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Coexpression cluster:C1145

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Full id: C1145_Hodgkin_chronic_acute_Reticulocytes_lymphoma_diffuse_Hep2



Phase1 CAGE Peaks

  Short description
Hg19::chr11:61560348..61560419,+ p1@FEN1
Hg19::chr11:65029421..65029459,+ p1@POLA2
Hg19::chr15:48624350..48624425,+ p1@DUT
Hg19::chr20:5100567..5100581,- p2@PCNA
Hg19::chr20:5100591..5100611,- p1@PCNA
Hg19::chr6:31126291..31126399,+ p1@TCF19
Hg19::chrX:48555110..48555164,+ p1@SUV39H1


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
0.0001805809699843390.01270086155556522100Pyrimidine metabolism (KEGG):00240
3.67416886898525e-081.16287444703383e-05336DNA replication (KEGG):03030
2.05925492603147e-050.00260701673635584234Base excision repair (KEGG):03410
8.58329659590162e-050.00679153343150715269G1 to S cell cycle control (Wikipathways):WP45
3.15809823992966e-050.00285582312267925242DNA Replication (Wikipathways):WP1806
0.0002067483186744810.01308716857209462107DNA Repair (Reactome):REACT_216
6.67157721853038e-060.001055777094832433200DNA Replication (Reactome):REACT_383
2.59719623007301e-050.002740042022727023315Cell Cycle, Mitotic (Reactome):REACT_152
3.75206069989847e-077.91684807678577e-05377Chromosome Maintenance (Reactome):REACT_22172
3.07978931231787e-081.16287444703383e-05334{PCNA,34} (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:0006260DNA replication3.23493187209283e-05
GO:0006259DNA metabolic process3.62539169331596e-05
GO:0005657replication fork0.00080180884438166
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00100012752440769
GO:0003887DNA-directed DNA polymerase activity0.00100012752440769
GO:0005634nucleus0.00100012752440769
GO:0044427chromosomal part0.00131180468070354
GO:0005694chromosome0.00175265536069073
GO:0000228nuclear chromosome0.00235908563354695
GO:0043283biopolymer metabolic process0.00235908563354695
GO:00171085'-flap endonuclease activity0.00235908563354695
GO:0043626PCNA complex0.00235908563354695
GO:0004170dUTP diphosphatase activity0.00235908563354695
GO:0030337DNA polymerase processivity factor activity0.00235908563354695
GO:0048015phosphoinositide-mediated signaling0.00264897946591783
GO:0043231intracellular membrane-bound organelle0.00300225166600379
GO:0043227membrane-bound organelle0.00300225166600379
GO:0047429nucleoside-triphosphate diphosphatase activity0.00300225166600379
GO:0048256flap endonuclease activity0.00300225166600379
GO:0006287base-excision repair, gap-filling0.00300225166600379
GO:0046974histone lysine N-methyltransferase activity (H3-K9 specific)0.00300225166600379
GO:0008309double-stranded DNA specific exodeoxyribonuclease activity0.00300225166600379
GO:0044428nuclear part0.00507998581710691
GO:0016779nucleotidyltransferase activity0.00507998581710691
GO:0005652nuclear lamina0.00507998581710691
GO:00084095'-3' exonuclease activity0.00507998581710691
GO:0032405MutLalpha complex binding0.00608285954516829
GO:0019932second-messenger-mediated signaling0.00608285954516829
GO:0043229intracellular organelle0.0063152511564931
GO:0043226organelle0.0063152511564931
GO:0009650UV protection0.00639000930182787
GO:0005663DNA replication factor C complex0.00684683280567824
GO:0005658alpha DNA polymerase:primase complex0.00684683280567824
GO:0043170macromolecule metabolic process0.00684683280567824
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.00686030240274865
GO:0000307cyclin-dependent protein kinase holoenzyme complex0.00686030240274865
GO:0032404mismatch repair complex binding0.00686030240274865
GO:0004529exodeoxyribonuclease activity0.00686030240274865
GO:0003677DNA binding0.00686030240274865
GO:0046080dUTP metabolic process0.0074267459690403
GO:0006281DNA repair0.0088115876286842
GO:0009200deoxyribonucleoside triphosphate metabolic process0.0100477932531831
GO:0009211pyrimidine deoxyribonucleoside triphosphate metabolic process0.0100477932531831
GO:0000287magnesium ion binding0.0100477932531831
GO:0006974response to DNA damage stimulus0.0100477932531831
GO:0009120deoxyribonucleoside metabolic process0.0100477932531831
GO:0043601nuclear replisome0.0100477932531831
GO:0030894replisome0.0100477932531831
GO:0046125pyrimidine deoxyribonucleoside metabolic process0.0100477932531831
GO:0044237cellular metabolic process0.0100477932531831
GO:0044238primary metabolic process0.0101510033057196
GO:0016888endodeoxyribonuclease activity, producing 5'-phosphomonoesters0.0101510033057196
