Coexpression cluster:C4007

Full id: C4007_Wilms_breast_ovary_mature_vagina_seminal_salivary

Phase1 CAGE Peaks

Hg19::chr1:92351643..92351652,-	p6@TGFBR3
Hg19::chr1:92351667..92351689,-	p1@TGFBR3
Hg19::chr1:92351701..92351724,-	p2@TGFBR3

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	3.44e-28	115

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	3	6.33620157696263	0.00393075003576489	0.0190277452136848
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00661017802473048
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279813136569857
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325796131947179
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322724297940918
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321088175760423
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00391576403331843
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128238863210424
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246161902707136
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.0030919873920548
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00136811278283022
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00664779820492753
REST#5978	3	9.65002871612802	0.00111263624711459	0.00768637498428368
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277171805972052
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00309399264458342
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246865742544011
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00614365491821704
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140389575186719
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109550666749562

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.