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Coexpression cluster:C138: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 10:40, 17 September 2013


Full id: C138_diffuse_Burkitt_lymphangiectasia_lymphoma_acute_CD19_pineal



Phase1 CAGE Peaks

Hg19::chr10:560037..560049,-p@chr10:560037..560049
-
Hg19::chr11:111224906..111224920,-p@chr11:111224906..111224920
-
Hg19::chr11:111229505..111229516,-p@chr11:111229505..111229516
-
Hg19::chr11:2407318..2407325,+p24@CD81
Hg19::chr11:2407761..2407778,+p26@CD81
Hg19::chr11:26122006..26122011,-p@chr11:26122006..26122011
-
Hg19::chr11:26124040..26124064,-p@chr11:26124040..26124064
-
Hg19::chr12:113494494..113494505,+p4@DTX1
Hg19::chr12:113494516..113494577,+p1@DTX1
Hg19::chr12:113495162..113495172,+p11@DTX1
Hg19::chr12:113495245..113495253,+p5@DTX1
Hg19::chr12:113495715..113495725,+p8@DTX1
Hg19::chr12:113496099..113496108,+p3@AB384763
Hg19::chr12:113496125..113496146,+p1@AB384763
Hg19::chr12:113533128..113533138,+p@chr12:113533128..113533138
+
Hg19::chr12:117256221..117256231,+p@chr12:117256221..117256231
+
Hg19::chr12:117256250..117256271,+p@chr12:117256250..117256271
+
Hg19::chr12:117256273..117256285,+p@chr12:117256273..117256285
+
Hg19::chr12:11905315..11905321,+p30@ETV6
Hg19::chr12:11905335..11905342,+p28@ETV6
Hg19::chr12:122435304..122435308,-p@chr12:122435304..122435308
-
Hg19::chr12:122458855..122458857,+p16@BCL7A
Hg19::chr12:122459183..122459198,+p10@BCL7A
Hg19::chr12:122459199..122459208,+p13@BCL7A
Hg19::chr12:122462311..122462330,-p@chr12:122462311..122462330
-
Hg19::chr12:122462770..122462775,+p@chr12:122462770..122462775
+
Hg19::chr12:2296602..2296621,+p@chr12:2296602..2296621
+
Hg19::chr12:4313305..4313315,+p@chr12:4313305..4313315
+
Hg19::chr12:4313331..4313334,+p@chr12:4313331..4313334
+
Hg19::chr12:8808206..8808209,-p@chr12:8808206..8808209
-
Hg19::chr12:94551874..94551884,+p16@PLXNC1
Hg19::chr13:103821459..103821470,+p@chr13:103821459..103821470
+
Hg19::chr13:61236926..61236943,+p@chr13:61236926..61236943
+
Hg19::chr14:106332392..106332397,-p@chr14:106332392..106332397
-
Hg19::chr14:106332402..106332439,-p@chr14:106332402..106332439
-
Hg19::chr14:106332443..106332451,-p@chr14:106332443..106332451
-
Hg19::chr14:106332453..106332464,-p@chr14:106332453..106332464
-
Hg19::chr14:106332480..106332490,-p@chr14:106332480..106332490
-
Hg19::chr14:106332501..106332515,-p@chr14:106332501..106332515
-
Hg19::chr14:106332518..106332527,-p@chr14:106332518..106332527
-
Hg19::chr14:106332629..106332637,-p@chr14:106332629..106332637
-
Hg19::chr14:33433362..33433367,-p@chr14:33433362..33433367
-
Hg19::chr14:33449602..33449615,-p@chr14:33449602..33449615
-
Hg19::chr14:53594794..53594799,+p@chr14:53594794..53594799
+
Hg19::chr14:75906948..75906962,+p@chr14:75906948..75906962
+
Hg19::chr14:91750002..91750014,-p21@CCDC88C
Hg19::chr14:96152757..96152769,+p1@TCL1B
Hg19::chr14:96181789..96181822,+p1@ENST00000556386
p1@uc001yfd.1
Hg19::chr14:96181832..96181839,+p2@uc001yfd.1
Hg19::chr14:96184093..96184099,+p@chr14:96184093..96184099
+
Hg19::chr15:66446160..66446166,-p@chr15:66446160..66446166
-
Hg19::chr15:66446174..66446184,-p@chr15:66446174..66446184
-
Hg19::chr15:66446191..66446202,-p@chr15:66446191..66446202
-
Hg19::chr15:66464730..66464736,-p@chr15:66464730..66464736
-
Hg19::chr15:67841330..67841348,+p4@MAP2K5
Hg19::chr15:84653070..84653073,+p@chr15:84653070..84653073
+
Hg19::chr16:86604624..86604648,+p@chr16:86604624..86604648
+
Hg19::chr16:87098907..87098937,-p@chr16:87098907..87098937
-
Hg19::chr17:3123719..3123724,-p@chr17:3123719..3123724
-
Hg19::chr17:74846230..74846245,+p1@uc002jtf.2
Hg19::chr17:74965032..74965049,-p@chr17:74965032..74965049
-
Hg19::chr17:74965255..74965298,-p1@AK123869
