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Coexpression cluster:C383: Difference between revisions

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{{Coexpression_clusters
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ubiquitination during ubiquitin-dependent protein catabolic process!0.00632874131637819!154214$GO:0016567!protein ubiquitination!0.0315382275599513!154214$GO:0032446!protein modification by small protein conjugation!0.0315382275599513!154214$GO:0004842!ubiquitin-protein ligase activity!0.0315382275599513!154214$GO:0008639!small protein conjugating enzyme activity!0.0315382275599513!154214$GO:0019787!small conjugating protein ligase activity!0.0315382275599513!154214$GO:0006511!ubiquitin-dependent protein catabolic process!0.0315382275599513!154214$GO:0043632!modification-dependent macromolecule catabolic process!0.0315382275599513!154214$GO:0019941!modification-dependent protein catabolic process!0.0315382275599513!154214$GO:0051603!proteolysis involved in cellular protein catabolic process!0.0315382275599513!154214$GO:0044257!cellular protein catabolic process!0.0315382275599513!154214$GO:0016881!acid-amino acid ligase activity!0.0315382275599513!154214$GO:0030163!protein catabolic 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402804,0.874158,0.94111,0.890936,0.577683,0.238895,0.859374,0.188088,0.618572,0.461383,0.123436,0.459903,0.643429,0.472985,0.523022,0.723689,0.660052,0.343642,0.476274,0.583648,0.294901,0.741602,0.881645,0.962097,0.610239,0.366899,0.759843,0.94217,0.936673,0.875556,0.910098,0.842284,0.292267,0.838887,0.955554,0.0710288,0.732516,0.804973,0.884183,0.343293,0.957395,0.919387,0.499662,0.682998,0.899309,0.906044,0.681197,0.867916,0.138961,0.596331,0.955303,0.748507,0.813435,0.422447,4.8754e-05,0.975393,0.908192,0.88628,0.609642,0.567665,0.689494,0.827615,0.801009,0.566339,0.497662,0.947399,0.629893,0.680403,0.835698,0.797508,0.395383,0.934118,0.883795,0.244621|tfbs_overrepresentation_for_novel_motifs=0.462305,0.13035,0.202592,0.388836,0.361268,0.386501,0.498842,0.156756,0.523572,1.83766,0.105867,0.194352,0.0987929,0.481329,0.156208,0.180739,0.323398,0.10615,2.05041,0.950822,0.202659,0.271835,0.375545,0.351266,0.928668,0.602605,0.0249841,0.372504,0.160764,0.265025,0.649669,0.352308,0.395527,0.603099,0.54364,0.355517,1.2288,1.26729,0.248146,0.2667,0.0298223,0.611871,0.0626908,0.154672,2.15959,0.878841,0.167225,0.329669,0.18135,0.160896,0.219219,0.174632,0.286878,0.414705,0.545525,0.161247,0.042927,0.141618,0.433805,0.857208,0.385258,0.168703,0.153907,0.302097,1.61388,0.276238,0.62433,0.968521,0.34408,0.814438,0.276665,0.0620601,0.279109,0.543765,0.361954,0.0803588,0.152757,0.289314,0.341516,0.532397,0.249025,3.12536,0.179843,0.160784,0.49889,0.438747,2.19651,0.622403,0.237365,1.06421,0.709557,0.475666,0.36573,0.414815,0.362732,0.0220366,0.1117,1.03439,0.240628,0.764638,0.