Coexpression cluster:C1162

Full id: C1162_embryonic_iPS_Keratinocyte_giant_teratocarcinoma_acute_chronic

Phase1 CAGE Peaks

Hg19::chr12:112847354..112847457,-	p1@RPL6
Hg19::chr1:24018269..24018274,+	p2@RPL11
Hg19::chr1:93297622..93297635,+	p2@RPL5
Hg19::chr2:55459786..55459807,+	p2@RPS27A
Hg19::chr3:185136568..185136602,-	p1@ENST00000422486
Hg19::chrX:71497077..71497133,-	p1@RPS4X
Hg19::chrX:71497148..71497163,-	p3@RPS4X

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
3.11437028550525e-13	1.04170377464436e-10	5	92	Ribosome (KEGG):03010
3.29132314263622e-13	1.04170377464436e-10	5	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1591439383194e-10	1.22289685492696e-08	5	296	Metabolism of proteins (Reactome):REACT_17015
9.29699977867239e-13	1.96166695329987e-10	5	114	Regulation of beta-cell development (Reactome):REACT_13698
6.81527814787627e-10	5.3925888345071e-08	5	421	Gene Expression (Reactome):REACT_71
1.5108164748526e-10	1.36620975511671e-08	5	312	Diabetes pathways (Reactome):REACT_15380
2.94043896828612e-12	3.72259573385023e-10	5	143	Influenza Infection (Reactome):REACT_6167
2.45472569124687e-12	3.72259573385023e-10	5	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:0005830	cytosolic ribosome (sensu Eukaryota)	1.80412952534817e-08
GO:0044445	cytosolic part	3.89335864396034e-07
GO:0033279	ribosomal subunit	4.50106557389469e-07
GO:0019843	rRNA binding	4.50106557389469e-07
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	4.6083793122753e-07
GO:0015934	large ribosomal subunit	7.85433413948777e-06
GO:0005829	cytosol	8.99367102257202e-06
GO:0003735	structural constituent of ribosome	2.76395189313524e-05
GO:0005840	ribosome	3.48041401227949e-05
GO:0003723	RNA binding	5.48133301770672e-05
GO:0030529	ribonucleoprotein complex	9.14479151801551e-05
GO:0006412	translation	0.000105937742458961
GO:0009059	macromolecule biosynthetic process	0.000273606126740663
GO:0044249	cellular biosynthetic process	0.000593938698888462
GO:0010467	gene expression	0.00117137004948452
GO:0044267	cellular protein metabolic process	0.00117327045102701
GO:0044260	cellular macromolecule metabolic process	0.00117327045102701
GO:0009058	biosynthetic process	0.00117327045102701
GO:0019538	protein metabolic process	0.00132208046366353
GO:0043232	intracellular non-membrane-bound organelle	0.00199327017675962
GO:0043228	non-membrane-bound organelle	0.00199327017675962
GO:0008582	regulation of synaptic growth at neuromuscular junction	0.00202360627664
GO:0051124	synaptic growth at neuromuscular junction	0.00202360627664
GO:0042062	long-term strengthening of neuromuscular junction	0.00202360627664
GO:0008097	5S rRNA binding	0.00291382148067808
GO:0005737	cytoplasm	0.00328504115132846
GO:0032991	macromolecular complex	0.0047323211441893
GO:0050806	positive regulation of synaptic transmission	0.00520233369326765
GO:0044446	intracellular organelle part	0.00541624347566376
GO:0044422	organelle part	0.00541624347566376
GO:0051971	positive regulation of transmission of nerve impulse	0.0054817063055444
GO:0031646	positive regulation of neurological process	0.00606867467450403
GO:0007528	neuromuscular junction development	0.00721681283175408
GO:0044444	cytoplasmic part	0.00721681283175408
GO:0030433	ER-associated protein catabolic process	0.00741595907656725
GO:0006515	misfolded or incompletely synthesized protein catabolic process	0.00741595907656725
GO:0048167	regulation of synaptic plasticity	0.0102161128062905
GO:0050804	regulation of synaptic transmission	0.0102161128062905
GO:0051969	regulation of transmission of nerve impulse	0.0109171849772188
GO:0050803	regulation of synapse structure and activity	0.0109171849772188
GO:0043229	intracellular organelle	0.0125611320158036
GO:0043226	organelle	0.0125611320158036
GO:0043161	proteasomal ubiquitin-dependent protein catabolic process	0.0129726795143152
GO:0031644	regulation of neurological process	0.0134724526218766
GO:0007416	synaptogenesis	0.0134724526218766
GO:0043170	macromolecule metabolic process	0.0136164574474217
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	0.0175335600722431
GO:0003676	nucleic acid binding	0.0181231096858235
GO:0048589	developmental growth	0.0182986050132503
GO:0050808	synapse organization and biogenesis	0.0188997388298272
GO:0048741	skeletal muscle fiber development	0.0195672790731445
GO:0048747	muscle fiber development	0.0195672790731445
GO:0044237	cellular metabolic process	0.0224350864349877
GO:0044238	primary metabolic process	0.0228668393165134
GO:0044424	intracellular part	0.0242061947206519
GO:0007411	axon guidance	0.0242061947206519
GO:0007519	skeletal muscle development	0.0284344745885562
GO:0016567	protein ubiquitination	0.0304359394801792
GO:0032446	protein modification by small protein conjugation	0.0315521008867531
GO:0043062	extracellular structure organization and biogenesis	0.0338328528209046
GO:0014706	striated muscle development	0.0348546835516022
GO:0005622	intracellular	0.0432642044174568
GO:0007409	axonogenesis	0.0436523682379881
GO:0048667	neuron morphogenesis during differentiation	0.0442085182750772
GO:0048812	neurite morphogenesis	0.0442085182750772
GO:0015935	small ribosomal subunit	0.0442085182750772
GO:0000904	cellular morphogenesis during differentiation	0.0453348748357801
GO:0031175	neurite development	0.0478334177117967

