Coexpression cluster:C3568

Full id: C3568_Mast_Eosinophils_CD4_immature_CD8_Neutrophils_Natural

Phase1 CAGE Peaks

Hg19::chr16:50776050..50776074,+	p3@CYLD
Hg19::chr1:100818080..100818094,+	p2@CDC14A
Hg19::chr9:2017714..2017737,+	p@chr9:2017714..2017737 +

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:0007049	cell cycle	0.0463706779592514
GO:0016788	hydrolase activity, acting on ester bonds	0.0463706779592514
GO:0005856	cytoskeleton	0.0469426303635197
GO:0008138	protein tyrosine/serine/threonine phosphatase activity	0.049963050018113
GO:0043687	post-translational protein modification	0.049963050018113
GO:0006464	protein modification process	0.049963050018113
GO:0043412	biopolymer modification	0.049963050018113
GO:0043232	intracellular non-membrane-bound organelle	0.049963050018113
GO:0043228	non-membrane-bound organelle	0.049963050018113
GO:0005813	centrosome	0.049963050018113
GO:0004221	ubiquitin thiolesterase activity	0.049963050018113
GO:0004843	ubiquitin-specific protease activity	0.049963050018113
GO:0019783	small conjugating protein-specific protease activity	0.049963050018113
GO:0005815	microtubule organizing center	0.049963050018113

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	6.91e-31	136
hematopoietic stem cell	1.03e-28	168
angioblastic mesenchymal cell	1.03e-28	168
hematopoietic cell	3.46e-27	177
hematopoietic oligopotent progenitor cell	4.36e-26	161
hematopoietic multipotent progenitor cell	4.36e-26	161
hematopoietic lineage restricted progenitor cell	3.08e-23	120
nongranular leukocyte	5.74e-22	115
myeloid leukocyte	6.22e-16	72
myeloid cell	1.32e-14	108
common myeloid progenitor	1.32e-14	108
granulocyte monocyte progenitor cell	2.98e-13	67
mature alpha-beta T cell	1.22e-12	18
alpha-beta T cell	1.22e-12	18
immature T cell	1.22e-12	18
mature T cell	1.22e-12	18
immature alpha-beta T cell	1.22e-12	18
myeloid lineage restricted progenitor cell	1.77e-11	66
lymphocyte	2.54e-11	53
common lymphoid progenitor	2.54e-11	53
lymphoid lineage restricted progenitor cell	2.93e-11	52
nucleate cell	1.11e-10	55
macrophage dendritic cell progenitor	1.58e-10	61
classical monocyte	2.44e-10	42
CD14-positive, CD16-negative classical monocyte	2.44e-10	42
monopoietic cell	9.75e-10	59
monocyte	9.75e-10	59
monoblast	9.75e-10	59
promonocyte	9.75e-10	59
T cell	8.24e-09	25
pro-T cell	8.24e-09	25
defensive cell	2.29e-08	48
phagocyte	2.29e-08	48
CD8-positive, alpha-beta T cell	2.37e-08	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.11e-19	98
blood island	1.11e-19	98
hemolymphoid system	1.19e-19	108
adult organism	8.02e-17	114
immune system	1.37e-13	93
bone marrow	4.98e-11	76
bone element	8.14e-11	82
skeletal element	1.00e-08	90
blood	2.41e-08	15
haemolymphatic fluid	2.41e-08	15
organism substance	2.41e-08	15
skeletal system	2.65e-07	100
lateral plate mesoderm	8.19e-07	203

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
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461426883748348
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027619740102932
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328802131221092

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.