Coexpression cluster:C2940

Full id: C2940_renal_hairy_Mesenchymal_leiomyoblastoma_small_Hep2_Wilms

Phase1 CAGE Peaks

Hg19::chr9:139744155..139744222,+	p2@PHPT1
Hg19::chr9:139744237..139744257,+	p8@PHPT1
Hg19::chr9:139744264..139744275,+	p10@PHPT1
Hg19::chr9:139744298..139744325,+	p5@PHPT1

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	2.90e-21	180
embryonic cell	1.45e-10	248
fibroblast	7.88e-10	75
contractile cell	2.91e-09	59
smooth muscle cell	3.99e-09	42
smooth muscle myoblast	3.99e-09	42
muscle precursor cell	8.08e-09	57
myoblast	8.08e-09	57
multi-potent skeletal muscle stem cell	8.08e-09	57
muscle cell	4.12e-08	54
mesodermal cell	5.09e-08	119
vascular associated smooth muscle cell	5.26e-07	32
electrically responsive cell	7.53e-07	60
electrically active cell	7.53e-07	60

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	4.60e-25	347
organism subdivision	1.22e-20	365
mesenchyme	6.26e-18	238
entire embryonic mesenchyme	6.26e-18	238
trunk	7.75e-14	216
trunk mesenchyme	1.91e-13	143
anatomical cluster	1.86e-12	286
somite	4.83e-12	83
paraxial mesoderm	4.83e-12	83
presomitic mesoderm	4.83e-12	83
presumptive segmental plate	4.83e-12	83
trunk paraxial mesoderm	4.83e-12	83
presumptive paraxial mesoderm	4.83e-12	83
multi-cellular organism	5.19e-12	659
epithelium	1.61e-11	309
cell layer	4.71e-11	312
multilaminar epithelium	7.19e-11	82
dermomyotome	1.79e-09	70
anatomical system	2.52e-09	625
anatomical group	2.72e-09	626
skeletal muscle tissue	4.65e-09	61
striated muscle tissue	4.65e-09	61
myotome	4.65e-09	61
endoderm-derived structure	6.93e-09	169
endoderm	6.93e-09	169
presumptive endoderm	6.93e-09	169
muscle tissue	7.52e-09	63
musculature	7.52e-09	63
musculature of body	7.52e-09	63
primordium	3.28e-08	168
anatomical conduit	5.25e-08	241
larynx	1.42e-07	9
surface structure	1.81e-07	95
embryo	2.51e-07	612
germ layer	3.60e-07	604
embryonic tissue	3.60e-07	604
presumptive structure	3.60e-07	604
epiblast (generic)	3.60e-07	604
embryonic structure	3.68e-07	605
developing anatomical structure	3.68e-07	605
digestive system	5.86e-07	155
digestive tract	5.86e-07	155
primitive gut	5.86e-07	155

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
BCL3#602	4	34.5471028037383	7.01262157705428e-07	3.15685855554298e-05
CCNT2#905	3	4.75215118272197	0.0138620699668949	0.0487520448973778
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106876696729689
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00999800005103913
EBF1#1879	4	8.906466846569	0.0001588790747201	0.00200207187315306
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101694312104451
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154882734080841
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00391060847438082
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186720850681579
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.0076962372471092
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00798551876587386
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323531956953721
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.000972671770985663
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0245189894768733
THAP1#55145	4	31.3691446028513	1.03171810326891e-06	4.3291123739374e-05
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0107139327293017
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00347375685642239
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.0025021800073161

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.