0.00585830455523893
GO:0045622	regulation of T-helper cell differentiation	0.00585830455523893
GO:0002294	CD4-positive, alpha-beta T cell differentiation during immune response	0.00585830455523893
GO:0002292	T cell differentiation during immune response	0.00585830455523893
GO:0042093	T-helper cell differentiation	0.00585830455523893
GO:0002366	leukocyte activation during immune response	0.00585830455523893
GO:0002285	lymphocyte activation during immune response	0.00585830455523893
GO:0002293	alpha-beta T cell differentiation during immune response	0.00585830455523893
GO:0002286	T cell activation during immune response	0.00585830455523893
GO:0002263	cell activation during immune response	0.00585830455523893
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.00585830455523893
GO:0045086	positive regulation of interleukin-2 biosynthetic process	0.00585830455523893
GO:0030433	ER-associated protein catabolic process	0.00585830455523893
GO:0006515	misfolded or incompletely synthesized protein catabolic process	0.00585830455523893
GO:0042088	T-helper 1 type immune response	0.00610029345454885
GO:0030134	ER to Golgi transport vesicle	0.00662708906093496
GO:0045076	regulation of interleukin-2 biosynthetic process	0.00662708906093496
GO:0015026	coreceptor activity	0.00662708906093496
GO:0042094	interleukin-2 biosynthetic process	0.00662708906093496
GO:0046632	alpha-beta T cell differentiation	0.00662708906093496
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.00678970780813472
GO:0046631	alpha-beta T cell activation	0.00732660892338999
GO:0032623	interleukin-2 production	0.00782767272809414
GO:0043161	proteasomal ubiquitin-dependent protein catabolic process	0.00803710586941609
GO:0042327	positive regulation of phosphorylation	0.00803710586941609
GO:0045937	positive regulation of phosphate metabolic process	0.00838605134778403
GO:0001934	positive regulation of protein amino acid phosphorylation	0.00838605134778403
GO:0033240	positive regulation of amine metabolic process	0.00838605134778403
GO:0045764	positive regulation of amino acid metabolic process	0.00838605134778403
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.00846147677070778
GO:0042108	positive regulation of cytokine biosynthetic process	0.0114266798003558
GO:0030217	T cell differentiation	0.0114266798003558
GO:0018108	peptidyl-tyrosine phosphorylation	0.0114266798003558
GO:0005793	ER-Golgi intermediate compartment	0.0114266798003558
GO:0018212	peptidyl-tyrosine modification	0.0114266798003558
GO:0001932	regulation of protein amino acid phosphorylation	0.0114266798003558
GO:0033238	regulation of amine metabolic process	0.0114266798003558
GO:0006521	regulation of amino acid metabolic process	0.0114266798003558
GO:0005769	early endosome	0.0119067654502945
GO:0005770	late endosome	0.0121287229252704
GO:0045727	positive regulation of translation	0.0123414047328301
GO:0042035	regulation of cytokine biosynthetic process	0.0132576707148612
GO:0031328	positive regulation of cellular biosynthetic process	0.0132576707148612
GO:0030133	transport vesicle	0.0132576707148612
GO:0042325	regulation of phosphorylation	0.0132576707148612
GO:0030098	lymphocyte differentiation	0.0132576707148612
GO:0042089	cytokine biosynthetic process	0.0132576707148612
GO:0042107	cytokine metabolic process	0.0132576707148612
GO:0051174	regulation of phosphorus metabolic process	0.0132576707148612
GO:0019220	regulation of phosphate metabolic process	0.0132576707148612
GO:0005798	Golgi-associated vesicle	0.0132576707148612
GO:0009891	positive regulation of biosynthetic process	0.0132576707148612
GO:0000502	proteasome complex (sensu Eukaryota)	0.0136963456940561
GO:0002250	adaptive immune response	0.0136963456940561
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0136963456940561
GO:0051247	positive regulation of protein metabolic process	0.0150731348966164
GO:0002521	leukocyte differentiation	0.0157092605783575
GO:0042110	T cell activation	0.0168404898544839
GO:0001816	cytokine production	0.019119673830591
GO:0018193	peptidyl-amino acid modification	0.0201653291102759
GO:0005813	centrosome	0.0211799199203176
GO:0045595	regulation of cell differentiation	0.0231093223870945
GO:0030135	coated vesicle	0.0231093223870945
GO:0005815	microtubule organizing center	0.0231093223870945
GO:0009967	positive regulation of signal transduction	0.023696587742515
GO:0046649	lymphocyte activation	0.023696587742515
GO:0030097	hemopoiesis	0.0242791059133819
GO:0048534	hemopoietic or lymphoid organ development	0.025736321880546
GO:0045321	leukocyte activation	0.0263156658080161
GO:0002520	immune system development	0.0263156658080161
GO:0006417	regulation of translation	0.0263156658080161
GO:0005768	endosome	0.0272498221085682
GO:0031326	regulation of cellular biosynthetic process	0.0277432975632526
GO:0001775	cell activation	0.0287734637137277
GO:0009889	regulation of biosynthetic process	0.0295070275349378
GO:0050793	regulation of developmental process	0.0316950642195714
GO:0045941	positive regulation of transcription	0.0361358867797147
GO:0006511	ubiquitin-dependent protein catabolic process	0.0361358867797147
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0361358867797147
GO:0019941	modification-dependent protein catabolic process	0.0361358867797147
GO:0043632	modification-dependent macromolecule catabolic process	0.0361358867797147
GO:0051603	proteolysis involved in cellular protein catabolic process	0.0361358867797147
GO:0044257	cellular protein catabolic process	0.0361358867797147
GO:0016563	transcription activator activity	0.0378099684071082
GO:0016023	cytoplasmic membrane-bound vesicle	0.0419746224953009
GO:0031988	membrane-bound vesicle	0.0421184849722903
GO:0030163	protein catabolic process	0.0421414493810656
GO:0031325	positive regulation of cellular metabolic process	0.0427463215061124
GO:0009893	positive regulation of metabolic process	0.045296838372318
GO:0044431	Golgi apparatus part	0.0477196729912479
GO:0051246	regulation of protein metabolic process	0.0477196729912479
GO:0031410	cytoplasmic vesicle	0.0477196729912479
GO:0031982	vesicle	0.0480156090498826
GO:0043285	biopolymer catabolic process	0.0499449550303376

