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Coexpression cluster:C559: Difference between revisions

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{{Coexpression_clusters
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cell fate commitment!0.0229580571962169!4654$GO:0007518!myoblast cell fate determination!0.0229580571962169!4654$GO:0000731!DNA synthesis during DNA repair!0.0306039852584672!56897$GO:0030174!regulation of DNA replication initiation!0.0306039852584672!56897$GO:0008536!Ran GTPase binding!0.0336599244224942!5902$GO:0045445!myoblast differentiation!0.0427812955751279!4654$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.0427812955751279!4654$GO:0005092!GDP-dissociation inhibitor activity!0.0427812955751279!5902$GO:0006275!regulation of DNA replication!0.0427812955751279!56897$GO:0001709!cell fate determination!0.0427812955751279!4654$GO:0004864!protein phosphatase inhibitor activity!0.0427812955751279!26472$GO:0019212!phosphatase inhibitor activity!0.0427812955751279!26472$GO:0006270!DNA replication initiation!0.0427812955751279!56897$GO:0048741!skeletal muscle fiber development!0.0427812955751279!4654$GO:0048747!muscle fiber 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4833,0.552042,0.689905,0.0615715,0.596464,0.527328,0.469901,0.739277,0.634865,0.0213784,0.419455,0.12146,0.862225,0.524857,0.377623,0.367255,0.00152465,0.0233139,0.254606,0.255313,0.582662,0.351578,0.198874,0.255153,0.338546,0.801772,0.718094,0.670087,0.0559055,0.674028,0.363759,0.42349,0.297824,0.500117,0.296723,0.118381,0.306508,0.344935,0.520488,0.0247817,0.213844,0.308984,0.393893,0.180997,0.538507,0.704612,0.845895,0.537704,0.396853,0.557415,0.224087,0.467551,0.0329765,0.747563,0.293544,0.78972,0.647685,0.530923,0.0258255,0.174613,0.607047,0.708249,0.694264,0.538145,0.762813,0.00582427,0.481329,0.730672,0.154881,0.139727,0.321688,0.677093,0.103124,0.00976432,0.0202209,0.249315,0.741876,0.407853,0.354953,0.158015,0.352603,0.415815,0.380706,0.602677,0.0811467,0.602504,0.0913704,0.325254,0.0906439,0.43333,0.738828,0.643716,0.598522,0.726332,0.204882,0.707691,0.908569|tfbs_overrepresentation_for_novel_motifs=0.157827,1.36836,0.152819,0.258928,0.789854,0.715112,0.318839,1.72849,0.463955,0.914578,0.234283,0.355038,0.643012,0.309388,0.124662,0.851457,0.511522,0.0927064,0.388593,1.48681,0.152859,1.05372,0.251588,0.12232,0.542899,0.374311,0.566593,0.249905,0.127478,0.274385,0.217756,0.544857,0.260283,0.363901,0.340569,0.785985,1.13501,0.717201,0.622505,0.419472,0.338389,0.205653,0.209746,0.123709,0.321633,0.173971,0.319738,0.641595,0.18831,0.798822,0.386472,0.878028,0.193889,0.615394,0.758742,0.311792,0.130259,0.2852,2.08479,0.284391,1.42397,0.321692,0.465207,0.48664,0.336598,0.456015,0.843028,2.69398,0.535417,1.04233,0.19602,0.836913,0.189549,0.756844,0.0383048,0.135657,0.847029,0.471562,1.31856,0.18023,0.400226,0.48568,1.60321,0.219253,1.68705,0.0705689,0.30235,1.15199,0.408949,1.29895,0.932961,0.68283,0.560183,0.0788172,1.87151,0.290488,0.684177,0.599297,1.06191,1.88154,1.04735,0.555021,0.594155,0.514828,0.445845,1.21768,0.500571,0.826592,1.03663,0.115618,0.160439,0.591605,0.891551,0.241506,0.886618,0.333119,0.318047,0.216858,0.453946,0.275094,0.748992,1.0486,0.255485,0.914205,0.993708,1.19002,0.313614,1.38691,0.78949,0.608973,0.683478,0.627156,0.803201,0.342946,0.945426,0.469273,0.21329,0.698255,0.904406,1.74999,1.35069,0.868456,0.315034,0.596045,0.447394,0.76278,0.432737,1.59165,0.58757,0.953427,0.336018,0.0889833,0.683836,0.0546497,0.321292,1.07219,0.394947,0.373254,0.184652,0.164414,2.015,0.66649,0.531753,0.166635,0.46162,0.335644,2.47056,0.317742,1.40687|tfbs_overrepresentation_jaspar=MA0003.1;0.114205,MA0004.1;0.238283,MA0006.1;0.392773,MA0007.1;0.223897,MA0009.1;0.644692,MA0014.1;0.111471,MA0017.1;0.150184,MA0019.1;0.359322,MA0024.1;0.547222,MA0025.1;0.771296,MA0027.1;2.23171,MA0028.1;0.134741,MA0029.1;0.565022,MA0030.1;0.554453,MA0031.1;0.495474,MA0038.1;0.321141,MA0040.1;0.570428,MA0041.1;0.252793,MA0042.1;0.227947,MA0043.1;1.55541,MA0046.1;0.634468,MA0048.1;3.2561,MA0050.1;0.228625,MA0051.1;0.317617,MA0052.1;0.574006,MA0055.1;9.61865,MA0056.1;0,MA0057.1;0.91959,MA0058.1;0.167587,MA0059.1;0.499176,MA0060.1;0.212419,MA0061.1;0.175447,MA0063.1;0,MA0066.1;0.321498,MA0067.1;0.948938,MA0068.1;0.303278,MA0069.1;0.630852,MA0070.1;0.620368,MA0071.1;0.289163,MA0072.1;1.49508,MA0073.1;2.32976,MA0074.1;0.316991,MA0076.1;0.528959,MA0077.1;0.608956,MA0078.1;1.039,MA0081.1;0.965129,MA0083.1;0.651755,MA0084.1;1.13204,MA0087.1;0.613875,MA0088.1;0.369952,MA0089.1;0,MA0090.1;0.189305,MA0091.1;2.72392,MA0092.1;0.607109,MA0093.1;0.12631,MA0095.1;0,MA0098.1;0,MA0100.1;0.885358,MA0101.1;0.128426,MA0103.1;1.24111,MA0105.1;1.1728,MA0106.1;0.355999,MA0107.1;0.285979,MA0108.2;0.492699,MA0109.1;0,MA0111.1;0.578093,MA0113.1;0.370073,MA0114.1;0.278245,MA0115.1;0.874839,MA0116.1;4.11635,MA0117.1;0.680135,MA0119.1;0.471628,MA0122.1;1.67968,MA0124.1;0.834787,MA0125.1;0.75419,MA0130.1;0,MA0131.1;0.418384,MA0132.1;0,MA0133.1;0,MA0135.1;0.673296,MA0136.1;0.327047,MA0139.1;2.47082,MA0140.1;0.286995,MA0141.1;0.165463,MA0142.1;1.17834,MA0143.1;0.370225,MA0144.1;0.25687,MA0145.1;0.113672,MA0146.1;1.16153,MA0147.1;0.0881384,MA0148.1;0.257816,MA0149.1;0.279141,MA0062.2;0.382208,MA0035.2;0.286421,MA0039.2;0.426118,MA0138.2;0.403517,MA0002.2;2.74818,MA0137.2;0.848496,MA0104.2;0.0580852,MA0047.2;0.345656,MA0112.2;1.20168,MA0065.2;0.246686,MA0150.1;0.185024,MA0151.1;0,MA0152.1;0.292357,MA0153.1;0.738108,MA0154.1;0.542249,MA0155.1;0.204406,MA0156.1;0.140505,MA0157.1;0.442323,MA0158.1;0,MA0159.1;0.29763,MA0160.1;0.26995,MA0161.1;0,MA0162.1;0.191058,MA0163.1;0.864319,MA0164.1;0.380804,MA0080.2;0.126365,MA0018.2;2.52953,MA0099.2;0.292649,MA0079.2;0.819043,MA0102.2;1.16862,MA0258.1;0.520754,MA0259.1;0.640339,MA0442.1;0}}
|full_id=C559_Skeletal_Pericytes_mesenchymal_Myoblast_rhabdomyosarcoma_skeletal_tongue
|id=C559
}}

