Coexpression cluster:C447

Full id: C447_Alveolar_Bronchial_Smooth_Renal_Tracheal_Keratocytes_Hepatic

Phase1 CAGE Peaks

Hg19::chr11:62341318..62341402,-	p1@EEF1G
Hg19::chr14:23299088..23299114,+	p1@MRPL52
Hg19::chr17:49230905..49231005,+	p1@NME1 p3@NME1-NME2 p3@NME2
Hg19::chr17:7210852..7210861,+	p5@EIF5A
Hg19::chr17:7210877..7210888,+	p4@EIF5A
Hg19::chr17:7210898..7210918,+	p2@EIF5A
Hg19::chr17:79670386..79670427,+	p2@MRPL12 p2@SLC25A10
Hg19::chr19:1438351..1438382,+	p2@RPS15
Hg19::chr19:1438383..1438409,+	p1@RPS15
Hg19::chr19:17970693..17970729,+	p1@RPL18A
Hg19::chr19:42364267..42364301,+	p2@RPS19
Hg19::chr19:5690266..5690296,+	p2@RPL36
Hg19::chr20:60962115..60962126,+	p2@RPS21
Hg19::chr22:24236562..24236621,+	p1@MIF
Hg19::chr22:30987849..30987904,-	p1@PES1
Hg19::chr2:73461410..73461463,+	p1@CCT7
Hg19::chr3:23958612..23958630,+	p1@RPL15
Hg19::chr3:39448443..39448499,+	p@chr3:39448443..39448499 +
Hg19::chr3:52029945..52029956,-	p3@RPL29
Hg19::chr3:52029958..52029974,-	p2@RPL29
Hg19::chr5:177580855..177580927,-	p1@NHP2
Hg19::chr9:132388423..132388477,+	p1@METTL11A

