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{{Coexpression_clusters
{
|full_id=C1011_acute_granulocyte_Hodgkin_neuroepithelioma_retinoblastoma_hepatoblastoma_merkel
|gostat_on_coexpression_clusters

Latest revision as of 11:35, 17 September 2013


Full id: C1011_acute_granulocyte_Hodgkin_neuroepithelioma_retinoblastoma_hepatoblastoma_merkel



Phase1 CAGE Peaks

Hg19::chr12:133263893..133263986,-p1@POLE
Hg19::chr19:10305581..10305646,-p1@DNMT1
Hg19::chr19:4402613..4402658,+p1@CHAF1A
Hg19::chr19:48673580..48673630,-p1@LIG1
Hg19::chr19:50887585..50887619,+p1@POLD1
Hg19::chr8:145669791..145669834,-p1@TONSL
Hg19::chr8:145743164..145743236,-p1@RECQL4
Hg19::chr8:145743237..145743261,-p2@RECQL4


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

p.valueFDRnGenesnPathwayName
0.0004788267146628310.02331517772165942163Purine metabolism (KEGG):00230
0.0001805809699843390.00952564616667392100Pyrimidine metabolism (KEGG):00240
3.67416886898525e-087.75249631355887e-06336DNA replication (KEGG):03030
3.07978931231787e-087.75249631355887e-06334Base excision repair (KEGG):03410
8.89191667316632e-081.40714581352857e-05348Nucleotide excision repair (KEGG):03420
9.29638856460575e-060.000653845995710604223Mismatch repair (KEGG):03430
3.15809823992966e-050.00181734198715952242DNA Replication (Wikipathways):WP1806
1.32453795997426e-060.00011977607552338629Mismatch repair (Wikipathways):WP531
1.01567335750795e-060.0001071535392170893107DNA Repair (Reactome):REACT_216
6.67157721853038e-060.0005278885474162163200DNA Replication (Reactome):REACT_383
2.59719623007301e-050.001644025213636213315Cell Cycle, Mitotic (Reactome):REACT_152
3.75206069989847e-074.75010884607146e-05377Chromosome Maintenance (Reactome):REACT_22172
3.07978931231787e-087.75249631355887e-06334{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

GO IDGO nameFDR corrected p-value
GO:0006281DNA repair1.36711281599438e-07
GO:0006974response to DNA damage stimulus1.36711281599438e-07
GO:0006259DNA metabolic process1.36711281599438e-07
GO:0009719response to endogenous stimulus2.2353665367932e-07
GO:0006260DNA replication5.81249790921492e-06
GO:0006950response to stress9.73788887599282e-06
GO:0000731DNA synthesis during DNA repair1.30963982036091e-05
GO:0003682chromatin binding1.70270067455608e-05
GO:0007049cell cycle9.94130900183607e-05
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00043621865655787
GO:0003887DNA-directed DNA polymerase activity0.000449255144653721
GO:0005634nucleus0.000449255144653721
GO:0051329interphase of mitotic cell cycle0.00119150193290442
GO:0051325interphase0.00124071983685884
GO:0043283biopolymer metabolic process0.00182299496202717
GO:0043231intracellular membrane-bound organelle0.00296693105816845
GO:0043227membrane-bound organelle0.00296693105816845
GO:0006335DNA replication-dependent nucleosome assembly0.00296693105816845
GO:0045875negative regulation of sister chromatid cohesion0.00296693105816845
GO:0007063regulation of sister chromatid cohesion0.00296693105816845
GO:0006310DNA recombination0.0039538293047545
GO:0016779nucleotidyltransferase activity0.00494415731932331
GO:0003891delta DNA polymerase activity0.00494415731932331
GO:0003910DNA ligase (ATP) activity0.00494415731932331
GO:0003886DNA (cytosine-5-)-methyltransferase activity0.00549310385928867
GO:0003893epsilon DNA polymerase activity0.00549310385928867
GO:0003909DNA ligase activity0.00549310385928867
GO:0043229intracellular organelle0.00574075701982397
GO:0043226organelle0.00574075701982397
GO:0009008DNA-methyltransferase activity0.00574075701982397
GO:0005678chromatin assembly complex0.00574075701982397
GO:0003676nucleic acid binding0.00618596197214122
GO:0043170macromolecule metabolic process0.00633756424988399
GO:0000278mitotic cell cycle0.00663322789314192
GO:0003677DNA binding0.00686763962456978
GO:0007062sister chromatid cohesion0.00741350756267838
GO:0022403cell cycle phase0.00778579769906605
GO:0016886ligase activity, forming phosphoric ester bonds0.0109211497937796
GO:0048705skeletal morphogenesis0.0112381757070516
GO:0044237cellular metabolic process0.0112381757070516
GO:0008270zinc ion binding0.0112381757070516
GO:0044238primary metabolic process0.0112443768708326
GO:0000084S phase of mitotic cell cycle0.0114891233863831
GO:0000166nucleotide binding0.0114891233863831
GO:0044424intracellular part0.0114891233863831
GO:0000792heterochromatin0.0127739844957742
GO:0051276chromosome organization and biogenesis0.0127739844957742
GO:0051320S phase0.0129621865307859
GO:0006305DNA alkylation0.0136268075946318
GO:0006306DNA methylation0.0136268075946318
GO:0022402cell cycle process0.0158980673489082
GO:0006304DNA modification0.0159452447403155
GO:0046914transition metal ion binding0.0161135256749198
GO:0005657replication fork0.0175430415041266
GO:0009411response to UV0.0177610225540556
GO:0000082G1/S transition of mitotic cell cycle0.0179711408745799
GO:0016458gene silencing0.0197272102767894
GO:0005622intracellular0.0205585703501337
GO:0016585chromatin remodeling complex0.0205585703501337
GO:0043414biopolymer methylation0.0221816836641472
GO:0003678DNA helicase activity0.023750440581921
GO:0007059chromosome segregation0.0281155259347484
GO:0040029regulation of gene expression, epigenetic0.0304696161599306
GO:0032259methylation0.0326956260140766
GO:0004527exonuclease activity0.0326956260140766
GO:0009653anatomical structure morphogenesis0.0333618840509839
GO:0016740transferase activity0.0350776076463905
GO:0009416response to light stimulus0.0350776076463905
GO:0043169cation binding0.0350776076463905
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0362262712413766
GO:0046872metal ion binding0.0411364456418694
GO:0009314response to radiation0.0413173911846125
GO:0043167ion binding0.0425175439882766