GO:0043596nuclear replication fork0.0105811634345431
GO:0044424intracellular part0.0106570737760598
GO:0006213pyrimidine nucleoside metabolic process0.0113942924920784
GO:0006886intracellular protein transport0.0114259662429928
GO:0009719response to endogenous stimulus0.0114259662429928
GO:0009219pyrimidine deoxyribonucleotide metabolic process0.0118930548377811
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0118930548377811
GO:0004523ribonuclease H activity0.0118930548377811
GO:0000060protein import into nucleus, translocation0.0118930548377811
GO:0018024histone-lysine N-methyltransferase activity0.0139067156443542
GO:0016278lysine N-methyltransferase activity0.0139067156443542
GO:0016279protein-lysine N-methyltransferase activity0.0139067156443542
GO:0006275regulation of DNA replication0.0141988607925667
GO:0000781chromosome, telomeric region0.0150233136872658
GO:0000794condensed nuclear chromosome0.0150233136872658
GO:0009262deoxyribonucleotide metabolic process0.0150233136872658
GO:0004520endodeoxyribonuclease activity0.0152820594469177
GO:0009411response to UV0.0155333432796311
GO:0005515protein binding0.0157953884552327
GO:0042054histone methyltransferase activity0.0157953884552327
GO:0006284base-excision repair0.0157953884552327
GO:0006302double-strand break repair0.0160259561931682
GO:0008283cell proliferation0.016940445835313
GO:0016891endoribonuclease activity, producing 5'-phosphomonoesters0.0173199076507755
GO:0005622intracellular0.0173199076507755
GO:0008276protein methyltransferase activity0.0198242929997908
GO:0051052regulation of DNA metabolic process0.0198242929997908
GO:0003684damaged DNA binding0.0198242929997908
GO:0008170N-methyltransferase activity0.0198242929997908
GO:0009147pyrimidine nucleoside triphosphate metabolic process0.0198242929997908
GO:0004536deoxyribonuclease activity0.0198242929997908
GO:0015031protein transport0.0198951299519024
GO:0000793condensed chromosome0.0198951299519024
GO:0009116nucleoside metabolic process0.0198951299519024
GO:0016893endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0207964623323496
GO:0046907intracellular transport0.0212665692053063
GO:0045184establishment of protein localization0.0213738883507893
GO:0043232intracellular non-membrane-bound organelle0.0213738883507893
GO:0043228non-membrane-bound organelle0.0213738883507893
GO:0008104protein localization0.0225955583078951
GO:0044454nuclear chromosome part0.0236785144343018
GO:0006220pyrimidine nucleotide metabolic process0.0241223676371893
GO:0033036macromolecule localization0.0241693364343283
GO:0004527exonuclease activity0.024387293458585
GO:0004521endoribonuclease activity0.024387293458585
GO:0003676nucleic acid binding0.0256838301287325
GO:0016740transferase activity0.0263206029691129
GO:0009416response to light stimulus0.0263206029691129
GO:0016043cellular component organization and biogenesis0.0263206029691129
GO:0051649establishment of cellular localization0.0263206029691129
GO:0051641cellular localization0.0271406759701018
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0271406759701018
GO:0006606protein import into nucleus0.029831475488504
GO:0051170nuclear import0.029831475488504
GO:0046872metal ion binding0.029831475488504
GO:0004540ribonuclease activity0.029831475488504
GO:0006950response to stress0.029831475488504
GO:0009314response to radiation0.029831475488504
GO:0032403protein complex binding0.029831475488504
GO:0046982protein heterodimerization activity0.0305734825634199
GO:0043167ion binding0.0305734825634199
GO:0003690double-stranded DNA binding0.0310435675766427
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0328864569882111
GO:0003682chromatin binding0.033308670484058
GO:0017038protein import0.034133394260944
GO:0031323regulation of cellular metabolic process0.0375000074527852
GO:0030145manganese ion binding0.0400260820590306
GO:0009141nucleoside triphosphate metabolic process0.0400260820590306
GO:0004519endonuclease activity0.0406235751363442
GO:0044446intracellular organelle part0.0406235751363442
GO:0006913nucleocytoplasmic transport0.0406235751363442
GO:0044422organelle part0.0406235751363442
GO:0051169nuclear transport0.0406235751363442
GO:0019222regulation of metabolic process0.0406235751363442
GO:0043566structure-specific DNA binding0.0408711770132874
GO:0006261DNA-dependent DNA replication0.0417374929281751
GO:0009628response to abiotic stimulus0.0417374929281751
GO:0005635nuclear envelope0.0485919622754928



