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MCL coexpression mm9:411: Difference between revisions

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{{MCL_coexpression_mm9
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metabolic process;0.0241694953161645;22427,14479,18045,242705,170755,74302,140917,66464,213054!GO:0044428;nuclear part;0.0241694953161645;242705,22427,66464,98386,18045!GO:0005654;nucleoplasm;0.0241694953161645;242705,22427,66464,18045!GO:0003677;DNA binding;0.0279517535285351;242705,22427,66464,98386,18045,213054!GO:0031981;nuclear lumen;0.0279517535285351;242705,22427,66464,18045!GO:0031974;membrane-enclosed lumen;0.0303499110055835;242705,22427,66464,18045!GO:0043233;organelle lumen;0.0303499110055835;242705,22427,66464,18045!GO:0040009;regulation of growth rate;0.0303499110055835;22427!GO:0001302;replicative cell aging;0.0303499110055835;22427!GO:0043170;macromolecule metabolic process;0.0303499110055835;22427,14479,18045,242705,170755,74302,140917,66464,213054!GO:0016986;transcription initiation factor activity;0.0401385621644419;66464!GO:0005667;transcription factor 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|gostat_on_MCL_coexpression=GO:0043283;biopolymer metabolic process;0.0241694953161645;22427,14479,18045,242705,170755,74302,140917,66464,213054!GO:0044428;nuclear part;0.0241694953161645;242705,22427,66464,98386,18045!GO:0005654;nucleoplasm;0.0241694953161645;242705,22427,66464,18045!GO:0003677;DNA binding;0.0279517535285351;242705,22427,66464,98386,18045,213054!GO:0031981;nuclear lumen;0.0279517535285351;242705,22427,66464,18045!GO:0031974;membrane-enclosed lumen;0.0303499110055835;242705,22427,66464,18045!GO:0043233;organelle lumen;0.0303499110055835;242705,22427,66464,18045!GO:0040009;regulation of growth rate;0.0303499110055835;22427!GO:0001302;replicative cell aging;0.0303499110055835;22427!GO:0043170;macromolecule metabolic process;0.0303499110055835;22427,14479,18045,242705,170755,74302,140917,66464,213054!GO:0016986;transcription initiation factor activity;0.0401385621644419;66464!GO:0005667;transcription factor complex;0.0416932852787422;242705,66464,18045!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001041!5.00e-11!80;UBERON:0004921!2.09e-09!114;UBERON:0001007!5.96e-09!116;UBERON:0001555!5.96e-09!116;UBERON:0007026!5.96e-09!116;UBERON:0004119!1.05e-08!118;UBERON:0000925!1.05e-08!118;UBERON:0006595!1.05e-08!118;UBERON:0002390!2.22e-07!45;UBERON:0003061!2.22e-07!45;UBERON:0004177!2.38e-07!29;UBERON:0005057!2.38e-07!29;UBERON:0000475!3.74e-07!150;UBERON:0002193!3.81e-07!48;UBERON:0002405!3.81e-07!48;UBERON:0001048!4.44e-07!134
|tfbs_overrepresentation_for_novel_motifs=0.48778,0.239198,0.873196,0.191238,0.271545,0.201606,0.270195,0.146885,0.15797,1.07523,0.665632,0.260789,0.340991,0.766078,0.295744,0,1.1241,0.0750368,0.307533,0.478834,0.121654,0.32474,0.764446,0.26934,0.457081,0.301898,0.121208,0.620162,0.691298,0.963927,0.206597,0.531719,0.257084,0.249044,0.296456,0.200104,1.34509,0.257981,0.468707,0.399439,0.0770075,0.604618,0.15533,0.0888852,1.81234,1.03234,0.372907,0.6478,0.0147531,0.699131,1.09109,0.323798,0.0737278,0.661847,0.67813,0.779015,0.110603,0.699566,0.111806,0.77532,1.27858,0.882655,0.172226,1.06984,0.799223,2.0008,0.806865,1.14503,0.509463,1.00145,1.33165,0.153772,3.19141,0.709559,4.28767,0.234413,0.101234,0.363297,0.498264,0.124234,0.0397272,1.15703,0.330377,0.139579,0.602212,2.18011,0.0669878,0.0797642,0.377064,1.30447,0.873554,0.606796,0.543309,0.280055,0.209139,0.0497835,0.334928,0.545856,0.373124,0.553251,0.523231,0.531465,1.55675,0.4269,1.09022,0.603853,1.20351,0.225669,0.79738,1.26837,0.476067,0.647285,0.787233,0.67478,0.880323,0.263255,2.63626,0.193921,1.12656,0.0675617,0.714636,0.398522,0.819386,0.951399,0.932468,0.501574,0.276618,0.53717,0.805419,0.284377,0.629874,1.0432,0.777296,0.296474,0.9011,0.00454122,0.501821,0.211406,0.853868,1.66928,1.27308,0.811357,0.313144,0.541193,0.420352,0.605406,0.375553,1.62988,0.169369,0.577124,0.40185,4.9471,0.66331,0.194002,0.29573,0.739975,0.324625,0.313539,0.160402,0.501353,0.862985,0.601424,0.501973,1.47253,0.417485,0.289792,0.52021,0.259556,0.171242
|tfbs_overrepresentation_jaspar=MA0003.1;2.45436,MA0004.1;0.191582,MA0006.1;0.604294,MA0007.1;1.02294,MA0009.1;0.5557,MA0014.1;6.47617,MA0017.1;1.11747,MA0019.1;0.394308,MA0024.1;1.28375,MA0025.1;0.773017,MA0027.1;2.16618,MA0028.1;1.05513,MA0029.1;0.496599,MA0030.1;0.502474,MA0031.1;0.470779,MA0038.1;0.301835,MA0040.1;0.567108,MA0041.1;0.433432,MA0042.1;0.412259,MA0043.1;0.644695,MA0046.1;0.58854,MA0048.1;0.558597,MA0050.1;0.219748,MA0051.1;0.309072,MA0052.1;0.574473,MA0055.1;0.0620752,MA0056.1;0,MA0057.1;0.772226,MA0058.1;0.401421,MA0059.1;0.421089,MA0060.1;2.06381,MA0061.1;0.060618,MA0063.1;0,MA0066.1;1.44836,MA0067.1;2.0392,MA0068.1;0.309163,MA0069.1;0.574784,MA0070.1;0.565924,MA0071.1;0.625332,MA0072.1;0.558195,MA0073.1;3.34094,MA0074.1;0.264633,MA0076.1;0.724696,MA0077.1;0.538513,MA0078.1;0.336143,MA0081.1;0.458627,MA0083.1;0.643958,MA0084.1;1.1979,MA0087.1;0.604077,MA0088.1;0.784071,MA0089.1;0,MA0090.1;0.167748,MA0091.1;0.582275,MA0092.1;0.502322,MA0093.1;0.316906,MA0095.1;0,MA0098.1;0,MA0100.1;0.255651,MA0101.1;0.435524,MA0103.1;0.345124,MA0105.1;0.0968542,MA0106.1;0.907208,MA0107.1;0.686139,MA0108.2;0.413973,MA0109.1;0,MA0111.1;0.177475,MA0113.1;0.319332,MA0114.1;1.23875,MA0115.1;0.647296,MA0116.1;1.01433,MA0117.1;0.617392,MA0119.1;0.141504,MA0122.1;0.635764,MA0124.1;0.828115,MA0125.1;0.757653,MA0130.1;0,MA0131.1;0.390422,MA0132.1;0,MA0133.1;0,MA0135.1;0.67864,MA0136.1;0.280269,MA0139.1;0.331714,MA0140.1;0.255562,MA0141.1;0.755244,MA0142.1;0.457961,MA0143.1;0.332773,MA0144.1;0.478562,MA0145.1;0.0967733,MA0146.1;0.903084,MA0147.1;0.509077,MA0148.1;0.203219,MA0149.1;0.144679,MA0062.2;0.760681,MA0035.2;0.259203,MA0039.2;2.78093,MA0138.2;0.383644,MA0002.2;0.338271,MA0137.2;0.371067,MA0104.2;0.371038,MA0047.2;0.301217,MA0112.2;0.370684,MA0065.2;0.372253,MA0150.1;0.180943,MA0151.1;0,MA0152.1;0.814717,MA0153.1;0.694211,MA0154.1;0.548533,MA0155.1;0.430598,MA0156.1;0.356573,MA0157.1;0.429861,MA0158.1;0,MA0159.1;0.534512,MA0160.1;0.592791,MA0161.1;0,MA0162.1;1.96131,MA0163.1;4.72245,MA0164.1;0.280556,MA0080.2;0.103116,MA0018.2;0.288261,MA0099.2;0.37828,MA0079.2;4.78498,MA0102.2;1.24942,MA0258.1;0.197969,MA0259.1;0.833105,MA0442.1;0
}}