0237478,0.361201,0.395756,0.870771,0.267745,0.690471,0.313992,0.476111,0.545532,1.81125,1.23774,0.39349,0.196387,0.110777,0.665507,0.28674,0.56488,0.0942716,0.274506,0.220726,0.536488,0.235652,0.120436,0.548966,0.767667,0.289886,0.162613,0.369745,1.40672,0.239526,0.476257,0.318749,0.586948,0.184959,0.721448,0.00253702,0.307029,0.373297,0.682384,1.50986,1.115,0.648318,0.491786,0.397438,0.269036,0.424352,0.256873,1.35281,1.50761,0.406,0.0664133,0.18816,0.476584,0.142269,0.1684,0.843272,0.641569,0.036138,0.0738458,0.482919,0.647214,0.460792,0.340895,0.489868,0.768518,0.53011,0.925221,0.496807,0.464344|tfbs_overrepresentation_jaspar=MA0003.1;3.18725,MA0004.1;0.108579,MA0006.1;1.90637,MA0007.1;0.668837,MA0009.1;0.441048,MA0014.1;1.06723,MA0017.1;0.0536635,MA0019.1;0.197704,MA0024.1;2.51603,MA0025.1;0.557187,MA0027.1;1.98963,MA0028.1;0.390084,MA0029.1;0.369985,MA0030.1;1.68881,MA0031.1;0.309631,MA0038.1;2.94424,MA0040.1;0.374747,MA0041.1;0.377723,MA0042.1;0.10161,MA0043.1;0.441316,MA0046.1;0.431829,MA0048.1;0.0100542,MA0050.1;0.102063,MA0051.1;0.165625,MA0052.1;0.377904,MA0055.1;0.12662,MA0056.1;0,MA0057.1;0.00886853,MA0058.1;0.22757,MA0059.1;0.226028,MA0060.1;0.7972,MA0061.1;0.00791773,MA0063.1;0,MA0066.1;0.168556,MA0067.1;0.724802,MA0068.1;0.720892,MA0069.1;0.428576,MA0070.1;0.419162,MA0071.1;0.444039,MA0072.1;0.415392,MA0073.1;0.0112799,MA0074.1;0.495413,MA0076.1;0.0703269,MA0077.1;0.408948,MA0078.1;0.232083,MA0081.1;0.0631538,MA0083.1;0.447432,MA0084.1;0.901266,MA0087.1;0.413345,MA0088.1;0.0265055,MA0089.1;0,MA0090.1;0.07671,MA0091.1;0.720043,MA0092.1;0.0907294,MA0093.1;0.158872,MA0095.1;0,MA0098.1;0,MA0100.1;0.17714,MA0101.1;0.0419777,MA0103.1;0.146349,MA0105.1;0.235956,MA0106.1;0.195103,MA0107.1;0.0213588,MA0108.2;0.307261,MA0109.1;0,MA0111.1;0.0829259,MA0113.1;0.206168,MA0114.1;0.698692,MA0115.1;0.654355,MA0116.1;0.733056,MA0117.1;0.473208,MA0119.1;0.207161,MA0122.1;1.24012,MA0124.1;0.616574,MA0125.1;0.541304,MA0130.1;0,MA0131.1;0.245067,MA0132.1;0,MA0133.1;0,MA0135.1;0.466979,MA0136.1;0.172767,MA0139.1;1.18995,MA0140.1;0.142924,MA0141.1;0.0623757,MA0142.1;0.285297,MA0143.1;0.206288,MA0144.1;0.389325,MA0145.1;0.746602,MA0146.1;0.584933,MA0147.1;1.49758,MA0148.1;0.38682,MA0149.1;0.137231,MA0062.2;0.00728391,MA0035.2;0.142505,MA0039.2;0.0999597,MA0138.2;0.232954,MA0002.2;0.0499028,MA0137.2;0.0475444,MA0104.2;1.90718,MA0047.2;0.548812,MA0112.2;0.691221,MA0065.2;2.24224,MA0150.1;0.9306,MA0151.1;0,MA0152.1;0.146841,MA0153.1;0.526421,MA0154.1;1.58447,MA0155.1;0.00860269,MA0156.1;0.0483557,MA0157.1;0.264816,MA0158.1;0,MA0159.1;0.0231298,MA0160.1;0.130642,MA0161.1;0,MA0162.1;0.220274,MA0163.1;4.36117,MA0164.1;0.214689,MA0080.2;0.158961,MA0018.2;0.570401,MA0099.2;0.450447,MA0079.2;0.0105902,MA0102.2;0.936833,MA0258.1;1.26013,MA0259.1;0.486136,MA0442.1;0}}
|full_id=C383_oral_liposarcoma_small_Small_skeletal_amniotic_Astrocyte
|id=C383
}}

