Coexpression cluster:C3288

Full id: C3288_Fibroblast_Urothelial_Preadipocyte_mesothelioma_Mallassezderived_Mesothelial_alveolar

Phase1 CAGE Peaks

Hg19::chr12:50616122..50616144,-	p3@LIMA1
Hg19::chr12:50616368..50616378,-	p4@LIMA1
Hg19::chr12:50616382..50616505,-	p1@LIMA1

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
fibroblast	4.62e-16	76
embryonic cell	3.42e-14	250
skin fibroblast	3.18e-09	23
non-terminally differentiated cell	5.64e-09	106
muscle precursor cell	1.12e-08	58
myoblast	1.12e-08	58
multi-potent skeletal muscle stem cell	1.12e-08	58
animal cell	1.84e-08	679
eukaryotic cell	1.84e-08	679
mesodermal cell	2.34e-08	121
muscle cell	8.33e-08	55
electrically responsive cell	1.95e-07	61
electrically active cell	1.95e-07	61
mesothelial cell	2.23e-07	19
squamous epithelial cell	5.61e-07	63
smooth muscle cell	6.80e-07	43
smooth muscle myoblast	6.80e-07	43
somatic cell	8.29e-07	588

Uber Anatomy

Ontology term	p-value	n
surface structure	1.32e-13	99
multilaminar epithelium	5.83e-11	83
integument	8.81e-11	46
integumental system	8.81e-11	46
skin of body	1.53e-10	41
somite	4.92e-08	71
presomitic mesoderm	4.92e-08	71
presumptive segmental plate	4.92e-08	71
dermomyotome	4.92e-08	71
trunk paraxial mesoderm	4.92e-08	71
dense mesenchyme tissue	5.67e-08	73
muscle tissue	6.43e-08	64
musculature	6.43e-08	64
musculature of body	6.43e-08	64
skeletal muscle tissue	7.61e-08	62
striated muscle tissue	7.61e-08	62
myotome	7.61e-08	62
paraxial mesoderm	1.36e-07	72
presumptive paraxial mesoderm	1.36e-07	72

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.01150120610628
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278651752219008
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320933194370105
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460594153401077
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255203027922757
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167023506115009
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186013762232309
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00718863367530119
MYC#4609	3	5.2222818716094	0.00702084375574015	0.029351128853004
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268881724239366
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00662391894669037
REST#5978	3	9.65002871612802	0.00111263624711459	0.00765851295145328
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308341382822021
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.010888267525125
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374138026237103
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541220694045268
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00196616911598359

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.