Latest revision as of 15:15, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:122633523..122633524,-p@chr10:122633523..122633524
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Mm9::chr10:122633972..122634017,-p1@Usp15
Mm9::chr10:82226781..82226825,-p1@Nfyb
Mm9::chr10:82226833..82226864,-p3@Nfyb
Mm9::chr11:4494860..4494878,-p2@Mtmr3
Mm9::chr15:35300864..35300893,+p2@Vps13b
Mm9::chr19:12647998..12648032,+p1@Fam111a
Mm9::chr19:37624887..37624958,+p1@Exoc6
Mm9::chr1:183746723..183746725,-p@chr1:183746723..183746725
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Mm9::chr1:183750776..183750778,-p@chr1:183750776..183750778
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Mm9::chr1:183772465..183772515,-p1@Lbr
Mm9::chr1:9788204..9788297,+p1@Sgk3
Mm9::chr3:103613201..103613332,-p1@Dclre1b
Mm9::chr3:95021853..95021911,-p1@Gabpb2
Mm9::chr4:131830300..131830348,+p1@Taf12
Mm9::chr4:135728860..135728871,+p@chr4:135728860..135728871
+
Mm9::chr8:34495942..34495989,-p1@Wrn
Mm9::chrX:48557952..48557965,-p@chrX:48557952..48557965
-


