Coexpression cluster:C1466

Full id: C1466_immature_Mast_CD14_Eosinophils_CD8_CD4_Basophils

Phase1 CAGE Peaks

Hg19::chr1:16163919..16163931,+	p@chr1:16163919..16163931 +
Hg19::chr9:102584241..102584261,+	p4@NR4A3
Hg19::chr9:102584262..102584276,+	p1@NR4A3
Hg19::chr9:102584278..102584285,+	p5@NR4A3
Hg19::chr9:102588066..102588078,+	p2@S81242
Hg19::chr9:102628236..102628245,+	p@chr9:102628236..102628245 +

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:0004887	thyroid hormone receptor activity	0.0123631225715295

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	9.03e-31	72
defensive cell	1.25e-27	48
phagocyte	1.25e-27	48
classical monocyte	1.55e-27	42
CD14-positive, CD16-negative classical monocyte	1.55e-27	42
granulocyte monocyte progenitor cell	4.74e-27	67
leukocyte	1.11e-25	136
macrophage dendritic cell progenitor	1.40e-24	61
myeloid lineage restricted progenitor cell	2.37e-23	66
monopoietic cell	5.22e-23	59
monocyte	5.22e-23	59
monoblast	5.22e-23	59
promonocyte	5.22e-23	59
myeloid cell	9.20e-17	108
common myeloid progenitor	9.20e-17	108
hematopoietic lineage restricted progenitor cell	1.44e-16	120
nongranular leukocyte	1.07e-15	115
hematopoietic stem cell	4.68e-15	168
angioblastic mesenchymal cell	4.68e-15	168
hematopoietic cell	1.15e-13	177
stuff accumulating cell	5.54e-13	87
hematopoietic oligopotent progenitor cell	6.55e-13	161
hematopoietic multipotent progenitor cell	6.55e-13	161
dendritic cell	1.63e-09	10
conventional dendritic cell	3.30e-08	8
granulocyte	1.37e-07	8
intermediate monocyte	5.25e-07	9
CD14-positive, CD16-positive monocyte	5.25e-07	9

Uber Anatomy

Ontology term	p-value	n
bone marrow	1.60e-25	76
bone element	3.82e-24	82
skeletal system	5.86e-22	100
hematopoietic system	1.91e-21	98
blood island	1.91e-21	98
skeletal element	1.11e-20	90
immune system	1.51e-19	93
hemolymphoid system	3.04e-17	108
adult organism	3.92e-09	114
musculoskeletal system	1.79e-07	167

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
BRCA1#672	3	10.0921153216119	0.00217104425335958	0.0125271652362774
CTCFL#140690	3	9.87323717948718	0.00231276002785771	0.0131194581798616
FOXA1#3169	3	5.54070987469273	0.0119217877786028	0.0433802380952372
JUN#3725	3	6.25641459616817	0.00848634685095487	0.032417907050727
RFX5#5993	3	6.02395541359755	0.00943790403633506	0.0356048713932523
STAT1#6772	3	10.3532937485996	0.00201668045992093	0.011722607589118
SUZ12#23512	3	25.0578904555315	0.000151757598305103	0.00195502797698121
TCF7L2#6934	3	5.38508828156867	0.0129048877993104	0.0464109358427058

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.