Hg19::chr18:3174522..3174533,-p@chr18:3174522..3174533
-
Hg19::chr18:71693057..71693059,-p@chr18:71693057..71693059
-
Hg19::chr18:71733441..71733451,-p@chr18:71733441..71733451
-
Hg19::chr19:29097532..29097550,+p@chr19:29097532..29097550
+
Hg19::chr19:29098223..29098234,+p@chr19:29098223..29098234
+
Hg19::chr1:160414041..160414045,-p@chr1:160414041..160414045
-
Hg19::chr1:167666666..167666680,+p4@RCSD1
Hg19::chr1:171125500..171125502,-p@chr1:171125500..171125502
-
Hg19::chr1:178636283..178636287,+p@chr1:178636283..178636287
+
Hg19::chr22:23234780..23234786,+p@chr22:23234780..23234786
+
Hg19::chr22:23235755..23235760,+p@chr22:23235755..23235760
+
Hg19::chr22:23235843..23235863,+p1@IGLJ1
Hg19::chr22:23235880..23235915,+p2@AK097035
Hg19::chr22:23235933..23235972,+p1@AK097035
Hg19::chr2:198220285..198220289,-p@chr2:198220285..198220289
-
Hg19::chr2:198220897..198220904,-p@chr2:198220897..198220904
-
Hg19::chr2:89162159..89162169,-p@chr2:89162159..89162169
-
Hg19::chr2:98534317..98534328,-p@chr2:98534317..98534328
-
Hg19::chr3:153480361..153480373,-p1@ENST00000493214
Hg19::chr3:19436672..19436686,+p@chr3:19436672..19436686
+
Hg19::chr3:62809350..62809370,+p@chr3:62809350..62809370
+
Hg19::chr3:77626663..77626683,+p@chr3:77626663..77626683
+
Hg19::chr4:176346295..176346296,-p@chr4:176346295..176346296
-
Hg19::chr4:176353908..176353917,-p@chr4:176353908..176353917
-
Hg19::chr4:176358284..176358287,-p@chr4:176358284..176358287
-
Hg19::chr4:71532616..71532662,-p5@IGJ
Hg19::chr4:8046897..8046900,+p@chr4:8046897..8046900
+
Hg19::chr4:8046990..8046993,-p@chr4:8046990..8046993
-
Hg19::chr4:86525299..86525314,+p27@ARHGAP24
Hg19::chr4:86525321..86525343,+p19@ARHGAP24
Hg19::chr4:86525345..86525360,+p17@ARHGAP24
Hg19::chr5:118755330..118755335,+p@chr5:118755330..118755335
+
Hg19::chr6:184352..184384,-p@chr6:184352..184384
-
Hg19::chr6:26220614..26220622,-p@chr6:26220614..26220622
-
Hg19::chr6:39962285..39962290,+p@chr6:39962285..39962290
+
Hg19::chr6:39962295..39962305,+p@chr6:39962295..39962305
+
Hg19::chr6:39962337..39962342,+p@chr6:39962337..39962342
+
Hg19::chr6:89324309..89324332,-p@chr6:89324309..89324332
-
Hg19::chr6:89324350..89324357,-p@chr6:89324350..89324357
-
Hg19::chr7:44140835..44140864,+p@chr7:44140835..44140864
+
Hg19::chr7:47131937..47131939,-p@chr7:47131937..47131939
-
Hg19::chr7:47143537..47143540,-p@chr7:47143537..47143540
-
Hg19::chr7:47143563..47143572,-p@chr7:47143563..47143572
-
Hg19::chr7:47225953..47225964,-p@chr7:47225953..47225964
-
Hg19::chr7:47225965..47225970,-p@chr7:47225965..47225970
-
Hg19::chr7:47226019..47226026,-p@chr7:47226019..47226026
-
Hg19::chr7:47226094..47226108,-p@chr7:47226094..47226108
-
Hg19::chr8:103211732..103211741,-p@chr8:103211732..103211741
-
Hg19::chr8:54811712..54811719,+p1@ENST00000508149
Hg19::chr8:9577966..9577972,+p26@TNKS
Hg19::chr8:9577986..9578004,+p12@TNKS
Hg19::chr8:9578005..9578014,+p22@TNKS
Hg19::chr9:120707790..120707797,-p@chr9:120707790..120707797
-
Hg19::chr9:120707817..120707824,-p@chr9:120707817..120707824
-
Hg19::chr9:138904824..138904829,+p@chr9:138904824..138904829
+
Hg19::chr9:71805723..71805737,+p@chr9:71805723..71805737
+
Hg19::chr9:96029287..96029296,+p15@WNK2
Hg19::chr9:96029313..96029322,+p9@WNK2
Hg19::chr9:96030923..96030932,-p@chr9:96030923..96030932
-
Hg19::chr9:96030936..96030946,-p@chr9:96030936..96030946
-
Hg19::chr9:96059957..96059996,+p@chr9:96059957..96059996
+
Hg19::chrX:42727011..42727017,-p@chrX:42727011..42727017
-
Hg19::chrX:42727038..42727047,-p@chrX:42727038..42727047
-
Hg19::chrX:42727059..42727068,-p@chrX:42727059..42727068
-
Hg19::chrX:47051618..47051644,+p@chrX:47051618..47051644
+
Hg19::chrX:47051652..47051664,+p@chrX:47051652..47051664
+
Hg19::chrX:89012355..89012363,+p@chrX:89012355..89012363
+


