Coexpression cluster:C1868

Full id: C1868_hereditary_teratocarcinoma_adrenal_epitheloid_large_acantholytic_Reticulocytes

Phase1 CAGE Peaks

Hg19::chr20:35402135..35402207,-	p1@DSN1
Hg19::chr3:155588375..155588512,+	p1@GMPS
Hg19::chr3:179280702..179280769,+	p1@ACTL6A
Hg19::chr3:186524234..186524303,-	p1@RFC4
Hg19::chr7:7680052..7680078,-	p2@RPA3

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
1.54262472139839e-05	0.00195296289729036	2	36	DNA replication (KEGG):03030
2.75970978623047e-05	0.0024955661352627	2	48	Nucleotide excision repair (KEGG):03420
6.20063328622183e-06	0.00195296289729036	2	23	Mismatch repair (KEGG):03430
2.10736705709464e-05	0.00222327224523484	2	42	DNA Replication (Wikipathways):WP1806
0.000165221094022206	0.0104584952516056	2	117	Cell Cycle Checkpoints (Reactome):REACT_1538
0.00013817077023549	0.0097180108398961	2	107	DNA Repair (Reactome):REACT_216
3.3531346989962e-06	0.00195296289729036	3	200	DNA Replication (Reactome):REACT_383
1.30932089172023e-05	0.00195296289729036	3	315	Cell Cycle, Mitotic (Reactome):REACT_152
7.14406195160067e-05	0.00565273901920403	2	77	Chromosome Maintenance (Reactome):REACT_22172
1.37386321379175e-05	0.00195296289729036	2	34	{PCNA,34} (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:0005657	replication fork	0.00144153184862913
GO:0044427	chromosomal part	0.00208358897940201
GO:0005694	chromosome	0.00212435165266929
GO:0003922	GMP synthase (glutamine-hydrolyzing) activity	0.00494524902861179
GO:0003921	GMP synthase activity	0.00494524902861179
GO:0043234	protein complex	0.00675618320106279
GO:0022616	DNA strand elongation	0.0077899374882706
GO:0006271	DNA strand elongation during DNA replication	0.0077899374882706
GO:0006259	DNA metabolic process	0.0077899374882706
GO:0000444	MIS12/MIND type complex	0.0077899374882706
GO:0006177	GMP biosynthetic process	0.0077899374882706
GO:0046037	GMP metabolic process	0.0077899374882706
GO:0032991	macromolecular complex	0.0077899374882706
GO:0003689	DNA clamp loader activity	0.0077899374882706
GO:0033170	DNA-protein loading ATPase activity	0.0077899374882706
GO:0035267	NuA4 histone acetyltransferase complex	0.0077899374882706
GO:0005662	DNA replication factor A complex	0.0077899374882706
GO:0044446	intracellular organelle part	0.0077899374882706
GO:0044422	organelle part	0.0077899374882706
GO:0005663	DNA replication factor C complex	0.0077899374882706
GO:0009113	purine base biosynthetic process	0.0077899374882706
GO:0043189	H4/H2A histone acetyltransferase complex	0.0077899374882706
GO:0006260	DNA replication	0.0077899374882706
GO:0000777	condensed chromosome kinetochore	0.0079091381939718
GO:0000779	condensed chromosome, pericentric region	0.0079091381939718
GO:0006281	DNA repair	0.00838626150757864
GO:0006144	purine base metabolic process	0.00915301729194821
GO:0006974	response to DNA damage stimulus	0.0101406475116562
GO:0000123	histone acetyltransferase complex	0.0110763505871249
GO:0046112	nucleobase biosynthetic process	0.0115300861109198
GO:0043601	nuclear replisome	0.0115808778598948
GO:0030894	replisome	0.0115808778598948
GO:0009719	response to endogenous stimulus	0.0119433952415913
GO:0016884	carbon-nitrogen ligase activity, with glutamine as amido-N-donor	0.0119985824167592
GO:0043596	nuclear replication fork	0.0119985824167592
GO:0009112	nucleobase metabolic process	0.0150556898479508
GO:0006541	glutamine metabolic process	0.0150556898479508
GO:0009167	purine ribonucleoside monophosphate metabolic process	0.0150556898479508
GO:0009168	purine ribonucleoside monophosphate biosynthetic process	0.0150556898479508
GO:0009127	purine nucleoside monophosphate biosynthetic process	0.0150556898479508
GO:0009126	purine nucleoside monophosphate metabolic process	0.0150556898479508
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0151320209506773
GO:0005634	nucleus	0.0169232163420361
GO:0000776	kinetochore	0.0173900211118302
GO:0009161	ribonucleoside monophosphate metabolic process	0.0174616809728728
GO:0009156	ribonucleoside monophosphate biosynthetic process	0.0174616809728728
GO:0005524	ATP binding	0.0174616809728728
GO:0032559	adenyl ribonucleotide binding	0.0175052163371643
GO:0046148	pigment biosynthetic process	0.0175379048208526
GO:0043232	intracellular non-membrane-bound organelle	0.0175379048208526
GO:0043228	non-membrane-bound organelle	0.0175379048208526
GO:0009124	nucleoside monophosphate biosynthetic process	0.0175379048208526
GO:0009123	nucleoside monophosphate metabolic process	0.0175379048208526
GO:0030554	adenyl nucleotide binding	0.0175379048208526
GO:0042440	pigment metabolic process	0.01883633608628
GO:0000793	condensed chromosome	0.0228912471177436
GO:0019748	secondary metabolic process	0.0229207899784339
GO:0044424	intracellular part	0.0233753563053392
GO:0007059	chromosome segregation	0.0246419545531916
GO:0003697	single-stranded DNA binding	0.0250261873742735
GO:0006338	chromatin remodeling	0.0250261873742735
GO:0032553	ribonucleotide binding	0.0250261873742735
GO:0032555	purine ribonucleotide binding	0.0250261873742735
GO:0044454	nuclear chromosome part	0.025724233707556
GO:0044428	nuclear part	0.025724233707556
GO:0017076	purine nucleotide binding	0.0264993261056813
GO:0000775	chromosome, pericentric region	0.0279241051497402
GO:0006950	response to stress	0.0291770609694501
GO:0009064	glutamine family amino acid metabolic process	0.0291770609694501
GO:0008094	DNA-dependent ATPase activity	0.0291770609694501
GO:0000228	nuclear chromosome	0.0342790856501484
GO:0000166	nucleotide binding	0.0374130305697161
GO:0005622	intracellular	0.0374130305697161
GO:0003682	chromatin binding	0.0391576713235763
GO:0043231	intracellular membrane-bound organelle	0.0398889373448718
GO:0043227	membrane-bound organelle	0.0398889373448718
GO:0048015	phosphoinositide-mediated signaling	0.0408986044603046
GO:0046483	heterocycle metabolic process	0.0408986044603046
GO:0009152	purine ribonucleotide biosynthetic process	0.0456158013559859
GO:0009150	purine ribonucleotide metabolic process	0.0469285643966661
GO:0009260	ribonucleotide biosynthetic process	0.0469285643966661
GO:0043566	structure-specific DNA binding	0.0469285643966661
GO:0006164	purine nucleotide biosynthetic process	0.0469285643966661
GO:0001558	regulation of cell growth	0.0472364507656931
GO:0006261	DNA-dependent DNA replication	0.0475367888405612
GO:0006163	purine nucleotide metabolic process	0.047558702635796
GO:0009259	ribonucleotide metabolic process	0.047558702635796

