Coexpression cluster:C2859

Full id: C2859_Dendritic_migratory_myeloma_adult_lymphangiectasia_xeroderma_cord

Phase1 CAGE Peaks

Hg19::chr6:391743..391759,+	p1@IRF4
Hg19::chr6:405020..405033,+	p@chr6:405020..405033 +
Hg19::chr6:407517..407528,+	p@chr6:407517..407528 +
Hg19::chr9:134497381..134497402,-	p6@RAPGEF1

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:0045368	positive regulation of interleukin-13 biosynthetic process	0.00213699113631954
GO:0045366	regulation of interleukin-13 biosynthetic process	0.00213699113631954
GO:0045082	positive regulation of interleukin-10 biosynthetic process	0.00213699113631954
GO:0042231	interleukin-13 biosynthetic process	0.00213699113631954
GO:0045074	regulation of interleukin-10 biosynthetic process	0.00213699113631954
GO:0032616	interleukin-13 production	0.00213699113631954
GO:0045404	positive regulation of interleukin-4 biosynthetic process	0.00213699113631954
GO:0042091	interleukin-10 biosynthetic process	0.00213699113631954
GO:0042097	interleukin-4 biosynthetic process	0.00213699113631954
GO:0045402	regulation of interleukin-4 biosynthetic process	0.00213699113631954
GO:0032633	interleukin-4 production	0.00259025416027356
GO:0032613	interleukin-10 production	0.00296795587240533
GO:0045622	regulation of T-helper cell differentiation	0.00339169993279774
GO:0002285	lymphocyte activation during immune response	0.00339169993279774
GO:0002293	alpha-beta T cell differentiation during immune response	0.00339169993279774
GO:0002294	CD4-positive, alpha-beta T cell differentiation during immune response	0.00339169993279774
GO:0002292	T cell differentiation during immune response	0.00339169993279774
GO:0042093	T-helper cell differentiation	0.00339169993279774
GO:0002366	leukocyte activation during immune response	0.00339169993279774
GO:0002286	T cell activation during immune response	0.00339169993279774
GO:0002263	cell activation during immune response	0.00339169993279774
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.0034063963100371
GO:0045086	positive regulation of interleukin-2 biosynthetic process	0.0034063963100371
GO:0045076	regulation of interleukin-2 biosynthetic process	0.00438273278584504
GO:0046632	alpha-beta T cell differentiation	0.00438273278584504
GO:0042094	interleukin-2 biosynthetic process	0.00438273278584504
GO:0046631	alpha-beta T cell activation	0.00501151475870867
GO:0032623	interleukin-2 production	0.00534106240657551
GO:0042108	positive regulation of cytokine biosynthetic process	0.00972973679009771
GO:0030217	T cell differentiation	0.00972973679009771
GO:0045727	positive regulation of translation	0.0121695889114223
GO:0042035	regulation of cytokine biosynthetic process	0.0129405954725452
GO:0031328	positive regulation of cellular biosynthetic process	0.0129405954725452
GO:0030098	lymphocyte differentiation	0.0133965329354952
GO:0042089	cytokine biosynthetic process	0.0134422564976761
GO:0042107	cytokine metabolic process	0.0134422564976761
GO:0009891	positive regulation of biosynthetic process	0.0134632306164145
GO:0051247	positive regulation of protein metabolic process	0.0159144746976325
GO:0002521	leukocyte differentiation	0.01641734330888
GO:0042110	T cell activation	0.0174276911454626
GO:0001816	cytokine production	0.0196007336599614
GO:0045595	regulation of cell differentiation	0.0243720698181301
GO:0046649	lymphocyte activation	0.0256195788897962
GO:0030097	hemopoiesis	0.0260042002809116
GO:0048534	hemopoietic or lymphoid organ development	0.0272332515236904
GO:0045321	leukocyte activation	0.0272332515236904
GO:0002520	immune system development	0.0272332515236904
GO:0006417	regulation of translation	0.0272332515236904
GO:0031326	regulation of cellular biosynthetic process	0.0288458775953045
GO:0001775	cell activation	0.0292418842593038
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0292418842593038
GO:0009889	regulation of biosynthetic process	0.0296324622673738
GO:0050793	regulation of developmental process	0.0316100824187841
GO:0003702	RNA polymerase II transcription factor activity	0.0359877839994034
GO:0045941	positive regulation of transcription	0.0359877839994034
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0366065852216123
GO:0007167	enzyme linked receptor protein signaling pathway	0.037138765578115
GO:0016563	transcription activator activity	0.037138765578115
GO:0005085	guanyl-nucleotide exchange factor activity	0.037138765578115
GO:0031325	positive regulation of cellular metabolic process	0.0431025408519966
GO:0009893	positive regulation of metabolic process	0.0453984533678038
GO:0051246	regulation of protein metabolic process	0.0481854091161337
GO:0008134	transcription factor binding	0.0485370818298729

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
leukocyte	9.05e-55	140
nongranular leukocyte	7.13e-48	119
hematopoietic lineage restricted progenitor cell	6.77e-45	124
hematopoietic stem cell	2.00e-40	172
angioblastic mesenchymal cell	2.00e-40	172
hematopoietic cell	1.51e-38	182
hematopoietic oligopotent progenitor cell	1.12e-37	165
hematopoietic multipotent progenitor cell	1.12e-37	165
lymphocyte	6.66e-28	53
common lymphoid progenitor	6.66e-28	53
lymphoid lineage restricted progenitor cell	3.75e-27	52
myeloid leukocyte	5.84e-20	76
granulocyte monocyte progenitor cell	1.00e-19	71
macrophage dendritic cell progenitor	3.63e-19	65
CD14-positive, CD16-negative classical monocyte	4.73e-19	42
monopoietic cell	4.89e-18	63
monocyte	4.89e-18	63
monoblast	4.89e-18	63
promonocyte	4.89e-18	63
lymphocyte of B lineage	2.38e-17	24
pro-B cell	2.38e-17	24
classical monocyte	2.82e-17	45
myeloid lineage restricted progenitor cell	6.36e-17	70
myeloid cell	2.84e-13	112
common myeloid progenitor	2.84e-13	112
B cell	4.58e-11	14
T cell	1.15e-09	25
pro-T cell	1.15e-09	25
dendritic cell	1.21e-09	10
mature alpha-beta T cell	6.29e-09	18
alpha-beta T cell	6.29e-09	18
immature T cell	6.29e-09	18
mature T cell	6.29e-09	18
immature alpha-beta T cell	6.29e-09	18
conventional dendritic cell	4.59e-08	8

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	9.75e-28	102
blood island	9.75e-28	102
hemolymphoid system	8.74e-26	112
bone marrow	2.55e-16	80
immune system	1.01e-14	115
bone element	1.21e-14	86
skeletal element	3.14e-10	101
skeletal system	3.14e-10	101
blood	7.63e-10	15
haemolymphatic fluid	7.63e-10	15
organism substance	7.63e-10	15
adult organism	6.63e-08	115

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
ZNF274#10782	1	355.436538461538	0.00281049764039454	0.0153855521053132

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.