Coexpression cluster:C3324

Full id: C3324_Smooth_Tracheal_mucinous_Bronchial_chronic_iPS_testicular

Phase1 CAGE Peaks

Hg19::chr12:6978028..6978039,+	p3@TPI1
Hg19::chr1:8927211..8927246,-	p@chr1:8927211..8927246 -
Hg19::chr1:8934931..8934947,-	p4@ENO1

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
5.10526184734612e-06	0.00161581537468505	2	65	Glycolysis / Gluconeogenesis (KEGG):00010
2.76862277106078e-06	0.00161581537468505	2	48	Glycolysis and Gluconeogenesis (Wikipathways):WP534
1.93288158883898e-05	0.00407838015245025	2	126	Metabolism of carbohydrates (Reactome):REACT_474

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:0006096	glycolysis	0.000540199366548864
GO:0006007	glucose catabolic process	0.000540199366548864
GO:0019320	hexose catabolic process	0.000540199366548864
GO:0046365	monosaccharide catabolic process	0.000540199366548864
GO:0046164	alcohol catabolic process	0.000540199366548864
GO:0044275	cellular carbohydrate catabolic process	0.000540199366548864
GO:0016052	carbohydrate catabolic process	0.000540199366548864
GO:0006006	glucose metabolic process	0.000540199366548864
GO:0019682	glyceraldehyde-3-phosphate metabolic process	0.000801364291142872
GO:0019318	hexose metabolic process	0.000801364291142872
GO:0005996	monosaccharide metabolic process	0.000801364291142872
GO:0006066	alcohol metabolic process	0.00194031033381917
GO:0044262	cellular carbohydrate metabolic process	0.00222563009254727
GO:0044265	cellular macromolecule catabolic process	0.00229801901433619
GO:0008243	plasminogen activator activity	0.0026687074290719
GO:0009057	macromolecule catabolic process	0.00287246063691723
GO:0004807	triose-phosphate isomerase activity	0.00381215860215283
GO:0005975	carbohydrate metabolic process	0.00381215860215283
GO:0044248	cellular catabolic process	0.00381215860215283
GO:0000015	phosphopyruvate hydratase complex	0.00381215860215283
GO:0004634	phosphopyruvate hydratase activity	0.00381215860215283
GO:0006098	pentose-phosphate shunt	0.00452466669138058
GO:0006740	NADPH regeneration	0.00452466669138058
GO:0009056	catabolic process	0.00464384082415092
GO:0006739	NADP metabolic process	0.00544320154386884
GO:0006081	aldehyde metabolic process	0.00738819991474676
GO:0006094	gluconeogenesis	0.00741089388558953
GO:0016861	intramolecular oxidoreductase activity, interconverting aldoses and ketoses	0.00771768936066741
GO:0006090	pyruvate metabolic process	0.00800329401828087
GO:0006769	nicotinamide metabolic process	0.0088031049041376
GO:0019319	hexose biosynthetic process	0.00894367264301036
GO:0046165	alcohol biosynthetic process	0.00894367264301036
GO:0019362	pyridine nucleotide metabolic process	0.00894367264301036
GO:0046364	monosaccharide biosynthetic process	0.00894367264301036
GO:0006733	oxidoreduction coenzyme metabolic process	0.0114297418328042
GO:0030308	negative regulation of cell growth	0.0116761834286374
GO:0045792	negative regulation of cell size	0.0116761834286374
GO:0045926	negative regulation of growth	0.0128413395414501
GO:0006767	water-soluble vitamin metabolic process	0.0131268421898135
GO:0016860	intramolecular oxidoreductase activity	0.0137975509083469
GO:0006633	fatty acid biosynthetic process	0.0142405352847658
GO:0046394	carboxylic acid biosynthetic process	0.0154359354486916
GO:0016053	organic acid biosynthetic process	0.0154359354486916
GO:0006766	vitamin metabolic process	0.0156296729918687
GO:0016836	hydro-lyase activity	0.0159922110028098
GO:0016835	carbon-oxygen lyase activity	0.0175538202251983
GO:0003714	transcription corepressor activity	0.0181993389241271
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0211448259831228
GO:0016051	carbohydrate biosynthetic process	0.0225037134075076
GO:0001558	regulation of cell growth	0.0258798910505056
GO:0044445	cytosolic part	0.0293265925339893
GO:0006631	fatty acid metabolic process	0.0293265925339893
GO:0016049	cell growth	0.0293639592890473
GO:0040008	regulation of growth	0.0293639592890473
GO:0045892	negative regulation of transcription, DNA-dependent	0.0293639592890473
GO:0008361	regulation of cell size	0.0293639592890473
GO:0016564	transcription repressor activity	0.0299656044669309
GO:0016829	lyase activity	0.0380323582947717
GO:0032787	monocarboxylic acid metabolic process	0.0380323582947717
GO:0006732	coenzyme metabolic process	0.0380323582947717
GO:0016481	negative regulation of transcription	0.0380323582947717
GO:0003712	transcription cofactor activity	0.0388270803655245
GO:0016853	isomerase activity	0.0397210780239578
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0397210780239578
GO:0008610	lipid biosynthetic process	0.0401829081725927
GO:0004252	serine-type endopeptidase activity	0.0401829081725927
GO:0009117	nucleotide metabolic process	0.0401829081725927
GO:0051186	cofactor metabolic process	0.0401829081725927
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.042131259085518
GO:0008236	serine-type peptidase activity	0.042131259085518
GO:0017171	serine hydrolase activity	0.042131259085518
GO:0031324	negative regulation of cellular metabolic process	0.042131259085518
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0461062077148254
GO:0008134	transcription factor binding	0.0462469925712618
GO:0009892	negative regulation of metabolic process	0.0462469925712618
GO:0000287	magnesium ion binding	0.0467822848085108
GO:0000902	cell morphogenesis	0.0487215706423031
GO:0032989	cellular structure morphogenesis	0.0487215706423031

