Coexpression cluster:C2019

Full id: C2019_mature_sacrococcigeal_gastric_Adipocyte_Synoviocyte_Mesenchymal_Chondrocyte

Phase1 CAGE Peaks

Hg19::chr9:129884902..129884922,-	p1@ANGPTL2
Hg19::chr9:129884924..129884937,-	p3@ANGPTL2
Hg19::chr9:129884944..129884979,-	p2@ANGPTL2
Hg19::chr9:129884994..129885007,-	p4@ANGPTL2
Hg19::chr9:129885010..129885017,-	p5@ANGPTL2

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
non-terminally differentiated cell	1.99e-24	180
fibroblast	6.22e-13	75
fat cell	9.19e-11	15
mesodermal cell	5.91e-09	119
stuff accumulating cell	1.04e-08	39
muscle precursor cell	2.47e-07	57
myoblast	2.47e-07	57
multi-potent skeletal muscle stem cell	2.47e-07	57
contractile cell	3.04e-07	59
muscle cell	4.77e-07	54
electrically responsive cell	7.76e-07	60
electrically active cell	7.76e-07	60

Uber Anatomy

Ontology term	p-value	n
organism subdivision	3.12e-15	365
multi-cellular organism	6.16e-12	659
epithelium	9.97e-12	309
cell layer	1.22e-11	312
adult organism	1.30e-10	115
multi-tissue structure	3.08e-10	347
splanchnic layer of lateral plate mesoderm	4.51e-10	84
anatomical cluster	5.70e-10	286
somite	2.12e-09	83
paraxial mesoderm	2.12e-09	83
presomitic mesoderm	2.12e-09	83
presumptive segmental plate	2.12e-09	83
trunk paraxial mesoderm	2.12e-09	83
presumptive paraxial mesoderm	2.12e-09	83
muscle tissue	2.48e-09	63
musculature	2.48e-09	63
musculature of body	2.48e-09	63
anatomical conduit	4.41e-09	241
dermomyotome	8.15e-09	70
skeletal muscle tissue	1.04e-08	61
striated muscle tissue	1.04e-08	61
myotome	1.04e-08	61
anatomical system	2.88e-08	625
anatomical group	4.57e-08	626
vasculature	6.17e-08	79
vascular system	6.17e-08	79
trunk mesenchyme	8.47e-08	143
primary circulatory organ	8.50e-08	27
unilaminar epithelium	1.08e-07	138
adipose tissue	1.65e-07	14
epithelial tube	2.06e-07	118
multilaminar epithelium	2.43e-07	82
tube	3.56e-07	194
vessel	6.45e-07	69
surface structure	7.67e-07	95
blood vessel	8.20e-07	60
epithelial tube open at both ends	8.20e-07	60
blood vasculature	8.20e-07	60
vascular cord	8.20e-07	60

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	5	5.36025637307503	0.000225927829993709	0.00250325447026447
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00323349497865782
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00675146798981547
MAX#4149	5	6.45255550900712	8.93743970843928e-05	0.00130859002622976
MYC#4609	5	5.2222818716094	0.000257394484885061	0.00276877357162539
PAX5#5079	5	6.66956553117783	7.57493746384605e-05	0.00117185438273829
SPI1#6688	5	8.20432350852273	2.68916109982495e-05	0.000575873069724457
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135586684136842
TAF7#6879	5	11.4330694049239	5.11611886715123e-06	0.000157617208957642
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00920585813997454
TCF7L2#6934	5	10.7701765631373	6.89693748574565e-06	0.000200308468874802
TFAP2A#7020	5	16.518634373045	8.12390055913032e-07	3.54555808815299e-05
TFAP2C#7022	5	10.8092286098602	6.77323239348459e-06	0.000197594865347245
ZNF263#10127	5	8.22184163701068	2.6606316672286e-05	0.000572817379290225

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.