Coexpression cluster:C1501

Full id: C1501_hepatocellular_acute_oral_signet_testicular_iPS_teratocarcinoma

Phase1 CAGE Peaks

Hg19::chr2:198364552..198364576,-	p1@HSPD1
Hg19::chr2:198364581..198364596,-	p2@HSPD1
Hg19::chr2:198365063..198365091,+	p2@HSPE1
Hg19::chr2:198365095..198365116,+	p1@HSPE1
Hg19::chr2:198365122..198365133,+	p3@HSPE1
Hg19::chr2:203776344..203776423,-	p1@WDR12

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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No results for this coexpression

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:0051087	chaperone binding	6.17474325659817e-05
GO:0006986	response to unfolded protein	0.000293224101723009
GO:0051789	response to protein stimulus	0.000293224101723009
GO:0031980	mitochondrial lumen	0.00170046604163955
GO:0005759	mitochondrial matrix	0.00170046604163955
GO:0051082	unfolded protein binding	0.00170046604163955
GO:0009607	response to biotic stimulus	0.00304274984538471
GO:0030150	protein import into mitochondrial matrix	0.00327824217005075
GO:0006457	protein folding	0.00337076692797348
GO:0019907	cyclin-dependent protein kinase activating kinase holoenzyme complex	0.00524472426633574
GO:0042981	regulation of apoptosis	0.0062930254510129
GO:0043067	regulation of programmed cell death	0.0062930254510129
GO:0044429	mitochondrial part	0.0062930254510129
GO:0042221	response to chemical stimulus	0.0062930254510129
GO:0043681	protein import into mitochondrion	0.00757415180743216
GO:0006915	apoptosis	0.0104087539166046
GO:0012501	programmed cell death	0.0104087539166046
GO:0006626	protein targeting to mitochondrion	0.0104087539166046
GO:0016265	death	0.0104087539166046
GO:0008219	cell death	0.0104087539166046
GO:0031974	membrane-enclosed lumen	0.0108082869144582
GO:0043233	organelle lumen	0.0108082869144582
GO:0005739	mitochondrion	0.0109590825739654
GO:0006950	response to stress	0.0150515336650597
GO:0048468	cell development	0.0150515336650597
GO:0006919	caspase activation	0.0150515336650597
GO:0006839	mitochondrial transport	0.0150515336650597
GO:0043280	positive regulation of caspase activity	0.0150515336650597
GO:0007219	Notch signaling pathway	0.0150515336650597
GO:0043281	regulation of caspase activity	0.0174546374220374
GO:0051345	positive regulation of hydrolase activity	0.0213859255099137
GO:0008632	apoptotic program	0.0232212881218106
GO:0007005	mitochondrion organization and biogenesis	0.0232212881218106
GO:0048869	cellular developmental process	0.0232212881218106
GO:0030154	cell differentiation	0.0232212881218106
GO:0017038	protein import	0.0295219359384132
GO:0043231	intracellular membrane-bound organelle	0.0456897064861589
GO:0043227	membrane-bound organelle	0.0456897064861589
GO:0005515	protein binding	0.0458582552281764
GO:0006605	protein targeting	0.0458582552281764
GO:0005524	ATP binding	0.0458582552281764
GO:0032559	adenyl ribonucleotide binding	0.0458582552281764
GO:0030554	adenyl nucleotide binding	0.0485713528048677

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
epithelial cell	1.46e-11	253

Uber Anatomy

Ontology term	p-value	n
larynx	9.78e-07	9

Disease

Ontology term	p-value	n
disease of cellular proliferation	4.67e-59	239
cancer	1.15e-57	235
cell type cancer	1.11e-30	143
organ system cancer	2.95e-28	137
carcinoma	1.26e-25	106
hematologic cancer	1.14e-17	51
immune system cancer	1.14e-17	51
leukemia	1.57e-14	39
myeloid leukemia	5.50e-12	31
germ cell and embryonal cancer	5.08e-07	22
germ cell cancer	5.08e-07	22