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
uberon_data
disease_data


Cell Type
Ontology termp-valuen
animal cell6.15e-22679
eukaryotic cell6.15e-22679
epithelial cell1.36e-17253
native cell2.19e-16722
embryonic cell2.06e-09250
migratory neural crest cell8.97e-0841
Uber Anatomy
Ontology termp-valuen
larynx1.62e-079
Disease
Ontology termp-valuen
cancer1.75e-36235
disease of cellular proliferation9.23e-36239
hematologic cancer1.38e-1951
immune system cancer1.38e-1951
organ system cancer5.10e-19137
leukemia2.18e-1539
cell type cancer4.47e-15143
carcinoma6.17e-14106
myeloid leukemia2.58e-1131


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)
MA0003.11.35295
MA0004.10.502801
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.10.367415
MA0017.10.380797
MA0019.10.652951
MA0024.13.33297
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.649431
MA0056.10
MA0057.10.744639
MA0058.11.04727
MA0059.10.404929
MA0060.11.86058
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.12.88764
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.14.03024
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.104569
MA0106.15.14579
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.11.71579
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.547931
MA0147.11.40486
MA0148.10.528066
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.21.82845
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.21.19136
MA0047.20.636643
MA0112.20.944394
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.55314
MA0163.11.72058
MA0164.10.678332
MA0080.20.344472
MA0018.21.56673
MA0099.20.572
MA0079.21.1389
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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
BRCA1#67238.650384561381610.003659293331202230.0184731697707574
CCNT2#90565.431029923110839.35028339706757e-050.00135780623985865
E2F1#186974.907389214879321.45832274679793e-050.000346701045647232
E2F4#1874712.66806031528441.90745058834676e-081.36633903975547e-06
E2F6#187675.017155731697391.24910426162553e-050.000308040613884082
EGR1#195864.275582081265830.0003762130619866450.0037359813616833
ELF1#199753.041498542005380.009719562269370750.0365604669134094
GABPB1#255344.038676477818380.00980113494696150.0368434198152004
GATA1#262335.811560633057330.01119311600820290.0411256936774213
GTF2B#2959313.69021282899610.0009761963170245720.0070152733195988
HDAC2#306635.749551529982680.01153041704040530.0421691783199528
HEY1#2346274.040111043105715.68979821988558e-050.000949563496782727
HMGN3#932455.841819802393280.0004629187191299590.00426300750438354
HNF4A#317239.913838726980150.002478654821661540.0139213891325361
IRF1#365966.546140360197633.13027310449255e-050.000631734478763474
MAX#414954.608968220719370.001424337014033610.0091779573919457
MYC#460953.730201336863860.003821944222306690.0188692461299749
NFKB1#479053.92004530299560.003036581424484610.0161163495981171
NFYA#4800410.5289032570460.0002657287183237080.00284436216183353
NFYB#480149.577024716306540.0003830061716016480.00376017875126006
NRF1#489958.721628176936366.71450045004423e-050.00107324106596598
POLR2A#543072.147453176558070.004747636447610280.02232701742399
POU2F2#545245.203499461567160.003866714310179810.0190623448591394
PRDM1#639237.66598736498880.0011773281945870.00799837242662277
RFX5#599346.884520472682910.001352207031528580.00890267604903318
SIN3A#2594275.408884726815147.3795239773719e-060.000211443101419134
SMARCB1#6598410.43012330351850.0002755863833009370.00293633608300006
SP1#666754.070272412957780.002549206128991580.014108236919387
SP2#6668311.20865592593340.001741515330916110.0107165990835227
SREBF1#6720320.14536404592360.0003158010261394680.00323606194750587
SRF#672235.913076398071920.01066868130167450.0393900521959057
TAF1#687273.343046285745290.0002142336319622450.0024646779344024
TAF7#687946.533182517099380.00164849410947510.0103106405736897
TBP#690873.706770687096390.0001039672097505110.00145047173645921
YY1#752853.507979107038470.005072570672808980.0236126853493269



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.