Coexpression cluster:C712

Full id: C712_thymus_biphenotypic_CD4_non_granulocyte_merkel_acute

Phase1 CAGE Peaks

Hg19::chr3:18480105..18480108,-	p48@SATB1
Hg19::chr3:18480151..18480162,-	p18@SATB1
Hg19::chr3:18480173..18480189,-	p6@SATB1
Hg19::chr3:18486202..18486209,-	p5@TBC1D5
Hg19::chr3:18486296..18486319,-	p3@TBC1D5
Hg19::chr3:18486324..18486338,-	p4@TBC1D5
Hg19::chr3:18486354..18486377,-	p2@SATB1
Hg19::chr3:18486459..18486481,+	p2@ENST00000414198
Hg19::chr3:18486486..18486500,+	p1@ENST00000414198
Hg19::chr3:18487033..18487044,-	p23@SATB1
Hg19::chr3:18487057..18487105,-	p4@SATB1
Hg19::chr8:66754259..66754276,-	p2@PDE7A

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:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.0284167707669588
GO:0016571	histone methylation	0.0284167707669588
GO:0005720	nuclear heterochromatin	0.0284167707669588
GO:0000792	heterochromatin	0.0284167707669588
GO:0008213	protein amino acid alkylation	0.0284167707669588
GO:0006479	protein amino acid methylation	0.0284167707669588
GO:0000790	nuclear chromatin	0.0284167707669588
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0360071200977271
GO:0043414	biopolymer methylation	0.0360071200977271
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0360071200977271
GO:0016570	histone modification	0.0360071200977271
GO:0016569	covalent chromatin modification	0.0360071200977271
GO:0044454	nuclear chromosome part	0.0444142842183568
GO:0032259	methylation	0.0444142842183568

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	8.80e-36	168
angioblastic mesenchymal cell	8.80e-36	168
hematopoietic cell	2.16e-34	177
hematopoietic oligopotent progenitor cell	6.27e-31	161
hematopoietic multipotent progenitor cell	6.27e-31	161
leukocyte	5.82e-28	136
nongranular leukocyte	1.66e-26	115
lymphoid lineage restricted progenitor cell	4.62e-25	52
lymphocyte	2.86e-24	53
common lymphoid progenitor	2.86e-24	53
hematopoietic lineage restricted progenitor cell	3.02e-23	120
nucleate cell	8.87e-23	55
T cell	4.51e-21	25
pro-T cell	4.51e-21	25
mature alpha-beta T cell	1.77e-18	18
alpha-beta T cell	1.77e-18	18
immature T cell	1.77e-18	18
mature T cell	1.77e-18	18
immature alpha-beta T cell	1.77e-18	18
CD8-positive, alpha-beta T cell	4.57e-12	11
myeloid cell	2.04e-10	108
common myeloid progenitor	2.04e-10	108
B cell	1.42e-09	14
CD4-positive, alpha-beta T cell	2.41e-07	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.04e-13	98
blood island	6.04e-13	98
blood	2.29e-12	15
haemolymphatic fluid	2.29e-12	15
organism substance	2.29e-12	15
hemolymphoid system	9.84e-12	108
neocortex	4.60e-09	20
adult organism	6.34e-09	114
regional part of cerebral cortex	8.11e-09	22
cerebral cortex	3.55e-07	25
pallium	3.55e-07	25

Disease

Ontology term	p-value	n
hematologic cancer	2.29e-11	51
immune system cancer	2.29e-11	51
leukemia	1.62e-10	39
myeloid leukemia	3.30e-09	31

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)
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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
CTCF#10664	7	3.1268162176271	0.00257034513840731	0.0142199531682446

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.