Coexpression cluster:C968

Full id: C968_Mesenchymal_testis_MCF7_mature_Adipocyte_Fibroblast_Alveolar

Phase1 CAGE Peaks

Hg19::chr10:104262056..104262066,+	p@chr10:104262056..104262066 +
Hg19::chr12:14927378..14927389,+	p3@H2AFJ
Hg19::chr1:110752586..110752596,-	p1@KCNC4-AS1
Hg19::chr20:60758060..60758074,-	p@chr20:60758060..60758074 -
Hg19::chr2:24346422..24346436,+	p2@AK098250
Hg19::chr3:44771012..44771024,-	p@chr3:44771012..44771024 -
Hg19::chr7:130080681..130080699,-	p4@CEP41
Hg19::chr8:103875754..103875768,+	p@chr8:103875754..103875768 +

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
contractile cell	4.20e-08	59
non-terminally differentiated cell	9.12e-08	180
muscle precursor cell	2.30e-07	57
myoblast	2.30e-07	57
multi-potent skeletal muscle stem cell	2.30e-07	57
fat cell	4.02e-07	15
electrically responsive cell	4.66e-07	60
electrically active cell	4.66e-07	60
muscle cell	8.42e-07	54

Uber Anatomy

Ontology term	p-value	n
cardiovascular system	1.63e-07	110
vasculature	2.67e-07	79
vascular system	2.67e-07	79
circulatory system	5.61e-07	113

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
CCNT2#905	5	3.96012598560165	0.0035982129138552	0.018224721557232
CHD2#1106	4	5.17201141705843	0.00443788460794178	0.0210046329452022
E2F1#1869	6	3.68054191115949	0.00136649155081914	0.00899332100800302
E2F6#1876	6	3.76286679877304	0.00120768002799781	0.00818699821135035
ELF1#1997	7	3.7258357139566	0.000250341272551272	0.00269901849530116
GABPB1#2553	7	6.1842233566594	7.95182205325426e-06	0.000221225451097448
HEY1#23462	6	3.03008328232928	0.00400172346648327	0.0191880995875326
HMGN3#9324	4	4.0892738616753	0.0103942462239878	0.0385909947169236
IRF1#3659	5	4.77322734597744	0.00152554848029467	0.00971445385851443
IRF3#3661	2	11.7454880528724	0.0116448804945314	0.042532687765558
NFYA#4800	3	6.90959276243645	0.00727972723713068	0.0301247100768164
NFYB#4801	3	6.28492247007617	0.00947376901248262	0.0356989090018283
PBX3#5090	4	10.9572563433721	0.000261492197563197	0.00280188607995309
POLR2A#5430	8	2.14745317655807	0.00221072578897191	0.012728003896055
SIN3A#25942	6	4.05666354511135	0.00079220890752307	0.00612825021056232
SP1#6667	6	4.27378603360567	0.000590472686428894	0.00494454593472958
SP2#6668	3	9.80757393519174	0.00270718466508561	0.0148886603073658
SREBF1#6720	2	11.7514623601221	0.0116335478572343	0.0424957540716203
TAF1#6872	8	3.34304628574529	6.40776711117462e-05	0.0010441890924075
YY1#7528	5	3.06948171865866	0.011259136535836	0.0413319142589167
ZNF143#7702	4	6.75043827611395	0.00165129218914978	0.0103262861470938

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.