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	4	14.9754496840058	5.47577390976406e-05	0.000927480297375688
BCLAF1#9774	5	18.0438730084349	1.21080990322265e-06	4.89948762040568e-05
BRCA1#672	5	16.8201922026865	1.71529178571936e-06	6.4766217935193e-05
CHD2#1106	5	8.62001902843071	4.6560374997265e-05	0.000815071908203044
E2F1#1869	5	4.08949101239944	0.00174981759776199	0.0107594465759591
E2F4#1874	5	10.5567169294037	1.71705502564041e-05	0.000392659316450315
E2F6#1876	6	5.01715573169739	6.26776799983417e-05	0.00102505390249715
ELF1#1997	5	3.54841496567295	0.00344683777572169	0.0175319870675789
ELK4#2005	6	16.235681658468	5.45305335722442e-08	3.4432372404786e-06
EP300#2033	5	5.64495143851933	0.000368813893181486	0.00367123086065394
ETS1#2113	6	9.72876092220234	1.17854759771003e-06	4.80618245049739e-05
FOS#2353	5	7.49829609074534	9.22669120642035e-05	0.00134340778322506
FOSL2#2355	5	14.1085005038014	4.09784291596229e-06	0.000130162596198353
FOXA1#3169	6	11.0814197493855	5.39600313513231e-07	2.50690912557866e-05
GABPB1#2553	5	5.88973653015181	0.000300017597367021	0.00309895538041879
GATA1#2623	6	13.5603081438004	1.60671883176178e-07	8.90679979142081e-06
GATA3#2625	5	22.6970969643383	3.87517465667206e-07	1.8868035709472e-05
GTF2B#2959	2	10.6479433114414	0.0135134586576011	0.0477252843480727
HDAC2#3066	5	11.1796835305219	1.29408913564529e-05	0.000317112565081319
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00253352302416356
HNF4A#3172	6	23.1322903629537	6.51490260560877e-09	5.13516915643151e-07
HNF4G#3174	6	28.7534225264468	1.76556713337063e-09	1.54046838631659e-07
HSF1#3297	5	136.908888888889	4.94363085166209e-11	5.56966410481917e-09
IRF4#3662	4	14.6096751244961	6.03404227507469e-05	0.000991487320903911
JUN#3725	5	10.4273576602803	1.82465747415735e-05	0.000415446701424721
JUND#3727	5	5.82888661822586	0.000315568248503075	0.00323462874721883
MAX#4149	6	6.45255550900712	1.3848964723355e-05	0.000334575995082692
MEF2A#4205	5	15.61935909137	2.47611227471544e-06	8.74248444418545e-05
MEF2C#4208	5	34.4261287438534	4.87546598482441e-08	3.1450820999943e-06
MXI1#4601	6	9.9615716287593	1.02262624227062e-06	4.30306454941583e-05
MYC#4609	6	5.2222818716094	4.92821127172503e-05	0.000854553307334702
NFKB1#4790	6	5.48806342419384	3.65870229532191e-05	0.000707744413819457
NR2C2#7182	6	32.6146109052409	8.2872822148748e-10	7.78341247517364e-08
NR3C1#2908	5	12.4775194426442	7.52342219908436e-06	0.000214976386060238
NRF1#4899	5	10.1752328730924	2.0585884796849e-05	0.000455501953876718
PAX5#5079	5	5.55797127598152	0.000397717619661286	0.00388707004302873
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380568055454884
POU2F2#5452	5	7.58843671478544	8.70203885493171e-05	0.00129095488063951
PPARGC1A#10891	5	291.70928030303	1.11748890111184e-12	1.56237514515688e-10
REST#5978	4	6.43335247741868	0.00145495422303207	0.00932633426006546
RFX5#5993	5	10.0399256893292	2.19894173045095e-05	0.00048267186924457
RXRA#6256	5	16.7288476159444	1.76223204684013e-06	6.62750279942156e-05
SETDB1#9869	5	33.6000218150087	5.50253359077372e-08	3.45567712379324e-06
SIN3A#25942	6	5.40888472681514	3.99207083571449e-05	0.000743319461599546
SIX5#147912	6	17.086715355459	4.01311308210759e-08	2.65269314672301e-06
SP1#6667	5	4.74865114845075	0.000852370402732661	0.00641822007865872
SRF#6722	6	13.7971782621678	1.44812893459755e-07	8.17519663786129e-06
STAT1#6772	5	17.2554895809993	1.51117799335256e-06	5.8195397657724e-05
STAT3#6774	5	8.76622083096187	4.28672496720299e-05	0.000766480515065421
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573519628776401
TAF7#6879	6	11.4330694049239	4.47357982339933e-07	2.12757833868854e-05
TBP#6908	6	3.70677068709639	0.00038541647290796	0.00378028841228723
TCF7L2#6934	5	8.97514713594779	3.818060286338e-05	0.000720033221821695
TFAP2C#7022	5	9.00769050821686	3.75071472654799e-05	0.000723934384265285
TRIM28#10155	6	18.5905250452625	2.41896703530258e-08	1.69553354496622e-06
USF1#7391	6	6.36149927720796	1.50818327938273e-05	0.000357010774060411
USF2#7392	5	10.8268311542247	1.51592052313491e-05	0.000358598467759201
YY1#7528	6	4.91117074985386	7.12445972864136e-05	0.00112414480978936
ZBTB33#10009	5	26.3872708583176	1.83222607625143e-07	1.00081516306288e-05
ZNF143#7702	6	13.5008765522279	1.64963374888971e-07	9.12532304556633e-06

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.