Coexpression cluster:C3538

Full id: C3538_iPS_Mallassezderived_Bronchial_HES3GFP_acute_chronic_hepatocellular

Phase1 CAGE Peaks

Hg19::chr16:18801619..18801630,-	p2@RPS15A
Hg19::chr2:55459808..55459860,+	p1@RPS27A
Hg19::chr3:197677089..197677100,+	p2@RPL35A

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
3.23952687815502e-08	1.05948726550059e-05	3	92	Ribosome (KEGG):03010
3.34751110742684e-08	1.05948726550059e-05	3	93	Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1037505066909e-06	0.00011644567845589	3	296	Metabolism of proteins (Reactome):REACT_17015
6.2031341872007e-08	1.30886131349935e-05	3	114	Regulation of beta-cell development (Reactome):REACT_13698
3.18533613032144e-06	0.000252039721311684	3	421	Gene Expression (Reactome):REACT_71
1.29326205516739e-06	0.000116947840131565	3	312	Diabetes pathways (Reactome):REACT_15380
1.23098667822397e-07	1.55842913463155e-05	3	143	Influenza Infection (Reactome):REACT_6167
1.10547371417187e-07	1.55842913463155e-05	3	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)	0.00204574031208939
GO:0044445	cytosolic part	0.00417978982585916
GO:0033279	ribosomal subunit	0.00417978982585916
GO:0008582	regulation of synaptic growth at neuromuscular junction	0.00417978982585916
GO:0051124	synaptic growth at neuromuscular junction	0.00417978982585916
GO:0042062	long-term strengthening of neuromuscular junction	0.00417978982585916
GO:0050806	positive regulation of synaptic transmission	0.0106074249154712
GO:0051971	positive regulation of transmission of nerve impulse	0.0106074249154712
GO:0031646	positive regulation of neurological process	0.0106074249154712
GO:0005829	cytosol	0.0106074249154712
GO:0007528	neuromuscular junction development	0.0106074249154712
GO:0030433	ER-associated protein catabolic process	0.0106074249154712
GO:0006515	misfolded or incompletely synthesized protein catabolic process	0.0106074249154712
GO:0048167	regulation of synaptic plasticity	0.0125334643717844
GO:0050804	regulation of synaptic transmission	0.0125334643717844
GO:0003735	structural constituent of ribosome	0.0125334643717844
GO:0051969	regulation of transmission of nerve impulse	0.0125334643717844
GO:0050803	regulation of synapse structure and activity	0.0125334643717844
GO:0005840	ribosome	0.0136205233382194
GO:0043161	proteasomal ubiquitin-dependent protein catabolic process	0.0136205233382194
GO:0000049	tRNA binding	0.0136205233382194
GO:0031644	regulation of neurological process	0.0136205233382194
GO:0007416	synaptogenesis	0.0136205233382194
GO:0003723	RNA binding	0.014385426350698
GO:0005843	cytosolic small ribosomal subunit (sensu Eukaryota)	0.0164385508748134
GO:0048589	developmental growth	0.0164385508748134
GO:0030529	ribonucleoprotein complex	0.0164385508748134
GO:0005842	cytosolic large ribosomal subunit (sensu Eukaryota)	0.0164385508748134
GO:0050808	synapse organization and biogenesis	0.0164385508748134
GO:0006412	translation	0.0164385508748134
GO:0048741	skeletal muscle fiber development	0.0164385508748134
GO:0048747	muscle fiber development	0.0164385508748134
GO:0010467	gene expression	0.0177973724591936
GO:0044267	cellular protein metabolic process	0.0185390426406863
GO:0044260	cellular macromolecule metabolic process	0.0187151417405112
GO:0007411	axon guidance	0.0194746956104163
GO:0019538	protein metabolic process	0.019669226711609
GO:0007519	skeletal muscle development	0.0220666113673117
GO:0009059	macromolecule biosynthetic process	0.0224279650682972
GO:0016567	protein ubiquitination	0.022836552979904
GO:0032446	protein modification by small protein conjugation	0.0234975929219407
GO:0043062	extracellular structure organization and biogenesis	0.025018250826649
GO:0014706	striated muscle development	0.0255970539033313
GO:0015934	large ribosomal subunit	0.0296229750907722
GO:0044249	cellular biosynthetic process	0.0296229750907722
GO:0007409	axonogenesis	0.0303299924990499
GO:0048667	neuron morphogenesis during differentiation	0.0303299924990499
GO:0048812	neurite morphogenesis	0.0303299924990499
GO:0015935	small ribosomal subunit	0.0303299924990499
GO:0005737	cytoplasm	0.0303299924990499
GO:0000904	cellular morphogenesis during differentiation	0.03086667314336
GO:0031175	neurite development	0.0324268433209433
GO:0048666	neuron development	0.0362723634105823
GO:0009058	biosynthetic process	0.0390181141743141
GO:0007517	muscle development	0.0390181141743141
GO:0040008	regulation of growth	0.0430991616255652
GO:0032990	cell part morphogenesis	0.0430991616255652
GO:0048858	cell projection morphogenesis	0.0430991616255652
GO:0030030	cell projection organization and biogenesis	0.0430991616255652
GO:0030182	neuron differentiation	0.0433450960231335
GO:0005515	protein binding	0.0433450960231335
GO:0016477	cell migration	0.0463453531660582
GO:0043232	intracellular non-membrane-bound organelle	0.0463453531660582
GO:0043228	non-membrane-bound organelle	0.0463453531660582
GO:0048699	generation of neurons	0.046355984662957
GO:0022008	neurogenesis	0.0484043620897308
GO:0051239	regulation of multicellular organismal process	0.0484043620897308
GO:0045941	positive regulation of transcription	0.0484043620897308
GO:0006511	ubiquitin-dependent protein catabolic process	0.0484043620897308
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0484043620897308
GO:0019941	modification-dependent protein catabolic process	0.0484043620897308
GO:0043632	modification-dependent macromolecule catabolic process	0.0484043620897308
GO:0051603	proteolysis involved in cellular protein catabolic process	0.0484043620897308
GO:0007268	synaptic transmission	0.0484043620897308
GO:0044257	cellular protein catabolic process	0.0484043620897308