Latest revision as of 11:21, 17 September 2013


Full id: C383_oral_liposarcoma_small_Small_skeletal_amniotic_Astrocyte



Phase1 CAGE Peaks

Hg19::chr10:99400163..99400169,-p@chr10:99400163..99400169
-
Hg19::chr11:30496173..30496192,+p@chr11:30496173..30496192
+
Hg19::chr11:30496199..30496218,+p@chr11:30496199..30496218
+
Hg19::chr17:70680022..70680046,-p@chr17:70680022..70680046
-
Hg19::chr18:3602688..3602692,+p1@MGC11082
Hg19::chr20:23120219..23120223,-p@chr20:23120219..23120223
-
Hg19::chr2:120974061..120974068,-p3@ENST00000455707
Hg19::chr2:209003854..209003858,-p@chr2:209003854..209003858
-
Hg19::chr3:54660709..54660712,-p@chr3:54660709..54660712
-
Hg19::chr6:102844491..102844494,+p@chr6:102844491..102844494
+
Hg19::chr6:123728153..123728175,-p@chr6:123728153..123728175
-
Hg19::chr6:125186828..125186832,+p@chr6:125186828..125186832
+
Hg19::chr6:125283093..125283144,+p@chr6:125283093..125283144
+
Hg19::chr6:125283157..125283197,+p1@RNF217
Hg19::chr6:125283201..125283226,+p6@RNF217
Hg19::chr6:125283242..125283303,+p2@RNF217
Hg19::chr6:125283415..125283431,+p7@RNF217
Hg19::chr6:125283436..125283477,+p5@RNF217
Hg19::chr6:125284075..125284181,+p4@RNF217
Hg19::chr6:125284314..125284343,+p8@RNF217
Hg19::chr6:125284359..125284375,+p9@RNF217
Hg19::chr6:125284405..125284429,-p4@ENST00000439075
Hg19::chr6:125284416..125284459,+p10@RNF217
Hg19::chr6:125284525..125284534,-p8@ENST00000439075
Hg19::chr6:125284540..125284551,-p7@ENST00000439075
Hg19::chr6:125314790..125314796,+p@chr6:125314790..125314796
+
Hg19::chr6:125426966..125426967,+p@chr6:125426966..125426967
+
Hg19::chr8:101661887..101661901,-p2@SNX31


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:0042787protein ubiquitination during ubiquitin-dependent protein catabolic process0.00632874131637819
GO:0016567protein ubiquitination0.0315382275599513
GO:0032446protein modification by small protein conjugation0.0315382275599513
GO:0004842ubiquitin-protein ligase activity0.0315382275599513
GO:0008639small protein conjugating enzyme activity0.0315382275599513
GO:0019787small conjugating protein ligase activity0.0315382275599513
GO:0006511ubiquitin-dependent protein catabolic process0.0315382275599513
GO:0043632modification-dependent macromolecule catabolic process0.0315382275599513
GO:0019941modification-dependent protein catabolic process0.0315382275599513
GO:0051603proteolysis involved in cellular protein catabolic process0.0315382275599513
GO:0044257cellular protein catabolic process0.0315382275599513
GO:0016881acid-amino acid ligase activity0.0315382275599513
GO:0030163protein catabolic process0.0335423289768044
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0335423289768044
GO:0043285biopolymer catabolic process0.038309980768476
GO:0044265cellular macromolecule catabolic process0.0408762233257838
GO:0006512ubiquitin cycle0.0408762233257838
GO:0009057macromolecule catabolic process0.0431020592810178
GO:0016874ligase activity0.0431020592810178



