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
non-terminally differentiated cell	8.41e-31	180
somatic cell	2.49e-28	591
multi fate stem cell	2.36e-25	430
somatic stem cell	1.58e-23	436
stem cell	3.65e-22	444
fibroblast	6.42e-18	75
mesodermal cell	3.17e-15	119
CD14-positive, CD16-negative classical monocyte	1.11e-14	42
connective tissue cell	7.34e-14	365
animal cell	1.62e-13	679
eukaryotic cell	1.62e-13	679
classical monocyte	1.04e-12	45
mesenchymal cell	1.93e-12	358
macrophage dendritic cell progenitor	2.86e-12	65
muscle precursor cell	3.42e-12	57
myoblast	3.42e-12	57
multi-potent skeletal muscle stem cell	3.42e-12	57
motile cell	4.24e-12	390
granulocyte monocyte progenitor cell	6.88e-12	71
monopoietic cell	7.19e-12	63
monocyte	7.19e-12	63
monoblast	7.19e-12	63
promonocyte	7.19e-12	63
contractile cell	1.46e-11	59
muscle cell	1.68e-11	54
myeloid lineage restricted progenitor cell	1.18e-10	70
myeloid leukocyte	1.85e-10	76
electrically responsive cell	2.55e-10	60
electrically active cell	2.55e-10	60
smooth muscle cell	6.06e-10	42
smooth muscle myoblast	6.06e-10	42
skin fibroblast	4.03e-09	23
vascular associated smooth muscle cell	8.13e-09	32
native cell	9.84e-09	722

Uber Anatomy

Ontology term	p-value	n
musculoskeletal system	1.70e-26	167
lateral plate mesoderm	3.77e-23	216
somite	1.15e-16	83
paraxial mesoderm	1.15e-16	83
presomitic mesoderm	1.15e-16	83
presumptive segmental plate	1.15e-16	83
trunk paraxial mesoderm	1.15e-16	83
presumptive paraxial mesoderm	1.15e-16	83
vasculature	2.35e-16	79
vascular system	2.35e-16	79
cardiovascular system	3.17e-15	110
dermomyotome	5.82e-15	70
vessel	8.01e-15	69
circulatory system	2.75e-14	113
connective tissue	3.40e-14	375
blood vessel	1.00e-13	60
epithelial tube open at both ends	1.00e-13	60
blood vasculature	1.00e-13	60
vascular cord	1.00e-13	60
skeletal element	1.09e-13	101
skeletal system	1.09e-13	101
splanchnic layer of lateral plate mesoderm	1.67e-13	84
artery	3.19e-13	42
arterial blood vessel	3.19e-13	42
arterial system	3.19e-13	42
mesoderm	4.73e-13	448
mesoderm-derived structure	4.73e-13	448
presumptive mesoderm	4.73e-13	448
bone marrow	8.14e-13	80
multilaminar epithelium	6.55e-12	82
bone element	6.76e-12	86
skeletal muscle tissue	1.38e-11	61
striated muscle tissue	1.38e-11	61
myotome	1.38e-11	61
muscle tissue	7.50e-11	63
musculature	7.50e-11	63
musculature of body	7.50e-11	63
systemic artery	1.78e-10	33
systemic arterial system	1.78e-10	33
hemolymphoid system	2.11e-09	112
hematopoietic system	1.69e-08	102
blood island	1.69e-08	102
aorta	7.05e-08	21
aortic system	7.05e-08	21
integument	2.41e-07	45
integumental system	2.41e-07	45

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.