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:0006468protein amino acid phosphorylation0.00792695412488815
GO:0016310phosphorylation0.00792695412488815
GO:0001932regulation of protein amino acid phosphorylation0.00792695412488815
GO:0033238regulation of amine metabolic process0.00792695412488815
GO:0006521regulation of amino acid metabolic process0.00792695412488815
GO:0042325regulation of phosphorylation0.00841869775108913
GO:0006793phosphorus metabolic process0.00841869775108913
GO:0006796phosphate metabolic process0.00841869775108913
GO:0051174regulation of phosphorus metabolic process0.00841869775108913
GO:0019220regulation of phosphate metabolic process0.00841869775108913
GO:0043126regulation of 1-phosphatidylinositol 4-kinase activity0.00841869775108913
GO:0043128positive regulation of 1-phosphatidylinositol 4-kinase activity0.00841869775108913
GO:0046813virion attachment, binding of host cell surface receptor0.00841869775108913
GO:0031648protein destabilization0.0156319629705365
GO:0018193peptidyl-amino acid modification0.0172743813151962
GO:0043687post-translational protein modification0.0172743813151962
GO:0018210peptidyl-threonine modification0.0172743813151962
GO:0018107peptidyl-threonine phosphorylation0.0172743813151962
GO:0019062virion attachment to host cell surface receptor0.0172743813151962
GO:0007165signal transduction0.0191047159318527
GO:0008593regulation of Notch signaling pathway0.0202675609349334
GO:0005515protein binding0.0202675609349334
GO:0007154cell communication0.0266769412154499
GO:0006661phosphatidylinositol biosynthetic process0.0272081182847486
GO:0006464protein modification process0.0272081182847486
GO:0043550regulation of lipid kinase activity0.0294342336391061
GO:0043412biopolymer modification0.0300437386506703
GO:0005112Notch binding0.0300437386506703
GO:0043621protein self-association0.0300437386506703
GO:0018209peptidyl-serine modification0.0300437386506703
GO:0018105peptidyl-serine phosphorylation0.0300437386506703
GO:0044409entry into host0.0300437386506703
GO:0045665negative regulation of neuron differentiation0.0300437386506703
GO:0052192movement in environment of other organism during symbiotic interaction0.0300437386506703
GO:0046718entry of virus into host cell0.0300437386506703
GO:0030260entry into host cell0.0300437386506703
GO:0019059initiation of viral infection0.0300437386506703
GO:0052126movement in host environment0.0300437386506703
GO:0051828entry into other organism during symbiotic interaction0.0300437386506703
GO:0051806entry into cell of other organism during symbiotic interaction0.0300437386506703
GO:0007004telomere maintenance via telomerase0.0441734036898593
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.0441734036898593
GO:0030165PDZ domain binding0.0495802336358574
GO:0005626insoluble fraction0.0495802336358574



