Coexpression cluster:C4710

Full id: C4710_Monocytederived_Mesenchymal_Macrophage_papillotubular_Dendritic_Alveolar_CD14CD16

Phase1 CAGE Peaks

Hg19::chr7:98972311..98972326,+	p2@ARPC1B
Hg19::chr7:98972327..98972338,+	p3@ARPC1B
Hg19::chr7:98972345..98972360,+	p1@ARPC1B

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
somatic cell	2.01e-45	588
native cell	5.47e-39	722
animal cell	1.76e-33	679
eukaryotic cell	1.76e-33	679
multi fate stem cell	3.78e-28	427
somatic stem cell	4.34e-28	433
stem cell	8.09e-26	441
monopoietic cell	9.13e-22	59
monocyte	9.13e-22	59
monoblast	9.13e-22	59
promonocyte	9.13e-22	59
connective tissue cell	2.23e-21	361
nongranular leukocyte	3.26e-21	115
mesenchymal cell	4.17e-21	354
myeloid leukocyte	8.86e-21	72
macrophage dendritic cell progenitor	1.16e-20	61
hematopoietic stem cell	1.58e-20	168
angioblastic mesenchymal cell	1.58e-20	168
leukocyte	2.75e-20	136
hematopoietic oligopotent progenitor cell	4.97e-20	161
hematopoietic multipotent progenitor cell	4.97e-20	161
hematopoietic cell	1.20e-19	177
defensive cell	7.95e-19	48
phagocyte	7.95e-19	48
myeloid cell	3.06e-18	108
common myeloid progenitor	3.06e-18	108
granulocyte monocyte progenitor cell	4.86e-18	67
myeloid lineage restricted progenitor cell	1.30e-17	66
hematopoietic lineage restricted progenitor cell	2.84e-17	120
motile cell	1.66e-16	386
classical monocyte	5.29e-15	42
CD14-positive, CD16-negative classical monocyte	5.29e-15	42
mesodermal cell	1.31e-14	121
stuff accumulating cell	4.63e-10	87
meso-epithelial cell	1.63e-08	45
endothelial cell	5.13e-08	36
lining cell	9.05e-08	58
barrier cell	9.05e-08	58
contractile cell	2.00e-07	59
smooth muscle cell	2.26e-07	43
smooth muscle myoblast	2.26e-07	43
muscle precursor cell	3.70e-07	58
myoblast	3.70e-07	58
multi-potent skeletal muscle stem cell	3.70e-07	58
vascular associated smooth muscle cell	3.89e-07	32
muscle cell	5.58e-07	55

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	3.21e-29	203
hemolymphoid system	1.19e-23	108
hematopoietic system	3.83e-23	98
blood island	3.83e-23	98
mesoderm	7.95e-21	315
mesoderm-derived structure	7.95e-21	315
presumptive mesoderm	7.95e-21	315
musculoskeletal system	3.15e-20	167
immune system	3.91e-20	93
bone marrow	1.22e-19	76
connective tissue	1.52e-19	371
skeletal element	4.29e-17	90
bone element	1.47e-16	82
skeletal system	6.65e-16	100
cardiovascular system	2.14e-11	109
circulatory system	2.11e-10	112
vessel	1.20e-09	68
epithelial tube open at both ends	3.37e-09	59
blood vessel	3.37e-09	59
blood vasculature	3.37e-09	59
vascular cord	3.37e-09	59
vasculature	9.95e-09	78
vascular system	9.95e-09	78
epithelial vesicle	1.18e-08	78
artery	1.83e-08	42
arterial blood vessel	1.83e-08	42
arterial system	1.83e-08	42
splanchnic layer of lateral plate mesoderm	5.01e-08	83
multilaminar epithelium	7.27e-08	83
epithelial tube	1.61e-07	117

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	0.0191181298833535
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662922083663422
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327790210208597
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324370010831998
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322540562188136
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465027815493772
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00765364469389672
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109236138296245
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296107055286413
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173684901665496
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.008857649942902
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278317337221431
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00204107676267796
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109430869275952
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545829166481088
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331298017527756
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140939207225153

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.