Coexpression cluster:C581

Full id: C581_Fibroblast_Keratocytes_Lens_CD14_Mesenchymal_Hepatic_Hair

Phase1 CAGE Peaks

Hg19::chr10:17271266..17271286,+	p1@VIM
Hg19::chr10:17271909..17272033,-	p1@uc001iot.1
Hg19::chr10:17272625..17272692,+	p@chr10:17272625..17272692 +
Hg19::chr10:17275575..17275660,+	p3@VIM
Hg19::chr10:17275758..17275914,+	p@chr10:17275758..17275914 +
Hg19::chr10:17276681..17276732,+	p@chr10:17276681..17276732 +
Hg19::chr10:17276737..17276787,+	p@chr10:17276737..17276787 +
Hg19::chr10:17277164..17277180,+	p@chr10:17277164..17277180 +
Hg19::chr10:17277196..17277231,+	p@chr10:17277196..17277231 +
Hg19::chr10:17277273..17277306,+	p@chr10:17277273..17277306 +
Hg19::chr10:17277329..17277340,+	p@chr10:17277329..17277340 +
Hg19::chr10:17277832..17277867,+	p@chr10:17277832..17277867 +
Hg19::chr10:17278284..17278356,+	p4@VIM
Hg19::chr10:17279217..17279304,+	p@chr10:17279217..17279304 +
Hg19::chr6:126923668..126923692,-	p@chr6:126923668..126923692 -

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:0045103	intermediate filament-based process	0.0101554221123278
GO:0005200	structural constituent of cytoskeleton	0.0287736959849288
GO:0045111	intermediate filament cytoskeleton	0.0399446603084893
GO:0005882	intermediate filament	0.0399446603084893
GO:0051674	localization of cell	0.0432169629891283
GO:0006928	cell motility	0.0432169629891283

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	1.61e-28	588
multi fate stem cell	1.05e-25	427
somatic stem cell	7.50e-24	433
stem cell	1.58e-22	441
fibroblast	8.21e-18	76
mesodermal cell	4.73e-16	121
defensive cell	6.80e-16	48
phagocyte	6.80e-16	48
classical monocyte	2.00e-14	42
CD14-positive, CD16-negative classical monocyte	2.00e-14	42
connective tissue cell	9.77e-14	361
stuff accumulating cell	1.37e-13	87
macrophage dendritic cell progenitor	1.38e-13	61
animal cell	1.89e-13	679
eukaryotic cell	1.89e-13	679
granulocyte monocyte progenitor cell	3.64e-13	67
monopoietic cell	3.94e-13	59
monocyte	3.94e-13	59
monoblast	3.94e-13	59
promonocyte	3.94e-13	59
non-terminally differentiated cell	5.67e-13	106
muscle precursor cell	1.05e-12	58
myoblast	1.05e-12	58
multi-potent skeletal muscle stem cell	1.05e-12	58
mesenchymal cell	2.49e-12	354
muscle cell	5.34e-12	55
motile cell	5.57e-12	386
contractile cell	6.45e-12	59
myeloid lineage restricted progenitor cell	9.39e-12	66
myeloid leukocyte	2.85e-11	72
electrically responsive cell	6.93e-11	61
electrically active cell	6.93e-11	61
smooth muscle cell	2.54e-10	43
smooth muscle myoblast	2.54e-10	43
skin fibroblast	5.41e-09	23
vascular associated smooth muscle cell	7.97e-09	32
native cell	1.85e-08	722

Uber Anatomy

Ontology term	p-value	n
musculoskeletal system	2.27e-29	167
mesoderm	3.52e-29	315
mesoderm-derived structure	3.52e-29	315
presumptive mesoderm	3.52e-29	315
lateral plate mesoderm	3.79e-24	203
vasculature	3.74e-16	78
vascular system	3.74e-16	78
skeletal system	1.02e-15	100
epithelial vesicle	1.30e-15	78
somite	1.48e-15	71
presomitic mesoderm	1.48e-15	71
presumptive segmental plate	1.48e-15	71
dermomyotome	1.48e-15	71
trunk paraxial mesoderm	1.48e-15	71
dense mesenchyme tissue	1.50e-15	73
paraxial mesoderm	5.10e-15	72
presumptive paraxial mesoderm	5.10e-15	72
cardiovascular system	5.33e-15	109
vessel	1.31e-14	68
bone marrow	4.42e-14	76
connective tissue	4.76e-14	371
circulatory system	4.92e-14	112
skeletal element	5.73e-14	90
epithelial tube open at both ends	1.47e-13	59
blood vessel	1.47e-13	59
blood vasculature	1.47e-13	59
vascular cord	1.47e-13	59
splanchnic layer of lateral plate mesoderm	1.77e-13	83
bone element	5.09e-13	82
artery	5.68e-13	42
arterial blood vessel	5.68e-13	42
arterial system	5.68e-13	42
multilaminar epithelium	1.49e-12	83
immune system	3.27e-12	93
skeletal muscle tissue	4.39e-12	62
striated muscle tissue	4.39e-12	62
myotome	4.39e-12	62
muscle tissue	2.41e-11	64
musculature	2.41e-11	64
musculature of body	2.41e-11	64
systemic artery	2.64e-10	33
systemic arterial system	2.64e-10	33
hemolymphoid system	6.60e-10	108
hematopoietic system	5.01e-09	98
blood island	5.01e-09	98
integument	8.07e-08	46
integumental system	8.07e-08	46
aorta	9.60e-08	21
aortic system	9.60e-08	21
unilaminar epithelium	8.93e-07	148

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
CTCF#10664	10	3.57350424871668	6.07197623972401e-05	0.000996309703850017
MAFK#7975	5	9.03357771260997	0.000150335733764987	0.00193694962974111
POLR2A#5430	13	1.86112608635033	0.00164205882674128	0.010274082303261
RAD21#5885	5	3.45167796515211	0.0110094794099265	0.0405008460758478
ZBTB33#10009	5	10.5549083433271	7.22167785884653e-05	0.00113570970320746

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.