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>

Uber Anatomy
Ontology termp-valuen
tonsil6.58e-501
mucosa-associated lymphoid tissue6.58e-501
lymphoid tissue6.58e-501
tonsillar ring6.58e-501
Disease
Ontology termp-valuen
lymphatic system cancer1.46e-501
lymphosarcoma1.46e-501
lymphoma4.18e-4510
hematologic cancer1.17e-0951
immune system cancer1.17e-0951


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)
MA0003.11.15181e-05
MA0004.10.404593
MA0006.10.104567
MA0007.10.501753
MA0009.10.212447
MA0014.11.08373e-05
MA0017.10.391098
MA0019.10.0752047
MA0024.10.0305442
MA0025.11.18642
MA0027.11.33422
MA0028.10.00277545
MA0029.10.592059
MA0030.10.130961
MA0031.10.222072
MA0038.10.372001
MA0040.11.35934
MA0041.10.657651
MA0042.10.939587
MA0043.10.46551
MA0046.10.77788
MA0048.10.120729
MA0050.10.944943
MA0051.10.215276
MA0052.10.146992
MA0055.10.000250868
MA0056.10
MA0057.10.00420579
MA0058.10.245507
MA0059.10.85166
MA0060.10.0436627
MA0061.10.124718
MA0063.10
MA0066.15.01251
MA0067.10.601587
MA0068.10.00208334
MA0069.11.1734
MA0070.10.420484
MA0071.10.438887
MA0072.10.412968
MA0073.17.21462e-13
MA0074.10.214012
MA0076.10.000668127
MA0077.10.707665
MA0078.10.112933
MA0081.10.661043
MA0083.10.826645
MA0084.10.336335
MA0087.10.182507
MA0088.10.371895
MA0089.10
MA0090.10.014359
MA0091.10.0874516
MA0092.10.0550314
MA0093.10.491584
MA0095.10
MA0098.10
MA0100.10.130507
MA0101.10.115343
MA0103.11.32649
MA0105.10.154882
MA0106.10.162663
MA0107.10.0505315
MA0108.20.41853
MA0109.10
MA0111.10.0180274
MA0113.10.777917
MA0114.10.450624
MA0115.10.164469
MA0116.11.5906
MA0117.10.0712115
MA0119.10.125218
MA0122.10.581478
MA0124.10.142292
MA0125.10.102222
MA0130.10
MA0131.10.129002
MA0132.10
MA0133.10
MA0135.11.85587
MA0136.10.390054
MA0139.10.00309064
MA0140.10.157732
MA0141.10.150911
MA0142.11.65891
MA0143.10.333261
MA0144.10.0556963
MA0145.10.0214992
MA0146.10.0174784
MA0147.10.148457
MA0148.10.0522085
MA0149.10.0704504
MA0062.20.00182123
MA0035.20.156737
MA0039.20.00054623
MA0138.20.11398
MA0002.20.93651
MA0137.20.0878199
MA0104.20.0427873
MA0047.20.275309
MA0112.20.692243
MA0065.20.213903
MA0150.10.618702
MA0151.10
MA0152.10.450925
MA0153.10.650326
MA0154.11.74105
MA0155.10.153498
MA0156.10.150581
MA0157.10.155229
MA0158.10
MA0159.10.0976126
MA0160.10.756503
MA0161.10
MA0162.18.00431e-11
MA0163.10.415418
MA0164.10.569214
MA0080.21.00909
MA0018.20.164398
MA0099.20.0836687
MA0079.21.44952e-09
MA0102.20.36416
MA0258.10.981492
MA0259.10.0398165
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

No analysis results for this cluster

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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