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Coexpression cluster:C4352: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;2.74347,MA0031.1;2.60497,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;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,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;0.0834661,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;0.257905,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;1.00436,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;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.757898,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;1.39232,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;0.8915,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;2.26143,MA0099.2;0.902716,MA0079.2;0.311277,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
}}

Revision as of 22:00, 22 January 2013


Full id: C4352_acute_hepatoblastoma_neuroepithelioma_giant_osteosarcoma_Myoblast_small



Phase1 CAGE Peaks

Hg19::chr3:99536663..99536692,+p3@C3orf26
Hg19::chr3:99536693..99536718,+p1@C3orf26
Hg19::chrX:153991088..153991168,+p1@DKC1


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

No results for this coexpression

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:0003720telomerase activity0.00448899093371011
GO:0005697telomerase holoenzyme complex0.00448899093371011
GO:0031119tRNA pseudouridine synthesis0.00598532124494681
GO:0007004telomere maintenance via telomerase0.00650903685387967
GO:0001522pseudouridine synthesis0.00650903685387967
GO:0006400tRNA modification0.00650903685387967
GO:0032200telomere organization and biogenesis0.00650903685387967
GO:0000723telomere maintenance0.00650903685387967
GO:0016439tRNA-pseudouridine synthase activity0.0065838533694415
GO:0009982pseudouridine synthase activity0.00664370658189096
GO:0009451RNA modification0.00734562152788927
GO:0003964RNA-directed DNA polymerase activity0.00748165155618352
GO:0006278RNA-dependent DNA replication0.00830463322736371
GO:0016866intramolecular transferase activity0.00830463322736371
GO:0006364rRNA processing0.00830463322736371
GO:0016072rRNA metabolic process0.00830463322736371
GO:0008033tRNA processing0.0097173450800313
GO:0042254ribosome biogenesis and assembly0.0110728443031516
GO:0005730nucleolus0.0155933369276246
GO:0006399tRNA metabolic process0.0195720004709761
GO:0016779nucleotidyltransferase activity0.0195805509298974
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0200780321762307
GO:0016853isomerase activity0.0245137939684343
GO:0006260DNA replication0.0265598630244515
GO:0005654nucleoplasm0.0356459131921277
GO:0006396RNA processing0.0356459131921277
GO:0051276chromosome organization and biogenesis0.0356459131921277
GO:0031981nuclear lumen0.0442486249179997
GO:0008283cell proliferation0.0461282516636419



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>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell5.92e-08253
Uber Anatomy
Ontology termp-valuen
organ system subdivision3.67e-07223
nervous system5.93e-0789
Disease
Ontology termp-valuen
cancer3.10e-63235
disease of cellular proliferation2.63e-61239
cell type cancer4.66e-40143
carcinoma3.21e-30106
organ system cancer3.09e-28137
hematologic cancer1.20e-1751
immune system cancer1.20e-1751
leukemia1.76e-1339
myeloid leukemia6.25e-1131
germ cell and embryonal cancer3.73e-0822
germ cell cancer3.73e-0822


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)
MA0003.11.0927
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.12.74347
MA0031.12.60497
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
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
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0113.11.00436
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
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
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BRCA1#672213.45615376214920.007119807716084560.0296390943104335
CEBPB#105137.971147625824820.001974187055288560.0115553506622923
CTCF#1066435.360256373075030.0064925092527670.028058891576998
E2F1#186934.907389214879320.008460985347239390.0326772002322437
E2F4#1874312.66806031528440.0004917987006298980.00438250550299368
E2F6#187635.017155731697390.00791769806886330.0323570382146664
ELF1#199734.258097958807540.01295179875054610.0463990981960101
FOSL2#2355211.28680040304110.0100534586973120.0376901849697955
GATA3#2625218.15767757147070.003944546819279620.018955713673158
IRF1#365937.63716375356390.002244692747297240.0128498939835001
MAFF#23764237.54357099329680.0009344774015560320.00677137898710264
MAFK#7975218.06715542521990.003983674744936810.0191164770578228
MAX#414936.452555509007120.003721913834265510.0187142149601298
MXI1#460139.96157162875930.001011470541259020.00721958528284247
MYC#460935.22228187160940.007020843755740150.0295498469011746
NFKB1#479035.488063424193840.006049381815655430.0270366050772526
NR3C1#290829.982015554115360.01278474365547170.0460629193305209
NRF1#4899312.21027944771090.0005492172401020010.00472563019764483
SETDB1#9869226.8800174520070.001814468907964410.0108977697555291
SIN3A#2594235.408884726815140.006318961977991520.0277673273875313
SMARCB1#6598212.16847718743830.008675002221921740.0330045738608898
SP1#666735.69838137814090.005403962701712170.0247395985010352
TRIM28#10155212.39368336350830.008368344129438470.0329332087020282



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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