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
granulocyte monocyte progenitor cell	2.84e-23	71
macrophage dendritic cell progenitor	1.78e-22	65
myeloid leukocyte	1.48e-21	76
myeloid lineage restricted progenitor cell	1.54e-21	70
monopoietic cell	2.79e-21	63
monocyte	2.79e-21	63
monoblast	2.79e-21	63
promonocyte	2.79e-21	63
classical monocyte	1.77e-20	45
CD14-positive, CD16-negative classical monocyte	4.90e-20	42
myeloid cell	6.03e-20	112
common myeloid progenitor	6.03e-20	112
leukocyte	1.55e-16	140
hematopoietic oligopotent progenitor cell	4.80e-15	165
hematopoietic multipotent progenitor cell	4.80e-15	165
hematopoietic stem cell	6.18e-15	172
angioblastic mesenchymal cell	6.18e-15	172
hematopoietic lineage restricted progenitor cell	2.04e-14	124
hematopoietic cell	2.73e-14	182
nongranular leukocyte	3.47e-14	119

Uber Anatomy

Ontology term	p-value	n
immune system	3.60e-22	115
bone marrow	3.54e-19	80
bone element	1.60e-18	86
hemolymphoid system	4.72e-17	112
hematopoietic system	2.04e-16	102
blood island	2.04e-16	102
skeletal element	1.82e-13	101
skeletal system	1.82e-13	101
mesoderm	1.31e-07	448
mesoderm-derived structure	1.31e-07	448
presumptive mesoderm	1.31e-07	448

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
BATF#10538	2	16.2385345282024	0.00491746240780997	0.0230024121650587
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280356889874197
FOSL1#8061	2	26.4757198109153	0.00186983370259098	0.0110273624747247
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376861265887285
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0330021694188353
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330329781723973

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.