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
bladder cell1.43e-101
lower urinary tract cell1.43e-101
Disease
Ontology termp-valuen
squamous cell carcinoma6.86e-1114
skin squamous cell carcinoma4.33e-101
keratoacanthoma4.33e-101
carcinoma3.58e-07106


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)
MA0003.13.18725
MA0004.10.108579
MA0006.11.90637
MA0007.10.668837
MA0009.10.441048
MA0014.11.06723
MA0017.10.0536635
MA0019.10.197704
MA0024.12.51603
MA0025.10.557187
MA0027.11.98963
MA0028.10.390084
MA0029.10.369985
MA0030.11.68881
MA0031.10.309631
MA0038.12.94424
MA0040.10.374747
MA0041.10.377723
MA0042.10.10161
MA0043.10.441316
MA0046.10.431829
MA0048.10.0100542
MA0050.10.102063
MA0051.10.165625
MA0052.10.377904
MA0055.10.12662
MA0056.10
MA0057.10.00886853
MA0058.10.22757
MA0059.10.226028
MA0060.10.7972
MA0061.10.00791773
MA0063.10
MA0066.10.168556
MA0067.10.724802
MA0068.10.720892
MA0069.10.428576
MA0070.10.419162
MA0071.10.444039
MA0072.10.415392
MA0073.10.0112799
MA0074.10.495413
MA0076.10.0703269
MA0077.10.408948
MA0078.10.232083
MA0081.10.0631538
MA0083.10.447432
MA0084.10.901266
MA0087.10.413345
MA0088.10.0265055
MA0089.10
MA0090.10.07671
MA0091.10.720043
MA0092.10.0907294
MA0093.10.158872
MA0095.10
MA0098.10
MA0100.10.17714
MA0101.10.0419777
MA0103.10.146349
MA0105.10.235956
MA0106.10.195103
MA0107.10.0213588
MA0108.20.307261
MA0109.10
MA0111.10.0829259
MA0113.10.206168
MA0114.10.698692
MA0115.10.654355
MA0116.10.733056
MA0117.10.473208
MA0119.10.207161
MA0122.11.24012
MA0124.10.616574
MA0125.10.541304
MA0130.10
MA0131.10.245067
MA0132.10
MA0133.10
MA0135.10.466979
MA0136.10.172767
MA0139.11.18995
MA0140.10.142924
MA0141.10.0623757
MA0142.10.285297
MA0143.10.206288
MA0144.10.389325
MA0145.10.746602
MA0146.10.584933
MA0147.11.49758
MA0148.10.38682
MA0149.10.137231
MA0062.20.00728391
MA0035.20.142505
MA0039.20.0999597
MA0138.20.232954
MA0002.20.0499028
MA0137.20.0475444
MA0104.21.90718
MA0047.20.548812
MA0112.20.691221
MA0065.22.24224
MA0150.10.9306
MA0151.10
MA0152.10.146841
MA0153.10.526421
MA0154.11.58447
MA0155.10.00860269
MA0156.10.0483557
MA0157.10.264816
MA0158.10
MA0159.10.0231298
MA0160.10.130642
MA0161.10
MA0162.10.220274
MA0163.14.36117
MA0164.10.214689
MA0080.20.158961
MA0018.20.570401
MA0099.20.450447
MA0079.20.0105902
MA0102.20.936833
MA0258.11.26013
MA0259.10.486136
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
CCNT2#905122.715514961555410.0005978892186740490.00499663536121461
CTCF#10664112.105815003708050.00883217986061110.0335329370533068
CTCFL#14069064.231387362637360.002416712809055170.0136188997499009
GATA3#262554.863663635215360.003229757208175820.0167326064320985
RAD21#588582.958581112987520.003993307231017140.019150381756828
TRIM28#1015574.647631261315630.0005646327218513030.00481739047769204



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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