Coexpression cluster:C4236

Full id: C4236_retinoblastoma_iPS_small_testicular_HES3GFP_teratocarcinoma_rhabdomyosarcoma

Phase1 CAGE Peaks

Hg19::chr2:47630255..47630333,+	p1@MSH2
Hg19::chr2:48010276..48010307,+	p1@MSH6
Hg19::chr2:48010312..48010328,+	p2@MSH6

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
6.20976561239697e-07	0.000131026054421576	2	23	Mismatch repair (KEGG):03430
0.000130824789291056	0.011830298803034	2	327	Pathways in cancer (KEGG):05200
4.64137026602477e-06	0.000587597475678735	2	62	Colorectal cancer (KEGG):05210
1.81874953311705e-06	0.000287817113615774	2	39	Integrated Cancer pathway (Wikipathways):WP1971
2.89159085690311e-05	0.00305062835403278	2	154	Integrated Breast Cancer Pathway (Wikipathways):WP1984
8.83603012040672e-08	5.59320706621745e-05	2	9	Mismatch repair (Wikipathways):WP531
2.94534337346891e-07	9.32201177702911e-05	2	16	{MLH1,20} (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:0032357	oxidized purine DNA binding	3.29271505890964e-08
GO:0032356	oxidized DNA binding	3.29271505890964e-08
GO:0000400	four-way junction DNA binding	3.29271505890964e-08
GO:0032301	MutSalpha complex	3.29271505890964e-08
GO:0032143	single thymine insertion binding	3.29271505890964e-08
GO:0032139	dinucleotide insertion or deletion binding	4.93907258836446e-08
GO:0032134	mispaired DNA binding	4.93907258836446e-08
GO:0032137	guanine/thymine mispair binding	4.93907258836446e-08
GO:0032142	single guanine insertion binding	4.93907258836446e-08
GO:0032300	mismatch repair complex	4.93907258836446e-08
GO:0032135	DNA insertion or deletion binding	7.59857321286842e-08
GO:0032138	single base insertion or deletion binding	7.59857321286842e-08
GO:0000217	DNA secondary structure binding	7.59857321286842e-08
GO:0032405	MutLalpha complex binding	1.1759696638963e-07
GO:0032404	mismatch repair complex binding	3.073200721649e-07
GO:0043531	ADP binding	3.70430444127335e-07
GO:0006284	base-excision repair	5.76225135309188e-06
GO:0003684	damaged DNA binding	1.07562025257715e-05
GO:0030983	mismatched DNA binding	2.09260707033337e-05
GO:0006298	mismatch repair	2.29392482437372e-05
GO:0045005	maintenance of fidelity during DNA-dependent DNA replication	2.29392482437372e-05
GO:0032403	protein complex binding	3.77913887443039e-05
GO:0003690	double-stranded DNA binding	4.13593643703911e-05
GO:0043566	structure-specific DNA binding	8.61662371978417e-05
GO:0006261	DNA-dependent DNA replication	8.91008694940949e-05
GO:0006260	DNA replication	0.000372850589695633
GO:0032302	MutSbeta complex	0.000372850589695633
GO:0000701	purine-specific mismatch base pair DNA N-glycosylase activity	0.000372850589695633
GO:0043570	maintenance of DNA repeat elements	0.000372850589695633
GO:0032181	dinucleotide repeat insertion binding	0.000372850589695633
GO:0006281	DNA repair	0.000407000824604192
GO:0000287	magnesium ion binding	0.000493471458313944
GO:0006974	response to DNA damage stimulus	0.000493471458313944
GO:0000700	mismatch base pair DNA N-glycosylase activity	0.000493471458313944
GO:0009719	response to endogenous stimulus	0.000656924877524407
GO:0016887	ATPase activity	0.000903237472812511
GO:0006301	postreplication repair	0.00105801164303689
GO:0017111	nucleoside-triphosphatase activity	0.00216842616708457
GO:0016462	pyrophosphatase activity	0.00224103793111858
GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.00224103793111858
GO:0016817	hydrolase activity, acting on acid anhydrides	0.00224103793111858
GO:0019104	DNA N-glycosylase activity	0.00234808105336975
GO:0044428	nuclear part	0.00234808105336975
GO:0006950	response to stress	0.00279144035012888
GO:0006259	DNA metabolic process	0.00285140343528084
GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds	0.00291701627068806
GO:0003697	single-stranded DNA binding	0.00725238356455489
GO:0008022	protein C-terminus binding	0.00861303260242305
GO:0005524	ATP binding	0.0130414729973987
GO:0032559	adenyl ribonucleotide binding	0.0130414729973987
GO:0043234	protein complex	0.0134110444302739
GO:0030554	adenyl nucleotide binding	0.0136319828171337
GO:0042803	protein homodimerization activity	0.0166344703124406
GO:0003677	DNA binding	0.0181049202533107
GO:0032553	ribonucleotide binding	0.0181049202533107
GO:0032555	purine ribonucleotide binding	0.0181049202533107
GO:0017076	purine nucleotide binding	0.0191399749681331
GO:0016798	hydrolase activity, acting on glycosyl bonds	0.020879621687379
GO:0032991	macromolecular complex	0.020879621687379
GO:0045786	negative regulation of progression through cell cycle	0.020879621687379
GO:0016787	hydrolase activity	0.020879621687379
GO:0044446	intracellular organelle part	0.0222817113393344
GO:0044422	organelle part	0.0222817113393344
GO:0000166	nucleotide binding	0.0233801187807446
GO:0000074	regulation of progression through cell cycle	0.029940926774321
GO:0051726	regulation of cell cycle	0.029940926774321
GO:0042802	identical protein binding	0.029940926774321
GO:0046983	protein dimerization activity	0.029940926774321
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0407929887479537
GO:0051276	chromosome organization and biogenesis	0.0424879627039622
GO:0005634	nucleus	0.0425424652209084
GO:0003676	nucleic acid binding	0.0464864505909484
GO:0022402	cell cycle process	0.047444133633493