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
1.80279937805575e-14	3.08438677416343e-12	7	92	Ribosome (KEGG):03010
0.000404506625599747	0.0284502993338489	2	57	Translation Factors (Wikipathways):WP107
1.94905957293108e-14	3.08438677416343e-12	7	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
3.54069343756762e-17	2.24125894598031e-14	10	296	Metabolism of proteins (Reactome):REACT_17015
8.42175523584154e-14	1.06619421285754e-11	7	114	Regulation of beta-cell development (Reactome):REACT_13698
1.23159185623497e-11	1.1137109214239e-09	8	421	Gene Expression (Reactome):REACT_71
1.0400835009089e-10	8.22966070094168e-09	7	312	Diabetes pathways (Reactome):REACT_15380
4.24738473644491e-13	4.48099089694938e-11	7	143	Influenza Infection (Reactome):REACT_6167
1.51898137154035e-15	4.80757604092522e-13	8	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:0044249	cellular biosynthetic process	1.63536519439817e-12
GO:0033279	ribosomal subunit	2.59202003269642e-12
GO:0009058	biosynthetic process	8.6750274201438e-12
GO:0006412	translation	8.6750274201438e-12
GO:0005830	cytosolic ribosome (sensu Eukaryota)	2.4732840086186e-11
GO:0044445	cytosolic part	4.20728102009308e-11
GO:0009059	macromolecule biosynthetic process	8.32198503670861e-11
GO:0003735	structural constituent of ribosome	2.43550401320784e-10
GO:0005840	ribosome	4.71495388940078e-10
GO:0030529	ribonucleoprotein complex	5.71573379108332e-09
GO:0015934	large ribosomal subunit	1.81502338481676e-08
GO:0005829	cytosol	4.47144288756933e-08
GO:0032991	macromolecular complex	7.70890439572307e-07
GO:0043232	intracellular non-membrane-bound organelle	7.70890439572307e-07
GO:0043228	non-membrane-bound organelle	7.70890439572307e-07
GO:0044267	cellular protein metabolic process	1.78090254612308e-06
GO:0044260	cellular macromolecule metabolic process	1.94152835452668e-06
GO:0019538	protein metabolic process	2.6494594484899e-06
GO:0005737	cytoplasm	2.6494594484899e-06
GO:0044444	cytoplasmic part	2.91903608333342e-06
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	5.23508541645072e-06
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	7.62170201263084e-06
GO:0010467	gene expression	1.51581020644333e-05
GO:0003723	RNA binding	2.47431966682721e-05
GO:0044446	intracellular organelle part	0.000147606563219062
GO:0044422	organelle part	0.000147606563219062
GO:0005762	mitochondrial large ribosomal subunit	0.000178278722220159
GO:0000315	organellar large ribosomal subunit	0.000178278722220159
GO:0015935	small ribosomal subunit	0.000178278722220159
GO:0005515	protein binding	0.000207267769744039
GO:0044237	cellular metabolic process	0.000207267769744039
GO:0044238	primary metabolic process	0.000228281165093755
GO:0044424	intracellular part	0.000285289357924009
GO:0043233	organelle lumen	0.000339362993530787
GO:0031974	membrane-enclosed lumen	0.000339362993530787
GO:0005730	nucleolus	0.00036235080550322
GO:0043229	intracellular organelle	0.0011593666543526
GO:0043226	organelle	0.0011593666543526
GO:0000313	organellar ribosome	0.00152367751972329
GO:0005761	mitochondrial ribosome	0.00152367751972329
GO:0043170	macromolecule metabolic process	0.00155370022125681
GO:0005622	intracellular	0.00201124067833298
GO:0007000	nucleolus organization and biogenesis	0.0026693105552166
GO:0050178	phenylpyruvate tautomerase activity	0.0026693105552166
GO:0003676	nucleic acid binding	0.00282955004644999
GO:0051323	metaphase	0.0074936979378262
GO:0000089	mitotic metaphase	0.0074936979378262
GO:0005832	chaperonin-containing T-complex	0.00958180233340283
GO:0043030	regulation of macrophage activation	0.00958180233340283
GO:0032502	developmental process	0.0110492591165849
GO:0006390	transcription from mitochondrial promoter	0.0115051858477387
GO:0005759	mitochondrial matrix	0.0145227496622909
GO:0031980	mitochondrial lumen	0.0145227496622909
GO:0031981	nuclear lumen	0.0155820216738653
GO:0008135	translation factor activity, nucleic acid binding	0.0168141455663711
GO:0008283	cell proliferation	0.0185141408805772
GO:0042116	macrophage activation	0.0185141408805772
GO:0043022	ribosome binding	0.0192183727001798
GO:0001516	prostaglandin biosynthetic process	0.0192183727001798
GO:0046457	prostanoid biosynthetic process	0.0192183727001798
GO:0016862	intramolecular oxidoreductase activity, interconverting keto- and enol-groups	0.0192183727001798
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0221078039902013
GO:0006915	apoptosis	0.0243405685871074
GO:0012501	programmed cell death	0.0245085795362319
GO:0043234	protein complex	0.0261257076792559
GO:0016265	death	0.0263258028457658
GO:0008219	cell death	0.0263258028457658
GO:0048869	cellular developmental process	0.0263258028457658
GO:0030154	cell differentiation	0.0263258028457658
GO:0007566	embryo implantation	0.0272612887625557
GO:0043021	ribonucleoprotein binding	0.0272612887625557
GO:0006693	prostaglandin metabolic process	0.0272612887625557
GO:0006692	prostanoid metabolic process	0.0272612887625557
GO:0048522	positive regulation of cellular process	0.0276967443860152
GO:0022414	reproductive process	0.0276967443860152
GO:0050679	positive regulation of epithelial cell proliferation	0.0277197817017431
GO:0051272	positive regulation of cell motility	0.0314910633148022
GO:0040017	positive regulation of locomotion	0.0314910633148022
GO:0048518	positive regulation of biological process	0.0350683770571089
GO:0005853	eukaryotic translation elongation factor 1 complex	0.0350683770571089
GO:0044428	nuclear part	0.038465921753742
GO:0002274	myeloid leukocyte activation	0.038465921753742
GO:0019079	viral genome replication	0.0408006772958901
GO:0050678	regulation of epithelial cell proliferation	0.0416965439544594
GO:0015669	gas transport	0.0437543521028632
GO:0030218	erythrocyte differentiation	0.0437543521028632
GO:0046456	icosanoid biosynthetic process	0.0437543521028632
GO:0050673	epithelial cell proliferation	0.0437543521028632
GO:0046051	UTP metabolic process	0.0440157626532768
GO:0004550	nucleoside diphosphate kinase activity	0.0440157626532768
GO:0006228	UTP biosynthetic process	0.0440157626532768
GO:0009208	pyrimidine ribonucleoside triphosphate metabolic process	0.0440157626532768
GO:0046036	CTP metabolic process	0.0440157626532768
GO:0009209	pyrimidine ribonucleoside triphosphate biosynthetic process	0.0440157626532768
GO:0006241	CTP biosynthetic process	0.0440157626532768
GO:0048468	cell development	0.0440157626532768
GO:0046039	GTP metabolic process	0.0440157626532768
GO:0006183	GTP biosynthetic process	0.0440157626532768
GO:0006997	nuclear organization and biogenesis	0.0447395533592941
GO:0009220	pyrimidine ribonucleotide biosynthetic process	0.0466041472028266
GO:0009218	pyrimidine ribonucleotide metabolic process	0.047286560910938