Latest revision as of 11:25, 17 September 2013


Full id: C559_Skeletal_Pericytes_mesenchymal_Myoblast_rhabdomyosarcoma_skeletal_tongue



Phase1 CAGE Peaks

Hg19::chr11:17716498..17716504,+p2@ENST00000524885
Hg19::chr11:17741111..17741124,+p1@MYOD1
Hg19::chr11:17741254..17741282,+p2@MYOD1
Hg19::chr11:64012815..64012824,-p20@PPP1R14B
Hg19::chr11:85090324..85090329,-p@chr11:85090324..85090329
-
Hg19::chr13:99582467..99582528,-p@chr13:99582467..99582528
-
Hg19::chr17:38502981..38502987,+p@chr17:38502981..38502987
+
Hg19::chr22:20103621..20103632,+p14@RANBP1
Hg19::chr22:20103644..20103662,+p10@RANBP1
Hg19::chr6:169588511..169588525,-p@chr6:169588511..169588525
-
Hg19::chr6:169588532..169588548,-p@chr6:169588532..169588548
-
Hg19::chr6:169588553..169588570,-p@chr6:169588553..169588570
-
Hg19::chr6:169588594..169588599,-p@chr6:169588594..169588599
-
Hg19::chr6:2783611..2783617,+p5@U56249
Hg19::chr6:2783684..2783703,+p1@U56249
Hg19::chr6:2783707..2783715,+p2@U56249


