Coexpression cluster:C3414

Full id: C3414_Smooth_Alveolar_Mallassezderived_mucinous_Placental_Bronchial_hepatocellular

Phase1 CAGE Peaks

Hg19::chr14:23504087..23504118,-	p1@PSMB5
Hg19::chr14:24701539..24701583,-	p1@NEDD8-MDP1 p1@NEDD8
Hg19::chr17:4699451..4699490,+	p1@PSMB6

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
2.42990828311186e-06	0.00104406531902726	2	45	Proteasome (KEGG):03050
4.94817686742777e-06	0.00104406531902726	2	64	Proteasome Degradation (Wikipathways):WP183
1.66559167769667e-05	0.00263579882995498	2	117	Cell Cycle Checkpoints (Reactome):REACT_1538
4.88436109433595e-05	0.00343533396968295	2	200	DNA Replication (Reactome):REACT_383
0.000121384963779088	0.00768366820721624	2	315	Cell Cycle, Mitotic (Reactome):REACT_152
3.28062162748213e-05	0.00343533396968295	2	164	Metabolism of RNA (Reactome):REACT_21257
4.94817686742777e-06	0.00104406531902726	2	64	Signaling by Wnt (Reactome):REACT_11045
2.63387331172458e-05	0.00333448361264332	2	147	Apoptosis (Reactome):REACT_578
4.59498110789263e-05	0.00343533396968295	2	194	HIV Infection (Reactome):REACT_6185
4.64259749243038e-05	0.00343533396968295	2	195	Metabolism of amino acids and derivatives (Reactome):REACT_13
0.00014649401603791	0.00843006474109064	2	346	{CDC2,351} (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:0004298	threonine endopeptidase activity	2.90963365692439e-05
GO:0005839	proteasome core complex (sensu Eukaryota)	2.90963365692439e-05
GO:0000502	proteasome complex (sensu Eukaryota)	6.0851107296576e-05
GO:0006511	ubiquitin-dependent protein catabolic process	0.000358939301823721
GO:0043632	modification-dependent macromolecule catabolic process	0.000358939301823721
GO:0019941	modification-dependent protein catabolic process	0.000358939301823721
GO:0051603	proteolysis involved in cellular protein catabolic process	0.000358939301823721
GO:0044257	cellular protein catabolic process	0.000358939301823721
GO:0030163	protein catabolic process	0.000474538006919738
GO:0043285	biopolymer catabolic process	0.000695007058246673
GO:0044265	cellular macromolecule catabolic process	0.000838715495874038
GO:0005829	cytosol	0.000906954100865701
GO:0009057	macromolecule catabolic process	0.00101380963655902
GO:0004175	endopeptidase activity	0.00147266438388624
GO:0044248	cellular catabolic process	0.00147266438388624
GO:0009056	catabolic process	0.00199753447215315
GO:0008233	peptidase activity	0.00303930587302639
GO:0006508	proteolysis	0.0032539008803968
GO:0043234	protein complex	0.0147781536685955
GO:0032991	macromolecular complex	0.0248985563881076
GO:0016787	hydrolase activity	0.0248985563881076
GO:0044444	cytoplasmic part	0.0323833408943997
GO:0044267	cellular protein metabolic process	0.0450366344531342
GO:0044260	cellular macromolecule metabolic process	0.0450366344531342
GO:0019538	protein metabolic process	0.0463788251414518
GO:0005634	nucleus	0.0476923425897552

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
embryonic cell	2.89e-31	250
mesodermal cell	2.65e-27	121
contractile cell	5.30e-21	59
animal cell	6.41e-21	679
eukaryotic cell	6.41e-21	679
electrically responsive cell	4.59e-20	61
electrically active cell	4.59e-20	61
muscle precursor cell	1.49e-19	58
myoblast	1.49e-19	58
multi-potent skeletal muscle stem cell	1.49e-19	58
muscle cell	3.45e-19	55
non-terminally differentiated cell	6.00e-18	106
smooth muscle cell	2.36e-17	43
smooth muscle myoblast	2.36e-17	43
epithelial cell	2.65e-15	253
vascular associated smooth muscle cell	2.61e-14	32
somatic cell	5.94e-13	588
meso-epithelial cell	2.69e-10	45
endothelial cell	3.34e-10	36
native cell	4.18e-10	722
lining cell	1.30e-08	58
barrier cell	1.30e-08	58
endothelial cell of vascular tree	2.42e-08	24
blood vessel endothelial cell	4.71e-08	18
embryonic blood vessel endothelial progenitor cell	4.71e-08	18
epithelial cell of nephron	1.31e-07	15

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	5.16e-25	78
unilaminar epithelium	2.76e-23	148
epithelial tube	7.42e-23	117
multilaminar epithelium	1.66e-21	83
somite	2.71e-21	71
presomitic mesoderm	2.71e-21	71
presumptive segmental plate	2.71e-21	71
dermomyotome	2.71e-21	71
trunk paraxial mesoderm	2.71e-21	71
dense mesenchyme tissue	4.12e-21	73
paraxial mesoderm	4.78e-21	72
presumptive paraxial mesoderm	4.78e-21	72
vasculature	4.58e-20	78
vascular system	4.58e-20	78
cell layer	8.11e-20	309
mesenchyme	1.03e-19	160
entire embryonic mesenchyme	1.03e-19	160
epithelium	1.95e-19	306
skeletal muscle tissue	3.35e-19	62
striated muscle tissue	3.35e-19	62
myotome	3.35e-19	62
trunk mesenchyme	3.05e-18	122
splanchnic layer of lateral plate mesoderm	4.75e-18	83
muscle tissue	9.40e-18	64
musculature	9.40e-18	64
musculature of body	9.40e-18	64
vessel	2.33e-17	68
epithelial tube open at both ends	1.10e-16	59
blood vessel	1.10e-16	59
blood vasculature	1.10e-16	59
vascular cord	1.10e-16	59
trunk	2.78e-16	199
organism subdivision	5.40e-16	264
multi-tissue structure	7.55e-16	342
artery	2.69e-15	42
arterial blood vessel	2.69e-15	42
arterial system	2.69e-15	42
anatomical cluster	2.51e-14	373
cardiovascular system	3.03e-13	109
circulatory system	3.38e-13	112
tube	5.42e-11	192
systemic artery	1.21e-10	33
systemic arterial system	1.21e-10	33
anatomical conduit	2.85e-10	240
multi-cellular organism	1.49e-08	656
simple squamous epithelium	3.66e-08	22
blood vessel endothelium	4.71e-08	18
endothelium	4.71e-08	18
cardiovascular system endothelium	4.71e-08	18
squamous epithelium	7.82e-08	25
nephron epithelium	1.31e-07	15
renal tubule	1.31e-07	15
nephron tubule	1.31e-07	15
nephron	1.31e-07	15
uriniferous tubule	1.31e-07	15
nephrogenic mesenchyme	1.31e-07	15
subdivision of trunk	7.12e-07	112
excretory tube	7.67e-07	16
kidney epithelium	7.67e-07	16

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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259480085086778
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460970866176487
MAFK#7975	2	18.0671554252199	0.00398367474493681	0.0191076975606896
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293769992390123
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269076400104445
NR2C2#7182	2	21.7430739368272	0.00276220797549601	0.0151370678325547
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.0048368040522365
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239339141678259
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328557058265238
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109124374806699

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.