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	3.07e-38	679
eukaryotic cell	3.07e-38	679
embryonic cell	1.23e-33	248
mesodermal cell	4.59e-25	119
epithelial cell	5.70e-23	254
non-terminally differentiated cell	7.67e-22	180
native cell	1.05e-21	722
somatic cell	1.13e-20	591
contractile cell	6.24e-19	59
muscle precursor cell	1.55e-17	57
myoblast	1.55e-17	57
multi-potent skeletal muscle stem cell	1.55e-17	57
electrically responsive cell	1.83e-17	60
electrically active cell	1.83e-17	60
muscle cell	4.36e-17	54
smooth muscle cell	6.20e-15	42
smooth muscle myoblast	6.20e-15	42
vascular associated smooth muscle cell	3.89e-12	32
squamous epithelial cell	2.28e-09	62
lining cell	3.46e-08	57
barrier cell	3.46e-08	57
meso-epithelial cell	2.95e-07	44
epithelial cell of nephron	3.04e-07	16
blood vessel endothelial cell	4.12e-07	18
embryonic blood vessel endothelial progenitor cell	4.12e-07	18
endothelial cell	4.60e-07	35

Uber Anatomy

Ontology term	p-value	n
multilaminar epithelium	3.61e-19	82
dermomyotome	7.06e-19	70
somite	2.03e-18	83
paraxial mesoderm	2.03e-18	83
presomitic mesoderm	2.03e-18	83
presumptive segmental plate	2.03e-18	83
trunk paraxial mesoderm	2.03e-18	83
presumptive paraxial mesoderm	2.03e-18	83
trunk mesenchyme	1.17e-17	143
mesenchyme	2.19e-16	238
entire embryonic mesenchyme	2.19e-16	238
unilaminar epithelium	2.39e-16	138
epithelial tube	6.82e-16	118
vasculature	6.97e-16	79
vascular system	6.97e-16	79
trunk	2.23e-15	216
skeletal muscle tissue	2.52e-15	61
striated muscle tissue	2.52e-15	61
myotome	2.52e-15	61
vessel	1.50e-14	69
blood vessel	2.75e-14	60
epithelial tube open at both ends	2.75e-14	60
blood vasculature	2.75e-14	60
vascular cord	2.75e-14	60
artery	4.93e-14	42
arterial blood vessel	4.93e-14	42
arterial system	4.93e-14	42
muscle tissue	9.83e-14	63
musculature	9.83e-14	63
musculature of body	9.83e-14	63
splanchnic layer of lateral plate mesoderm	4.70e-13	84
cell layer	5.51e-10	312
systemic artery	6.14e-10	33
systemic arterial system	6.14e-10	33
epithelium	2.00e-09	309
cardiovascular system	6.94e-09	110
circulatory system	3.12e-08	113
simple squamous epithelium	1.36e-07	22
multi-tissue structure	1.59e-07	347
nephron epithelium	3.04e-07	16
nephron	3.04e-07	16
uriniferous tubule	3.04e-07	16
metanephric mesenchyme	3.04e-07	16
nephrogenic mesenchyme	3.04e-07	16
endothelium	4.12e-07	18
blood vessel endothelium	4.12e-07	18
cardiovascular system endothelium	4.12e-07	18
squamous epithelium	9.58e-07	25

Disease

Ontology term	p-value	n
disease of cellular proliferation	1.09e-08	239
cancer	3.45e-08	235

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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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.