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
neural cell	3.80e-07	25

Disease

Ontology term	p-value	n
cancer	7.96e-54	235
disease of cellular proliferation	4.16e-52	239
cell type cancer	5.96e-34	143
carcinoma	7.60e-28	106
organ system cancer	3.31e-24	137
hematologic cancer	2.78e-12	51
immune system cancer	2.78e-12	51
leukemia	2.51e-10	39
myeloid leukemia	9.06e-10	31
germ cell and embryonal cancer	1.27e-07	22
germ cell cancer	1.27e-07	22
disease of anatomical entity	2.31e-07	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)
MA0003.1	3.8806
MA0004.1	0.826076
MA0006.1	0.639288
MA0007.1	0.804807
MA0009.1	1.3275
MA0014.1	2.44638
MA0017.1	0.686276
MA0019.1	0.990656
MA0024.1	2.72668
MA0025.1	1.46617
MA0027.1	2.95767
MA0028.1	0.658629
MA0029.1	1.23771
MA0030.1	1.22561
MA0031.1	1.15713
MA0038.1	0.94098
MA0040.1	1.24388
MA0041.1	0.847069
MA0042.1	0.810843
MA0043.1	1.32783
MA0046.1	1.31611
MA0048.1	0.341392
MA0050.1	0.81185
MA0051.1	0.936307
MA0052.1	1.24796
MA0055.1	2.37507
MA0056.1	0
MA0057.1	0.333427
MA0058.1	0.716037
MA0059.1	0.714521
MA0060.1	3.15662
MA0061.1	0.456531
MA0063.1	0
MA0066.1	0.941452
MA0067.1	1.65513
MA0068.1	0.405474
MA0069.1	1.31207
MA0070.1	1.30033
MA0071.1	0.897953
MA0072.1	1.29561
MA0073.1	0.211629
MA0074.1	0.935474
MA0076.1	0.734647
MA0077.1	1.28751
MA0078.1	1.04495
MA0081.1	0.714712
MA0083.1	1.33535
MA0084.1	1.84562
MA0087.1	1.29304
MA0088.1	0.715722
MA0089.1	0
MA0090.1	0.751469
MA0091.1	0.829044
MA0092.1	0.785956
MA0093.1	0.642957
MA0095.1	0
MA0098.1	0
MA0100.1	0.956299
MA0101.1	0.646932
MA0103.1	0.628063
MA0105.1	0.31555
MA0106.1	0.986396
MA0107.1	0.556367
MA0108.2	1.15387
MA0109.1	0
MA0111.1	0.767139
MA0113.1	2.29491
MA0114.1	0.549955
MA0115.1	1.57693
MA0116.1	0.560723
MA0117.1	1.36676
MA0119.1	0.695578
MA0122.1	1.39371
MA0124.1	1.53432
MA0125.1	1.44766
MA0130.1	0
MA0131.1	1.06461
MA0132.1	0
MA0133.1	0
MA0135.1	1.35921
MA0136.1	0.948776
MA0139.1	1.12079
MA0140.1	0.894983
MA0141.1	0.712476
MA0142.1	1.12317
MA0143.1	1.00455
MA0144.1	0.531867
MA0145.1	0.752137
MA0146.1	1.16674
MA0147.1	0.565108
MA0148.1	0.854239
MA0149.1	0.884158
MA0062.2	0.449458
MA0035.2	0.894194
MA0039.2	4.75888
MA0138.2	1.04628
MA0002.2	0.476938
MA0137.2	0.666381
MA0104.2	1.2307
MA0047.2	0.973066
MA0112.2	0.731309
MA0065.2	0.277623
MA0150.1	0.744617
MA0151.1	0
MA0152.1	0.902317
MA0153.1	1.43021
MA0154.1	0.312019
MA0155.1	0.256269
MA0156.1	0.669101
MA0157.1	1.09377
MA0158.1	0
MA0159.1	0.565904
MA0160.1	0.871361
MA0161.1	0
MA0162.1	3.52399
MA0163.1	0.387745
MA0164.1	1.01792
MA0080.2	0.643061
MA0018.2	0.987913
MA0099.2	0.902716
MA0079.2	2.28794
MA0102.2	1.88331
MA0258.1	0.519674
MA0259.1	1.40979
MA0442.1	0

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	0.0326373720657557
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437914268011646
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032320362267501
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321517602055861
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046360931888415
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154485546181527
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128414475150623
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295284270701412
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.0047221288663055
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277556491575664
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329997653270911
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247157635473666
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0390260223993406
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140547248792395
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109684967041549

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.