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	1.01e-40	679
eukaryotic cell	1.01e-40	679
embryonic cell	1.43e-27	250
native cell	2.08e-24	722
epithelial cell	7.80e-24	253
somatic cell	4.46e-15	588
mesodermal cell	1.50e-14	121
non-terminally differentiated cell	3.64e-11	106
electrically responsive cell	5.34e-11	61
electrically active cell	5.34e-11	61
muscle precursor cell	1.18e-09	58
myoblast	1.18e-09	58
multi-potent skeletal muscle stem cell	1.18e-09	58
muscle cell	3.73e-09	55
contractile cell	4.86e-09	59
squamous epithelial cell	3.92e-08	63
smooth muscle cell	4.93e-07	43
smooth muscle myoblast	4.93e-07	43

Uber Anatomy

Ontology term	p-value	n
unilaminar epithelium	3.76e-12	148
epithelial vesicle	1.14e-10	78
trunk	5.27e-10	199
somite	1.23e-09	71
presomitic mesoderm	1.23e-09	71
presumptive segmental plate	1.23e-09	71
dermomyotome	1.23e-09	71
trunk paraxial mesoderm	1.23e-09	71
multilaminar epithelium	1.25e-09	83
paraxial mesoderm	2.90e-09	72
presumptive paraxial mesoderm	2.90e-09	72
dense mesenchyme tissue	3.45e-09	73
trunk mesenchyme	7.05e-09	122
organism subdivision	1.93e-08	264
mesenchyme	3.94e-08	160
entire embryonic mesenchyme	3.94e-08	160
skeletal muscle tissue	4.48e-08	62
striated muscle tissue	4.48e-08	62
myotome	4.48e-08	62
epithelial tube	6.04e-08	117
vasculature	4.35e-07	78
vascular system	4.35e-07	78
muscle tissue	4.97e-07	64
musculature	4.97e-07	64
musculature of body	4.97e-07	64
artery	9.69e-07	42
arterial blood vessel	9.69e-07	42
arterial system	9.69e-07	42

Disease

Ontology term	p-value	n
cancer	1.33e-23	235
disease of cellular proliferation	1.68e-23	239
cell type cancer	3.01e-12	143
carcinoma	1.17e-11	106
organ system cancer	3.08e-11	137
hematologic cancer	2.58e-07	51
immune system cancer	2.58e-07	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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324682851513938
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461300995705857
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000627318133236668
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.0043341692450175
KAT2A#2648	1	205.363333333333	0.00486154522073778	0.0227530773609067
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186263337455966
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293993785736637
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.026920251712695
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00881081094282167
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00484033284896721
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298249371182131
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276104957752262
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370672859627738
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0246058534509359
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00154672529988785
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541808247528257
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328716314110035
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.0038853153331239
ZZZ3#26009	1	79.8044041450777	0.012478437908258	0.0451587226411364

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.