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>

Cell Type
Ontology termp-valuen
epithelial cell2.02e-14253
migratory neural crest cell9.42e-0741
Disease
Ontology termp-valuen
cancer1.26e-44235
disease of cellular proliferation1.23e-42239
hematologic cancer4.11e-2551
immune system cancer4.11e-2551
organ system cancer1.31e-22137
leukemia5.06e-2239
cell type cancer1.20e-21143
myeloid leukemia1.64e-1831
carcinoma1.05e-17106


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

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.15.21858
MA0004.10.455723
MA0006.11.47431
MA0007.10.437331
MA0009.10.918715
MA0014.14.92777
MA0017.10.337901
MA0019.10.602411
MA0024.13.16573
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.11.08711
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.524515
MA0056.10
MA0057.10.632427
MA0058.10.950944
MA0059.10.361075
MA0060.12.3723
MA0061.10.961853
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.326687
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.11.6523
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.291333
MA0105.10.988431
MA0106.11.45807
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.11.60834
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.830366
MA0146.14.05934
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.27.27445
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.20.55506
MA0047.20.586412
MA0112.20.79629
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.577214
MA0155.10.764865
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.17.09066
MA0163.10.493198
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.25.96581
MA0102.21.46209
MA0258.10.603127
MA0259.11.99938
MA0442.10



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

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

TF#promotersEnrichmentp-valueq-value
ATF3#46738.423690447253280.004171166389609930.0198701170664327
BRCA1#672512.61514415201491.47177326411908e-050.000349342108934846
CCNT2#90586.336201576962633.84606837428661e-071.87437953776071e-05
CHD2#110667.758017125587641.92157406469162e-050.000434200073003738
E2F1#186984.907389214879322.97124777369457e-060.000101443003019577
E2F4#1874812.66806031528441.5050509647149e-091.3332147387944e-07
E2F6#187685.017155731697392.48928731545241e-068.77713294863383e-05
EGR1#195874.364656707958878.58120841941444e-050.00128581467161438
ELF1#199784.258097958807549.24826870984006e-060.000246397942802803
HEY1#2346284.040111043105711.4081650274634e-050.000338864855537443
HMGN3#932455.111592327094120.001109515975889930.00770764527111667
IRF1#365987.63716375356398.63190100943299e-085.12802678910223e-06
IRF3#3661211.74548805287240.01164488049453140.0425297130356821
MAX#414964.839416631755340.0002917504313705360.0030965572461288
MXI1#460156.225982267974560.0004393954903539430.00409403386716705
MYC#460974.569496637658236.28392411465611e-050.00102641030749229
NFYA#480036.909592762436450.007279727237130680.030121129627142
NFYB#480148.379896626768230.0007296914029278550.00581609100437932
NRF1#489957.631424654819320.0001668882994718450.00204525312233513
PAX5#507965.002174148383370.0002416084515475770.00262874727275523
PBX3#509038.217942257529050.004473206582808440.0211660575526428
POLR2A#543082.147453176558070.002210725788971910.0127139862706188
RFX5#599346.023955413597550.00252649680619860.0139907104953645
SIN3A#2594285.408884726815141.36410592556506e-065.34781752102437e-05
SP1#666785.69838137814098.98832477855329e-073.86150411989851e-05
SP2#666839.807573935191740.002707184665085610.0148855248624237
SRF#672246.89858913108390.001522071904568780.00970000412748713
TAF1#687283.343046285745296.40776711117462e-050.00104304985867202
TBP#690883.706770687096392.80450451364125e-050.000591836021216767
TFAP2A#702036.194487889891860.009861483862380290.0370462757851565
YY1#752863.683378062390390.001360631154992740.0089564450520791
ZNF143#770258.438047845142440.0001031017321729180.00144167114826715



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

This analysis result is provided for C0 - C305 clusters.

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