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:0048625myoblast cell fate commitment0.0229580571962169
GO:0007518myoblast cell fate determination0.0229580571962169
GO:0000731DNA synthesis during DNA repair0.0306039852584672
GO:0030174regulation of DNA replication initiation0.0306039852584672
GO:0008536Ran GTPase binding0.0336599244224942
GO:0045445myoblast differentiation0.0427812955751279
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0427812955751279
GO:0005092GDP-dissociation inhibitor activity0.0427812955751279
GO:0006275regulation of DNA replication0.0427812955751279
GO:0001709cell fate determination0.0427812955751279
GO:0004864protein phosphatase inhibitor activity0.0427812955751279
GO:0019212phosphatase inhibitor activity0.0427812955751279
GO:0006270DNA replication initiation0.0427812955751279
GO:0048741skeletal muscle fiber development0.0427812955751279
GO:0048747muscle fiber development0.0427812955751279
GO:0042692muscle cell differentiation0.0439194635543592
GO:0051052regulation of DNA metabolic process0.0440259557804808



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><br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue3.95e-1962
striated muscle tissue3.95e-1962
myotome3.95e-1962
muscle tissue1.65e-1864
musculature1.65e-1864
musculature of body1.65e-1864
somite1.30e-1671
presomitic mesoderm1.30e-1671
presumptive segmental plate1.30e-1671
dermomyotome1.30e-1671
trunk paraxial mesoderm1.30e-1671
paraxial mesoderm2.26e-1672
presumptive paraxial mesoderm2.26e-1672
dense mesenchyme tissue3.88e-1673
epithelial vesicle4.70e-1578
multilaminar epithelium4.22e-1483
trunk mesenchyme2.49e-09122
throat6.42e-092
unilaminar epithelium1.56e-07148
mesenchyme6.70e-07160
entire embryonic mesenchyme6.70e-07160


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)
MA0003.10.114205
MA0004.10.238283
MA0006.10.392773
MA0007.10.223897
MA0009.10.644692
MA0014.10.111471
MA0017.10.150184
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.11.55541
MA0046.10.634468
MA0048.13.2561
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.19.61865
MA0056.10
MA0057.10.91959
MA0058.10.167587
MA0059.10.499176
MA0060.10.212419
MA0061.10.175447
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.303278
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.11.49508
MA0073.12.32976
MA0074.10.316991
MA0076.10.528959
MA0077.10.608956
MA0078.11.039
MA0081.10.965129
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.369952
MA0089.10
MA0090.10.189305
MA0091.12.72392
MA0092.10.607109
MA0093.10.12631
MA0095.10
MA0098.10
MA0100.10.885358
MA0101.10.128426
MA0103.11.24111
MA0105.11.1728
MA0106.10.355999
MA0107.10.285979
MA0108.20.492699
MA0109.10
MA0111.10.578093
MA0113.10.370073
MA0114.10.278245
MA0115.10.874839
MA0116.14.11635
MA0117.10.680135
MA0119.10.471628
MA0122.11.67968
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.12.47082
MA0140.10.286995
MA0141.10.165463
MA0142.11.17834
MA0143.10.370225
MA0144.10.25687
MA0145.10.113672
MA0146.11.16153
MA0147.10.0881384
MA0148.10.257816
MA0149.10.279141
MA0062.20.382208
MA0035.20.286421
MA0039.20.426118
MA0138.20.403517
MA0002.22.74818
MA0137.20.848496
MA0104.20.0580852
MA0047.20.345656
MA0112.21.20168
MA0065.20.246686
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.542249
MA0155.10.204406
MA0156.10.140505
MA0157.10.442323
MA0158.10
MA0159.10.29763
MA0160.10.26995
MA0161.10
MA0162.10.191058
MA0163.10.864319
MA0164.10.380804
MA0080.20.126365
MA0018.22.52953
MA0099.20.292649
MA0079.20.819043
MA0102.21.16862
MA0258.10.520754
MA0259.10.640339
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

This analysis result is provided for C0 - C305 clusters.

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