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	1.37e-38	679
eukaryotic cell	1.37e-38	679
embryonic cell	1.03e-24	250
native cell	5.24e-23	722
epithelial cell	1.62e-21	253
somatic cell	5.05e-12	588
electrically responsive cell	2.70e-11	61
electrically active cell	2.70e-11	61
non-terminally differentiated cell	9.70e-11	106
mesodermal cell	1.55e-10	121
muscle precursor cell	1.88e-10	58
myoblast	1.88e-10	58
multi-potent skeletal muscle stem cell	1.88e-10	58
squamous epithelial cell	3.11e-10	63
muscle cell	8.00e-10	55
contractile cell	4.24e-08	59
smooth muscle cell	2.46e-07	43
smooth muscle myoblast	2.46e-07	43
endo-epithelial cell	3.64e-07	42
vascular associated smooth muscle cell	4.59e-07	32

Uber Anatomy

Ontology term	p-value	n
unilaminar epithelium	1.35e-12	148
somite	3.51e-11	71
presomitic mesoderm	3.51e-11	71
presumptive segmental plate	3.51e-11	71
dermomyotome	3.51e-11	71
trunk paraxial mesoderm	3.51e-11	71
paraxial mesoderm	1.08e-10	72
presumptive paraxial mesoderm	1.08e-10	72
dense mesenchyme tissue	1.51e-10	73
multilaminar epithelium	1.92e-10	83
epithelial vesicle	4.07e-10	78
skeletal muscle tissue	9.85e-09	62
striated muscle tissue	9.85e-09	62
myotome	9.85e-09	62
trunk	5.06e-08	199
muscle tissue	8.51e-08	64
musculature	8.51e-08	64
musculature of body	8.51e-08	64
artery	1.05e-07	42
arterial blood vessel	1.05e-07	42
arterial system	1.05e-07	42
organism subdivision	1.13e-07	264
trunk mesenchyme	1.80e-07	122
larynx	5.29e-07	9
surface structure	5.79e-07	99

Disease

Ontology term	p-value	n
disease of cellular proliferation	9.63e-30	239
cancer	2.20e-28	235
cell type cancer	2.43e-14	143
carcinoma	1.14e-13	106
organ system cancer	6.96e-13	137
hematologic cancer	7.83e-08	51
immune system cancer	7.83e-08	51

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
BCLAF1#9774	4	12.3729414914982	0.00014216266196968	0.00185128756277449
ELF1#1997	6	3.64979825040646	0.000937747978262069	0.00678942537966809
ELK4#2005	4	9.27753237626744	0.000432817858966577	0.00404176183589148
ETS1#2113	4	5.55929195554419	0.00302256447530346	0.0160492964175209
GABPB1#2553	6	6.05801471672758	4.93271023131083e-05	0.000853632682432265
GTF2B#2959	6	27.3804256579922	6.39564885927993e-09	5.05261097741555e-07
GTF2F1#2962	6	10.9197093229351	1.52580683448537e-06	5.86722164899918e-05
HEY1#23462	6	3.46295232266204	0.00126789009587212	0.00850518168943341
KAT2A#2648	3	264.038571428571	1.47466334870275e-07	8.31151459660908e-06
MAX#4149	6	5.53076186486325	8.40673768319711e-05	0.00126166299309588
MXI1#4601	4	5.69232664500531	0.00276690540539156	0.0151612189734359
MYC#4609	6	4.47624160423663	0.000288361195091082	0.00306369835748906
NFKB1#4790	6	4.70405436359472	0.00021611506140197	0.00247677393808409
NRF1#4899	5	8.72162817693636	6.71450045004423e-05	0.00107340534593934
POU2F2#5452	6	7.80524919235073	1.11144903558223e-05	0.000284576184915844
RAD21#5885	4	5.91716222597504	0.00239318493722796	0.0135535947974162
RDBP#7936	3	65.8450302814393	9.4409612230599e-06	0.000250955599179219
REST#5978	5	6.89287765437716	0.000209438858484651	0.00243852674930641
RFX5#5993	5	8.60565059085364	7.16524263203101e-05	0.00112734374095614
SIN3A#25942	6	4.63618690869869	0.000235167814635783	0.00256535318495368
SIX5#147912	4	9.76383734597657	0.000355537135106872	0.00355874476264391
SMC3#9126	4	8.59710448281877	0.000579846628016137	0.00486649003402261
SP2#6668	4	14.9448745679112	6.81071539656055e-05	0.00108778759030645
SPI1#6688	4	4.68818486201299	0.00568568052914417	0.0256648134495954
SRF#6722	3	5.91307639807192	0.0106686813016745	0.0393914447594423
STAT2#6773	2	18.6467917675545	0.00468275705257902	0.0220935337827205
TAF1#6872	6	2.86546824492454	0.00372833020747146	0.0185854173327341
TAF7#6879	6	9.79977377564907	2.89681485118392e-06	9.9454453071268e-05
TBP#6908	6	3.17723201751119	0.00207411205185266	0.0120183193843453
TCF12#6938	6	9.1152556304455	4.4461156654571e-06	0.000139109608743162
YY1#7528	6	4.20957492844616	0.00041168337886575	0.00392190097649914
ZNF143#7702	6	11.5721799019096	1.08146108094101e-06	4.49628637867825e-05
ZNF263#10127	5	5.8727440264362	0.000451394263989067	0.00419796665509832
ZZZ3#26009	3	102.605662472243	2.50907428413451e-06	8.831992219775e-05

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.