Coexpression cluster:C3415

Full id: C3415_Mesenchymal_colon_osteosarcoma_Corneal_seminal_retina_ductus

Phase1 CAGE Peaks

Hg19::chr14:23623503..23623514,-	p6@SLC7A8
Hg19::chr14:23623516..23623531,-	p4@SLC7A8
Hg19::chr14:23623577..23623630,-	p3@SLC7A8

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
fat cell	4.64e-09	15
fibroblast	8.60e-09	75
stuff accumulating cell	5.40e-07	39

Uber Anatomy

Ontology term	p-value	n
surface structure	7.90e-18	95
integument	7.91e-09	45
integumental system	7.91e-09	45
organ component layer	9.43e-09	57
organ	1.77e-08	511
mouth	2.57e-08	28
stomodeum	2.57e-08	28
adult organism	5.87e-08	115
subdivision of head	1.59e-07	48
skin of body	1.80e-07	40
organism subdivision	1.93e-07	365
multi-cellular organism	2.60e-07	659

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	0.0189592020960259
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321219931093506
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460986575915306
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00895890321949828
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.0058033053194202
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000849945177562468
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00390515603972988
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127812379148935
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186120641099763
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293781762492786
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199173835680911
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245209369086932
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460263992634888

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.