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

GO IDGO nameFDR corrected p-value
GO:0043283biopolymer metabolic process0.0241694953161645
GO:0044428nuclear part0.0241694953161645
GO:0005654nucleoplasm0.0241694953161645
GO:0003677DNA binding0.0279517535285351
GO:0031981nuclear lumen0.0279517535285351
GO:0031974membrane-enclosed lumen0.0303499110055835
GO:0043233organelle lumen0.0303499110055835
GO:0040009regulation of growth rate0.0303499110055835
GO:0001302replicative cell aging0.0303499110055835
GO:0043170macromolecule metabolic process0.0303499110055835
GO:0016986transcription initiation factor activity0.0401385621644419
GO:0005667transcription factor complex0.0416932852787422



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
foregut5.00e-1180
subdivision of digestive tract2.09e-09114
digestive system5.96e-09116
digestive tract5.96e-09116
primitive gut5.96e-09116
endoderm-derived structure1.05e-08118
endoderm1.05e-08118
presumptive endoderm1.05e-08118
hematopoietic system2.22e-0745
blood island2.22e-0745
hemopoietic organ2.38e-0729
immune organ2.38e-0729
organism subdivision3.74e-07150
hemolymphoid system3.81e-0748
immune system3.81e-0748
primordium4.44e-07134


TFBS overrepresentation<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)
MA0003.12.45436
MA0004.10.191582
MA0006.10.604294
MA0007.11.02294
MA0009.10.5557
MA0014.16.47617
MA0017.11.11747
MA0019.10.394308
MA0024.11.28375
MA0025.10.773017
MA0027.12.16618
MA0028.11.05513
MA0029.10.496599
MA0030.10.502474
MA0031.10.470779
MA0038.10.301835
MA0040.10.567108
MA0041.10.433432
MA0042.10.412259
MA0043.10.644695
MA0046.10.58854
MA0048.10.558597
MA0050.10.219748
MA0051.10.309072
MA0052.10.574473
MA0055.10.0620752
MA0056.10
MA0057.10.772226
MA0058.10.401421
MA0059.10.421089
MA0060.12.06381
MA0061.10.060618
MA0063.10
MA0066.11.44836
MA0067.12.0392
MA0068.10.309163
MA0069.10.574784
MA0070.10.565924
MA0071.10.625332
MA0072.10.558195
MA0073.13.34094
MA0074.10.264633
MA0076.10.724696
MA0077.10.538513
MA0078.10.336143
MA0081.10.458627
MA0083.10.643958
MA0084.11.1979
MA0087.10.604077
MA0088.10.784071
MA0089.10
MA0090.10.167748
MA0091.10.582275
MA0092.10.502322
MA0093.10.316906
MA0095.10
MA0098.10
MA0100.10.255651
MA0101.10.435524
MA0103.10.345124
MA0105.10.0968542
MA0106.10.907208
MA0107.10.686139
MA0108.20.413973
MA0109.10
MA0111.10.177475
MA0113.10.319332
MA0114.11.23875
MA0115.10.647296
MA0116.11.01433
MA0117.10.617392
MA0119.10.141504
MA0122.10.635764
MA0124.10.828115
MA0125.10.757653
MA0130.10
MA0131.10.390422
MA0132.10
MA0133.10
MA0135.10.67864
MA0136.10.280269
MA0139.10.331714
MA0140.10.255562
MA0141.10.755244
MA0142.10.457961
MA0143.10.332773
MA0144.10.478562
MA0145.10.0967733
MA0146.10.903084
MA0147.10.509077
MA0148.10.203219
MA0149.10.144679
MA0062.20.760681
MA0035.20.259203
MA0039.22.78093
MA0138.20.383644
MA0002.20.338271
MA0137.20.371067
MA0104.20.371038
MA0047.20.301217
MA0112.20.370684
MA0065.20.372253
MA0150.10.180943
MA0151.10
MA0152.10.814717
MA0153.10.694211
MA0154.10.548533
MA0155.10.430598
MA0156.10.356573
MA0157.10.429861
MA0158.10
MA0159.10.534512
MA0160.10.592791
MA0161.10
MA0162.11.96131
MA0163.14.72245
MA0164.10.280556
MA0080.20.103116
MA0018.20.288261
MA0099.20.37828
MA0079.24.78498
MA0102.21.24942
MA0258.10.197969
MA0259.10.833105
MA0442.10
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