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	1.11e-14	254
animal cell	2.99e-10	679
eukaryotic cell	2.99e-10	679
native cell	6.33e-08	722

Disease

Ontology term	p-value	n
cancer	2.85e-66	235
disease of cellular proliferation	1.18e-64	239
cell type cancer	2.04e-37	143
carcinoma	2.95e-33	106
organ system cancer	4.71e-30	137
hematologic cancer	6.00e-19	51
immune system cancer	6.00e-19	51
leukemia	1.19e-14	39
myeloid leukemia	6.74e-11	31
disease of anatomical entity	6.63e-09	39

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	5	4.90738921487932	0.000351281809925646	0.00353070165978486
E2F4#1874	5	12.6680603152844	3.06319883889696e-06	0.000103499651742336
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.00322967964534967
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00573496488639466
ELK4#2005	3	9.74140899508082	0.0021255865657434	0.0122872715636063
ETS1#2113	3	5.8372565533214	0.00925327904563143	0.0349765910331777
GABPB1#2553	5	7.06768383618217	5.6685482528729e-05	0.00094889807818848
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00674583433319369
HMGN3#9324	4	6.54283817868047	0.0010080127776835	0.00722106087444182
IRF1#3659	4	6.10973100285112	0.00131552526476799	0.00881114237972837
IRF3#3661	2	18.7927808845958	0.00433962977712151	0.0205899779344354
MAX#4149	5	6.45255550900712	8.93743970843928e-05	0.0013073070948315
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329544972337304
MYC#4609	5	5.2222818716094	0.000257394484885061	0.00276649404208201
NANOG#79923	2	11.6979113924051	0.0109116495195608	0.0402302313754867
NFKB1#4790	4	4.39045073935507	0.00470773269252496	0.0222073574830449
PAX5#5079	4	5.33565242494226	0.00222338958618779	0.012780482414655
POU2F2#5452	3	5.46367443464551	0.0111565009446978	0.0410200247197074
REST#5978	3	5.79001722967681	0.00946878869443394	0.0357046186394911
RFX5#5993	3	7.22874649631706	0.0050291827895866	0.0234682463411659
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00248280920635418
SP2#6668	2	10.4614121975379	0.0135319118334714	0.0477839917492534
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135461834519773
TAF7#6879	3	6.85984164295435	0.00584328640701904	0.0262503006307064
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00919507977513232
THAP1#55145	3	18.8214867617108	0.000308522194815001	0.00317518225308276
TRIM28#10155	3	11.1543150271575	0.00143315927152925	0.00920244212476135
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00352765312185522
ZBTB7A#51341	4	5.88152744630072	0.00152494756104223	0.00971536621287683
ZNF143#7702	4	10.8007012417823	0.000141522343086319	0.00184432892308361

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.