Coexpression cluster:C2446

Full id: C2446_Mast_CD4_CD8_CD19_Natural_Neutrophils_Peripheral

Phase1 CAGE Peaks

Hg19::chr17:8059638..8059683,-	p1@PER1
Hg19::chr6:138188358..138188371,+	p2@TNFAIP3
Hg19::chrX:106957890..106957911,-	p@chrX:106957890..106957911 -
Hg19::chrX:106960285..106960299,-	p1@TSC22D3

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:0009649	entrainment of circadian clock	0.0235747706921152
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.0235747706921152
GO:0000155	two-component sensor activity	0.0350534801834528
GO:0000160	two-component signal transduction system (phosphorelay)	0.0350534801834528
GO:0004673	protein histidine kinase activity	0.0350534801834528
GO:0007623	circadian rhythm	0.0350534801834528
GO:0016775	phosphotransferase activity, nitrogenous group as acceptor	0.0350534801834528
GO:0048523	negative regulation of cellular process	0.0350534801834528
GO:0048519	negative regulation of biological process	0.0350534801834528
GO:0050794	regulation of cellular process	0.0421090180801356
GO:0050789	regulation of biological process	0.0477491028920505

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	3.03e-22	140
CD14-positive, CD16-negative classical monocyte	2.25e-16	42
hematopoietic lineage restricted progenitor cell	3.39e-16	124
nongranular leukocyte	4.84e-16	119
classical monocyte	2.71e-14	45
myeloid leukocyte	4.38e-12	76
hematopoietic stem cell	9.65e-11	172
angioblastic mesenchymal cell	9.65e-11	172
mature alpha-beta T cell	4.16e-10	18
alpha-beta T cell	4.16e-10	18
immature T cell	4.16e-10	18
mature T cell	4.16e-10	18
immature alpha-beta T cell	4.16e-10	18
hematopoietic cell	5.34e-10	182
granulocyte monocyte progenitor cell	1.17e-09	71
hematopoietic oligopotent progenitor cell	4.24e-09	165
hematopoietic multipotent progenitor cell	4.24e-09	165
macrophage dendritic cell progenitor	1.60e-08	65
lymphoid lineage restricted progenitor cell	2.14e-08	52
myeloid lineage restricted progenitor cell	7.72e-08	70
monopoietic cell	8.57e-08	63
monocyte	8.57e-08	63
monoblast	8.57e-08	63
promonocyte	8.57e-08	63
lymphocyte	1.04e-07	53
common lymphoid progenitor	1.04e-07	53

Uber Anatomy

Ontology term	p-value	n
adult organism	4.17e-26	115
hematopoietic system	1.90e-14	102
blood island	1.90e-14	102
hemolymphoid system	1.98e-12	112
bone marrow	4.09e-09	80
immune system	4.71e-08	115
bone element	6.26e-08	86

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
BHLHE40#8553	2	22.4359067734887	0.00289146449685312	0.0156394251689286
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0466206177908537
MEF2C#4208	2	20.655677246312	0.00340257057944504	0.0173566996554977
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428380504769958
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227613227786074
USF1#7391	3	4.77112445790597	0.0137046588718802	0.048304170224437
USF2#7392	3	9.7441480388022	0.00171834184841007	0.0107199034888059

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.