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
animal cell	3.01e-18	679
eukaryotic cell	3.01e-18	679
embryonic cell	7.86e-14	250
native cell	1.27e-13	722
somatic cell	3.27e-11	588
mesodermal cell	3.86e-11	121
electrically responsive cell	4.88e-09	61
electrically active cell	4.88e-09	61
epithelial cell	1.28e-08	253
muscle precursor cell	1.47e-08	58
myoblast	1.47e-08	58
multi-potent skeletal muscle stem cell	1.47e-08	58
muscle cell	4.68e-08	55
contractile cell	5.45e-08	59
non-terminally differentiated cell	5.63e-08	106
smooth muscle cell	7.64e-08	43
smooth muscle myoblast	7.64e-08	43
vascular associated smooth muscle cell	2.51e-07	32

Uber Anatomy

Ontology term	p-value	n
artery	5.36e-11	42
arterial blood vessel	5.36e-11	42
arterial system	5.36e-11	42
epithelial vesicle	1.39e-10	78
unilaminar epithelium	1.85e-09	148
dense mesenchyme tissue	3.31e-09	73
somite	3.50e-09	71
presomitic mesoderm	3.50e-09	71
presumptive segmental plate	3.50e-09	71
dermomyotome	3.50e-09	71
trunk paraxial mesoderm	3.50e-09	71
paraxial mesoderm	3.73e-09	72
presumptive paraxial mesoderm	3.73e-09	72
epithelial tube open at both ends	5.11e-09	59
blood vessel	5.11e-09	59
blood vasculature	5.11e-09	59
vascular cord	5.11e-09	59
epithelial tube	5.18e-09	117
multilaminar epithelium	2.55e-08	83
vessel	4.57e-08	68
vasculature	9.04e-08	78
vascular system	9.04e-08	78
splanchnic layer of lateral plate mesoderm	9.23e-08	83
systemic artery	1.27e-07	33
systemic arterial system	1.27e-07	33
trunk mesenchyme	2.87e-07	122
skeletal muscle tissue	5.44e-07	62
striated muscle tissue	5.44e-07	62
myotome	5.44e-07	62

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.