Coexpression cluster:C3332

Full id: C3332_leiomyoma_Fibroblast_Mallassezderived_Smooth_CD14_Osteoblast_mesenchymal

Phase1 CAGE Peaks

Hg19::chr12:75874525..75874549,+	p1@GLIPR1
Hg19::chr12:75874561..75874574,+	p3@GLIPR1
Hg19::chr12:75874580..75874611,+	p2@GLIPR1

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
multi fate stem cell	4.77e-38	427
somatic stem cell	1.65e-35	433
stem cell	7.10e-33	441
somatic cell	2.89e-30	588
connective tissue cell	3.60e-24	361
mesenchymal cell	1.58e-23	354
macrophage dendritic cell progenitor	1.14e-22	61
monopoietic cell	3.75e-22	59
monocyte	3.75e-22	59
monoblast	3.75e-22	59
promonocyte	3.75e-22	59
defensive cell	2.68e-21	48
phagocyte	2.68e-21	48
myeloid leukocyte	1.22e-20	72
classical monocyte	2.28e-18	42
CD14-positive, CD16-negative classical monocyte	2.28e-18	42
granulocyte monocyte progenitor cell	1.74e-17	67
motile cell	3.72e-17	386
myeloid lineage restricted progenitor cell	7.12e-16	66
muscle precursor cell	1.97e-15	58
myoblast	1.97e-15	58
multi-potent skeletal muscle stem cell	1.97e-15	58
vascular associated smooth muscle cell	2.61e-14	32
muscle cell	2.69e-14	55
smooth muscle cell	3.31e-14	43
smooth muscle myoblast	3.31e-14	43
native cell	7.06e-14	722
leukocyte	4.62e-13	136
contractile cell	5.15e-13	59
nongranular leukocyte	4.71e-12	115
animal cell	1.65e-11	679
eukaryotic cell	1.65e-11	679
fibroblast	5.26e-11	76
electrically responsive cell	7.84e-11	61
electrically active cell	7.84e-11	61
hematopoietic lineage restricted progenitor cell	2.18e-09	120
stuff accumulating cell	1.67e-08	87
myeloid cell	4.47e-08	108
common myeloid progenitor	4.47e-08	108
mesodermal cell	1.40e-07	121
skin fibroblast	2.43e-07	23

Uber Anatomy

Ontology term	p-value	n
musculoskeletal system	4.99e-32	167
mesoderm	1.12e-26	315
mesoderm-derived structure	1.12e-26	315
presumptive mesoderm	1.12e-26	315
lateral plate mesoderm	9.34e-26	203
connective tissue	3.92e-24	371
bone marrow	4.13e-19	76
hematopoietic system	5.56e-19	98
blood island	5.56e-19	98
skeletal element	5.97e-19	90
skeletal system	2.14e-18	100
bone element	1.45e-16	82
hemolymphoid system	2.33e-16	108
immune system	5.48e-15	93
somite	7.88e-14	71
presomitic mesoderm	7.88e-14	71
presumptive segmental plate	7.88e-14	71
dermomyotome	7.88e-14	71
trunk paraxial mesoderm	7.88e-14	71
artery	1.12e-13	42
arterial blood vessel	1.12e-13	42
arterial system	1.12e-13	42
dense mesenchyme tissue	1.17e-13	73
paraxial mesoderm	1.79e-13	72
presumptive paraxial mesoderm	1.79e-13	72
skeletal muscle tissue	8.74e-13	62
striated muscle tissue	8.74e-13	62
myotome	8.74e-13	62
multilaminar epithelium	2.06e-12	83
muscle tissue	4.28e-12	64
musculature	4.28e-12	64
musculature of body	4.28e-12	64
systemic artery	1.04e-11	33
systemic arterial system	1.04e-11	33
epithelial vesicle	1.05e-11	78
cardiovascular system	1.25e-11	109
circulatory system	1.39e-10	112
splanchnic layer of lateral plate mesoderm	1.97e-09	83
epithelial tube open at both ends	3.06e-09	59
blood vessel	3.06e-09	59
blood vasculature	3.06e-09	59
vascular cord	3.06e-09	59
vasculature	5.45e-09	78
vascular system	5.45e-09	78
tissue	2.96e-07	773
vessel	6.44e-07	68

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115037729100754
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460688273860188
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167089959989228
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00895666405348491
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00443452042671051
MEF2A#4205	3	18.7432309096441	0.000151824390562247	0.00194939605679007
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268938952598858
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172501750411808
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00880576176749627
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374243685097944
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.0064170959523002
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328385724454543

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.