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Coexpression cluster:C4236

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Full id: C4236_retinoblastoma_iPS_small_testicular_HES3GFP_teratocarcinoma_rhabdomyosarcoma



Phase1 CAGE Peaks

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


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


p.valueFDRnGenesnPathwayName
6.20976561239697e-070.000131026054421576223Mismatch repair (KEGG):03430
0.0001308247892910560.0118302988030342327Pathways in cancer (KEGG):05200
4.64137026602477e-060.000587597475678735262Colorectal cancer (KEGG):05210
1.81874953311705e-060.000287817113615774239Integrated Cancer pathway (Wikipathways):WP1971
2.89159085690311e-050.003050628354032782154Integrated Breast Cancer Pathway (Wikipathways):WP1984
8.83603012040672e-085.59320706621745e-0529Mismatch repair (Wikipathways):WP531
2.94534337346891e-079.32201177702911e-05216{MLH1,20} (Static Module):NA



Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0032357oxidized purine DNA binding3.29271505890964e-08
GO:0032356oxidized DNA binding3.29271505890964e-08
GO:0000400four-way junction DNA binding3.29271505890964e-08
GO:0032301MutSalpha complex3.29271505890964e-08
GO:0032143single thymine insertion binding3.29271505890964e-08
GO:0032139dinucleotide insertion or deletion binding4.93907258836446e-08
GO:0032134mispaired DNA binding4.93907258836446e-08
GO:0032137guanine/thymine mispair binding4.93907258836446e-08
GO:0032142single guanine insertion binding4.93907258836446e-08
GO:0032300mismatch repair complex4.93907258836446e-08
GO:0032135DNA insertion or deletion binding7.59857321286842e-08
GO:0032138single base insertion or deletion binding7.59857321286842e-08
GO:0000217DNA secondary structure binding7.59857321286842e-08
GO:0032405MutLalpha complex binding1.1759696638963e-07
GO:0032404mismatch repair complex binding3.073200721649e-07
GO:0043531ADP binding3.70430444127335e-07
GO:0006284base-excision repair5.76225135309188e-06
GO:0003684damaged DNA binding1.07562025257715e-05
GO:0030983mismatched DNA binding2.09260707033337e-05
GO:0006298mismatch repair2.29392482437372e-05
GO:0045005maintenance of fidelity during DNA-dependent DNA replication2.29392482437372e-05
GO:0032403protein complex binding3.77913887443039e-05
GO:0003690double-stranded DNA binding4.13593643703911e-05
GO:0043566structure-specific DNA binding8.61662371978417e-05
GO:0006261DNA-dependent DNA replication8.91008694940949e-05
GO:0006260DNA replication0.000372850589695633
GO:0032302MutSbeta complex0.000372850589695633
GO:0000701purine-specific mismatch base pair DNA N-glycosylase activity0.000372850589695633
GO:0043570maintenance of DNA repeat elements0.000372850589695633
GO:0032181dinucleotide repeat insertion binding0.000372850589695633
GO:0006281DNA repair0.000407000824604192
GO:0000287magnesium ion binding0.000493471458313944
GO:0006974response to DNA damage stimulus0.000493471458313944
GO:0000700mismatch base pair DNA N-glycosylase activity0.000493471458313944
GO:0009719response to endogenous stimulus0.000656924877524407
GO:0016887ATPase activity0.000903237472812511
GO:0006301postreplication repair0.00105801164303689
GO:0017111nucleoside-triphosphatase activity0.00216842616708457
GO:0016462pyrophosphatase activity0.00224103793111858
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.00224103793111858
GO:0016817hydrolase activity, acting on acid anhydrides0.00224103793111858
GO:0019104DNA N-glycosylase activity0.00234808105336975
GO:0044428nuclear part0.00234808105336975
GO:0006950response to stress0.00279144035012888
GO:0006259DNA metabolic process0.00285140343528084
GO:0016799hydrolase activity, hydrolyzing N-glycosyl compounds0.00291701627068806
GO:0003697single-stranded DNA binding0.00725238356455489
GO:0008022protein C-terminus binding0.00861303260242305
GO:0005524ATP binding0.0130414729973987
GO:0032559adenyl ribonucleotide binding0.0130414729973987
GO:0043234protein complex0.0134110444302739
GO:0030554adenyl nucleotide binding0.0136319828171337
GO:0042803protein homodimerization activity0.0166344703124406
GO:0003677DNA binding0.0181049202533107
GO:0032553ribonucleotide binding0.0181049202533107
GO:0032555purine ribonucleotide binding0.0181049202533107
GO:0017076purine nucleotide binding0.0191399749681331
GO:0016798hydrolase activity, acting on glycosyl bonds0.020879621687379
GO:0032991macromolecular complex0.020879621687379
GO:0045786negative regulation of progression through cell cycle0.020879621687379
GO:0016787hydrolase activity0.020879621687379
GO:0044446intracellular organelle part0.0222817113393344
GO:0044422organelle part0.0222817113393344
GO:0000166nucleotide binding0.0233801187807446
GO:0000074regulation of progression through cell cycle0.029940926774321
GO:0051726regulation of cell cycle0.029940926774321
GO:0042802identical protein binding0.029940926774321
GO:0046983protein dimerization activity0.029940926774321
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0407929887479537
GO:0051276chromosome organization and biogenesis0.0424879627039622
GO:0005634nucleus0.0425424652209084
GO:0003676nucleic acid binding0.0464864505909484
GO:0022402cell cycle process0.047444133633493



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data

disease_data


Cell Type
Ontology termp-valuen
neural cell3.80e-0725
Disease
Ontology termp-valuen
cancer7.96e-54235
disease of cellular proliferation4.16e-52239
cell type cancer5.96e-34143
carcinoma7.60e-28106
organ system cancer3.31e-24137
hematologic cancer2.78e-1251
immune system cancer2.78e-1251
leukemia2.51e-1039
myeloid leukemia9.06e-1031
germ cell and embryonal cancer1.27e-0722
germ cell cancer1.27e-0722
disease of anatomical entity2.31e-0739


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.13.8806
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.12.72668
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.13.15662
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.13.52399
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0326373720657557
E2F4#1874312.66806031528440.0004917987006298980.00437914268011646
E2F6#187635.017155731697390.00791769806886330.032320362267501
EGR1#195834.988179094810140.008056488137383440.0321517602055861
ELF1#199734.258097958807540.01295179875054610.046360931888415
GABPB1#255337.067683836182170.002832212825417420.0154485546181527
IRF1#365937.63716375356390.002244692747297240.0128414475150623
MYC#460935.22228187160940.007020843755740150.0295284270701412
NRF1#4899312.21027944771090.0005492172401020010.0047221288663055
SIN3A#2594235.408884726815140.006318961977991520.0277556491575664
SMARCB1#6598212.16847718743830.008675002221921740.0329997653270911
SP1#666735.69838137814090.005403962701712170.0247157635473666
TFAP2A#7020211.01242291536330.01054990655215560.0390260223993406
ZBTB7A#5134137.35190930787590.002516255860282270.0140547248792395
ZNF263#1012738.221841637010680.001799043925565870.0109684967041549



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.