Coexpression cluster:C3131

Full id: C3131_CD8_Natural_Peripheral_CD4_Eosinophils_CD14_Basophils

Phase1 CAGE Peaks

Hg19::chr11:207734..207745,+	p7@RIC8A
Hg19::chr11:208610..208627,-	p@chr11:208610..208627 -
Hg19::chr11:236025..236096,+	p3@PSMD13

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:0001965	G-protein alpha-subunit binding	0.00188387666372531
GO:0005838	proteasome regulatory particle (sensu Eukaryota)	0.00565079814737156
GO:0000502	proteasome complex (sensu Eukaryota)	0.0232098562760032

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
somatic cell	2.68e-23	591
multi fate stem cell	6.38e-23	430
stem cell	2.73e-22	444
somatic stem cell	4.25e-22	436
leukocyte	8.78e-22	140
native cell	1.28e-21	722
myeloid leukocyte	2.43e-19	76
mesenchymal cell	3.28e-17	358
animal cell	5.20e-17	679
eukaryotic cell	5.20e-17	679
connective tissue cell	1.16e-16	365
CD14-positive, CD16-negative classical monocyte	3.06e-16	42
hematopoietic cell	3.80e-16	182
hematopoietic lineage restricted progenitor cell	6.99e-16	124
nongranular leukocyte	1.05e-15	119
granulocyte monocyte progenitor cell	2.74e-15	71
hematopoietic stem cell	3.62e-15	172
angioblastic mesenchymal cell	3.62e-15	172
classical monocyte	1.15e-14	45
macrophage dendritic cell progenitor	2.47e-14	65
motile cell	4.05e-14	390
myeloid lineage restricted progenitor cell	4.62e-14	70
monopoietic cell	2.48e-13	63
monocyte	2.48e-13	63
monoblast	2.48e-13	63
promonocyte	2.48e-13	63
hematopoietic oligopotent progenitor cell	9.28e-13	165
hematopoietic multipotent progenitor cell	9.28e-13	165
myeloid cell	2.48e-10	112
common myeloid progenitor	2.48e-10	112
blood cell	3.72e-07	11
intermediate monocyte	7.12e-07	9
CD14-positive, CD16-positive monocyte	7.12e-07	9

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	1.62e-19	216
connective tissue	2.43e-15	375
hematopoietic system	3.75e-15	102
blood island	3.75e-15	102
bone element	9.56e-15	86
hemolymphoid system	1.30e-14	112
bone marrow	1.44e-14	80
musculoskeletal system	7.16e-13	167
skeletal element	5.68e-12	101
skeletal system	5.68e-12	101
immune system	1.99e-11	115
artery	2.53e-09	42
arterial blood vessel	2.53e-09	42
arterial system	2.53e-09	42
cardiovascular system	6.56e-09	110
circulatory system	4.64e-08	113
vasculature	5.61e-08	79
vascular system	5.61e-08	79
systemic artery	5.18e-07	33
systemic arterial system	5.18e-07	33
vessel	6.58e-07	69

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189190102302064
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319115395979895
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108318760524705
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.017232440111392
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027548258057249
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032800697761854

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.