Coexpression cluster:C1236

Full id: C1236_acute_Mesenchymal_iPS_Skeletal_Bronchial_chronic_embryonic

Phase1 CAGE Peaks

Hg19::chr18:47018869..47018896,-	p2@RPL17
Hg19::chr18:47018897..47018922,-	p3@RPL17
Hg19::chr1:45241186..45241289,+	p1@RPS8
Hg19::chr2:3622817..3622828,+	p4@RPS7
Hg19::chr2:3622829..3622838,+	p5@RPS7
Hg19::chr2:3622840..3622882,+	p1@RPS7
Hg19::chr4:109541684..109541697,+	p4@RPL34

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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p.value	FDR	nGenes	nPathway	Name
1.01011768964648e-10	3.34070889167409e-08	4	92	Ribosome (KEGG):03010
1.05551623749576e-10	3.34070889167409e-08	4	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.133023502997e-08	1.19533979566183e-06	4	296	Metabolism of proteins (Reactome):REACT_17015
2.41231788802606e-10	5.08999074373498e-08	4	114	Regulation of beta-cell development (Reactome):REACT_13698
4.66478822294209e-08	3.69101368140293e-06	4	421	Gene Expression (Reactome):REACT_71
1.40005596835204e-08	1.2660506113812e-06	4	312	Diabetes pathways (Reactome):REACT_15380
6.03784237646204e-10	7.64390844860094e-08	4	143	Influenza Infection (Reactome):REACT_6167
5.22856572235584e-10	7.64390844860094e-08	4	138	{RPS27A,138} (Static Module):NA

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:0033279	ribosomal subunit	8.46541406768146e-08
GO:0005830	cytosolic ribosome (sensu Eukaryota)	9.49265585536572e-07
GO:0003735	structural constituent of ribosome	4.18593866862922e-06
GO:0005840	ribosome	4.45499684263136e-06
GO:0003723	RNA binding	5.25917983946982e-06
GO:0044445	cytosolic part	5.25917983946982e-06
GO:0030529	ribonucleoprotein complex	8.23244723203298e-06
GO:0006412	translation	9.11860074703107e-06
GO:0009059	macromolecule biosynthetic process	2.28763759932242e-05
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	2.6799510277966e-05
GO:0044249	cellular biosynthetic process	4.41598008983352e-05
GO:0005829	cytosol	7.04056771737254e-05
GO:0009058	biosynthetic process	9.61263843812998e-05
GO:0043232	intracellular non-membrane-bound organelle	0.000162564217958898
GO:0043228	non-membrane-bound organelle	0.000162564217958898
GO:0015934	large ribosomal subunit	0.000162564217958898
GO:0015935	small ribosomal subunit	0.000203313742897541
GO:0032991	macromolecular complex	0.000435587953843731
GO:0044446	intracellular organelle part	0.000501752069462546
GO:0044422	organelle part	0.000501752069462546
GO:0044444	cytoplasmic part	0.000730416704183392
GO:0010467	gene expression	0.00138774622843352
GO:0044267	cellular protein metabolic process	0.00145860309969479
GO:0044260	cellular macromolecule metabolic process	0.00147134878170099
GO:0019538	protein metabolic process	0.00162540887295163
GO:0003676	nucleic acid binding	0.00219499584095007
GO:0005737	cytoplasm	0.00400598022910381
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	0.00753137890643941
GO:0043229	intracellular organelle	0.0154713065329693
GO:0043226	organelle	0.0154713065329693
GO:0043170	macromolecule metabolic process	0.0171758779144423
GO:0005730	nucleolus	0.0269440353263539
GO:0044237	cellular metabolic process	0.0269440353263539
GO:0044238	primary metabolic process	0.026953438245518
GO:0044424	intracellular part	0.0278120385522976
GO:0005622	intracellular	0.0473496982711292
GO:0043234	protein complex	0.0478253109342925

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
animal cell	1.35e-41	679
eukaryotic cell	1.35e-41	679
embryonic cell	3.91e-27	248
native cell	5.43e-26	722
epithelial cell	9.83e-20	254
somatic cell	2.89e-19	591
non-terminally differentiated cell	8.71e-16	180
electrically responsive cell	6.44e-14	60
electrically active cell	6.44e-14	60
muscle precursor cell	9.87e-14	57
myoblast	9.87e-14	57
multi-potent skeletal muscle stem cell	9.87e-14	57
mesodermal cell	1.90e-13	119
muscle cell	7.14e-13	54
contractile cell	4.53e-12	59
smooth muscle cell	5.90e-10	42
smooth muscle myoblast	5.90e-10	42
endo-epithelial cell	1.96e-07	43
squamous epithelial cell	2.60e-07	62
vascular associated smooth muscle cell	3.47e-07	32

Uber Anatomy

Ontology term	p-value	n
multilaminar epithelium	1.46e-14	82
somite	2.66e-14	83
paraxial mesoderm	2.66e-14	83
presomitic mesoderm	2.66e-14	83
presumptive segmental plate	2.66e-14	83
trunk paraxial mesoderm	2.66e-14	83
presumptive paraxial mesoderm	2.66e-14	83
dermomyotome	6.27e-14	70
mesenchyme	4.76e-13	238
entire embryonic mesenchyme	4.76e-13	238
unilaminar epithelium	1.85e-12	138
skeletal muscle tissue	1.40e-11	61
striated muscle tissue	1.40e-11	61
myotome	1.40e-11	61
trunk mesenchyme	1.61e-11	143
trunk	5.22e-11	216
muscle tissue	2.80e-10	63
musculature	2.80e-10	63
musculature of body	2.80e-10	63
artery	2.54e-07	42
arterial blood vessel	2.54e-07	42
arterial system	2.54e-07	42
vasculature	6.11e-07	79
vascular system	6.11e-07	79

Disease

Ontology term	p-value	n
disease of cellular proliferation	2.03e-18	239
cancer	1.58e-17	235
organ system cancer	1.09e-08	137
cell type cancer	2.48e-08	143
hematologic cancer	1.13e-07	51
immune system cancer	1.13e-07	51
carcinoma	2.46e-07	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.