Coexpression cluster:C2487

Full id: C2487_Alveolar_Mesenchymal_Renal_Placental_Bronchial_acute_Tracheal

Phase1 CAGE Peaks

Hg19::chr19:39421556..39421632,+	p1@MRPS12
Hg19::chr19:39971470..39971498,+	p1@TIMM50
Hg19::chr1:26496382..26496457,+	p1@ZNF593
Hg19::chr21:46359907..46359962,+	p1@FAM207A

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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GO ID	GO name	FDR corrected p-value
GO:0044429	mitochondrial part	0.0469200548296613
GO:0005744	mitochondrial inner membrane presequence translocase complex	0.0469200548296613
GO:0043021	ribonucleoprotein binding	0.0469200548296613
GO:0007006	mitochondrial membrane organization and biogenesis	0.0469200548296613
GO:0031974	membrane-enclosed lumen	0.0469200548296613
GO:0043233	organelle lumen	0.0469200548296613
GO:0005739	mitochondrion	0.0469200548296613

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	5.00e-30	254
embryonic cell	6.66e-25	248
animal cell	1.55e-23	679
eukaryotic cell	1.55e-23	679
mesodermal cell	2.33e-14	119
native cell	4.73e-11	722
contractile cell	8.90e-10	59
non-terminally differentiated cell	5.05e-09	180
electrically responsive cell	2.65e-08	60
electrically active cell	2.65e-08	60
somatic cell	5.87e-08	591
squamous epithelial cell	6.24e-08	62
muscle cell	8.17e-08	54
muscle precursor cell	1.02e-07	57
myoblast	1.02e-07	57
multi-potent skeletal muscle stem cell	1.02e-07	57
epithelial cell of nephron	1.45e-07	16
kidney cell	2.84e-07	18
kidney epithelial cell	2.84e-07	18

Uber Anatomy

Ontology term	p-value	n
mesenchyme	1.99e-16	238
entire embryonic mesenchyme	1.99e-16	238
trunk	6.84e-15	216
trunk mesenchyme	8.45e-13	143
unilaminar epithelium	1.38e-11	138
multilaminar epithelium	9.60e-11	82
epithelial tube	1.59e-10	118
dermomyotome	6.49e-10	70
somite	8.58e-09	83
paraxial mesoderm	8.58e-09	83
presomitic mesoderm	8.58e-09	83
presumptive segmental plate	8.58e-09	83
trunk paraxial mesoderm	8.58e-09	83
presumptive paraxial mesoderm	8.58e-09	83
subdivision of trunk	1.18e-08	113
trunk region element	6.32e-08	107
skeletal muscle tissue	8.06e-08	61
striated muscle tissue	8.06e-08	61
myotome	8.06e-08	61
cell layer	9.97e-08	312
nephron epithelium	1.45e-07	16
nephron	1.45e-07	16
uriniferous tubule	1.45e-07	16
metanephric mesenchyme	1.45e-07	16
nephrogenic mesenchyme	1.45e-07	16
epithelium	2.09e-07	309
cortex	2.24e-07	16
primordium	4.56e-07	168
muscle tissue	6.96e-07	63
musculature	6.96e-07	63
musculature of body	6.96e-07	63
multi-tissue structure	8.07e-07	347

Disease

Ontology term	p-value	n
cancer	2.76e-18	235
disease of cellular proliferation	3.71e-18	239
cell type cancer	1.70e-10	143
organ system cancer	2.17e-08	137
hematologic cancer	7.57e-08	51
immune system cancer	7.57e-08	51
carcinoma	9.84e-08	106

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)
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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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No analysis results for this cluster

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.