Coexpression cluster:C1561

Full id: C1561_Mast_Eosinophils_Neutrophils_CD14_immature_Whole_Hep2

Phase1 CAGE Peaks

Hg19::chr10:106113292..106113306,-	p3@ENST00000435434
Hg19::chr14:35452304..35452319,+	p4@SRP54
Hg19::chr1:203273760..203273784,-	p1@ENST00000425698
Hg19::chr6:31702698..31702709,+	p@chr6:31702698..31702709 +
Hg19::chr8:22553096..22553123,+	p@chr8:22553096..22553123 +

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:0005786	signal recognition particle, endoplasmic reticulum targeting	0.00671140939597315
GO:0048500	signal recognition particle	0.00671140939597315
GO:0045047	protein targeting to ER	0.00671140939597315
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	0.00671140939597315
GO:0008312	7S RNA binding	0.00671140939597315
GO:0006613	cotranslational protein targeting to membrane	0.00735900153067232
GO:0006612	protein targeting to membrane	0.00908311046071554
GO:0016607	nuclear speck	0.0183239138113741
GO:0016604	nuclear body	0.0211939244083363
GO:0006605	protein targeting	0.0385022960084776
GO:0045045	secretory pathway	0.0385344080151568
GO:0032940	secretion by cell	0.0437124690921936

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
hematopoietic stem cell	1.75e-34	172
angioblastic mesenchymal cell	1.75e-34	172
hematopoietic cell	1.52e-33	182
hematopoietic oligopotent progenitor cell	1.70e-32	165
hematopoietic multipotent progenitor cell	1.70e-32	165
myeloid cell	3.33e-31	112
common myeloid progenitor	3.33e-31	112
leukocyte	1.05e-29	140
myeloid leukocyte	7.06e-27	76
stem cell	1.87e-25	444
multi fate stem cell	2.75e-24	430
CD14-positive, CD16-negative classical monocyte	2.99e-24	42
hematopoietic lineage restricted progenitor cell	3.29e-24	124
somatic stem cell	1.52e-23	436
classical monocyte	3.63e-23	45
myeloid lineage restricted progenitor cell	4.77e-23	70
granulocyte monocyte progenitor cell	6.79e-23	71
nongranular leukocyte	5.45e-21	119
macrophage dendritic cell progenitor	1.42e-20	65
monopoietic cell	2.00e-19	63
monocyte	2.00e-19	63
monoblast	2.00e-19	63
promonocyte	2.00e-19	63
mesenchymal cell	4.20e-19	358
native cell	6.04e-19	722
animal cell	1.41e-18	679
eukaryotic cell	1.41e-18	679
connective tissue cell	3.01e-17	365
motile cell	4.45e-14	390
somatic cell	7.61e-11	591

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.33e-24	102
blood island	1.33e-24	102
hemolymphoid system	1.41e-21	112
bone marrow	2.39e-20	80
bone element	7.97e-19	86
connective tissue	1.89e-16	375
lateral plate mesoderm	4.49e-16	216
skeletal element	6.79e-16	101
skeletal system	6.79e-16	101
immune system	2.49e-15	115
musculoskeletal system	9.76e-15	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)
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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
EBF1#1879	3	5.3438801079414	0.0118761556386811	0.0432232303717668
ELF1#1997	4	3.40647836704603	0.0123506610529955	0.0447195496364511
ELK4#2005	3	9.74140899508082	0.0021255865657434	0.0122852316181337
POU2F2#5452	4	7.28489924619402	0.000663122328874386	0.00542247360674225

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.