Coexpression cluster:C3456

Full id: C3456_Basophils_Eosinophils_Mast_CD14_CD34_Natural_CD8

Phase1 CAGE Peaks

Hg19::chr14:75744049..75744066,+	p@chr14:75744049..75744066 +
Hg19::chr1:110438789..110438831,+	p1@BC015716
Hg19::chr20:4795556..4795568,+	p@chr20:4795556..4795568 +

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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No GOStat results

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	2.34e-83	72
classical monocyte	7.67e-79	42
CD14-positive, CD16-negative classical monocyte	7.67e-79	42
leukocyte	1.07e-75	136
defensive cell	1.60e-67	48
phagocyte	1.60e-67	48
granulocyte monocyte progenitor cell	1.70e-64	67
hematopoietic stem cell	8.31e-64	168
angioblastic mesenchymal cell	8.31e-64	168
myeloid lineage restricted progenitor cell	1.01e-62	66
hematopoietic cell	1.13e-59	177
macrophage dendritic cell progenitor	5.71e-58	61
monopoietic cell	2.34e-57	59
monocyte	2.34e-57	59
monoblast	2.34e-57	59
promonocyte	2.34e-57	59
myeloid cell	2.60e-57	108
common myeloid progenitor	2.60e-57	108
hematopoietic oligopotent progenitor cell	5.98e-55	161
hematopoietic multipotent progenitor cell	5.98e-55	161
hematopoietic lineage restricted progenitor cell	6.21e-54	120
nongranular leukocyte	6.09e-52	115
stuff accumulating cell	4.05e-32	87
mesenchymal cell	5.87e-21	354
granulocyte	7.98e-21	8
connective tissue cell	3.31e-20	361
motile cell	1.46e-17	386
intermediate monocyte	2.83e-16	9
CD14-positive, CD16-positive monocyte	2.83e-16	9
blood cell	1.12e-14	11
multi fate stem cell	2.45e-14	427
stem cell	4.98e-14	441
somatic stem cell	6.81e-14	433
basophil	3.52e-09	3
histamine secreting cell	4.55e-09	5
biogenic amine secreting cell	4.55e-09	5
granulocytopoietic cell	4.55e-09	5
mast cell	4.55e-09	5
mast cell progenitor	4.55e-09	5
basophil mast progenitor cell	4.55e-09	5
natural killer cell	8.47e-09	3
pro-NK cell	8.47e-09	3
neutrophil	2.43e-08	3
single nucleate cell	5.44e-08	3
mononuclear cell	5.44e-08	3
mature alpha-beta T cell	2.97e-07	18
alpha-beta T cell	2.97e-07	18
immature T cell	2.97e-07	18
mature T cell	2.97e-07	18
immature alpha-beta T cell	2.97e-07	18
plasmacytoid dendritic cell	3.08e-07	3

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.54e-58	98
blood island	2.54e-58	98
bone marrow	4.16e-58	76
bone element	6.24e-53	82
hemolymphoid system	1.34e-51	108
immune system	2.46e-47	93
skeletal element	4.27e-47	90
skeletal system	4.13e-41	100
lateral plate mesoderm	8.62e-21	203
musculoskeletal system	1.50e-19	167
connective tissue	3.51e-19	371
mesoderm	1.15e-08	315
mesoderm-derived structure	1.15e-08	315
presumptive mesoderm	1.15e-08	315

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
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319794597157155
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461112292383938
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225838474478152

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.