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MCL coexpression mm9:1276: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!7.54e-18!54;UBERON:0001049!1.46e-17!52;UBERON:0005068!1.46e-17!52;UBERON:0006241!1.46e-17!52;UBERON:0007135!1.46e-17!52;UBERON:0002020!2.39e-16!34;UBERON:0002346!1.08e-15!64;UBERON:0003075!1.08e-15!64;UBERON:0007284!1.08e-15!64;UBERON:0000955!2.73e-15!47;UBERON:0006238!2.73e-15!47;UBERON:0002616!1.28e-14!46;UBERON:0001017!1.71e-14!73;UBERON:0003056!1.95e-14!49;UBERON:0001016!5.36e-14!75;UBERON:0003528!7.02e-14!29;UBERON:0002791!7.02e-14!29;UBERON:0001893!7.02e-14!29;UBERON:0003080!7.60e-14!40;UBERON:0010371!1.35e-13!73;UBERON:0002780!2.10e-13!39;UBERON:0001890!2.10e-13!39;UBERON:0006240!2.10e-13!39;UBERON:0004121!9.84e-13!95;UBERON:0000924!9.84e-13!95;UBERON:0006601!9.84e-13!95;UBERON:0000956!4.96e-10!21;UBERON:0001869!4.96e-10!21;UBERON:0000203!4.96e-10!21;UBERON:0010314!6.44e-10!92;UBERON:0002619!8.68e-08!17
|ontology_enrichment_uberon=UBERON:0000073!7.54e-18!54;UBERON:0001049!1.46e-17!52;UBERON:0005068!1.46e-17!52;UBERON:0006241!1.46e-17!52;UBERON:0007135!1.46e-17!52;UBERON:0002020!2.39e-16!34;UBERON:0002346!1.08e-15!64;UBERON:0003075!1.08e-15!64;UBERON:0007284!1.08e-15!64;UBERON:0000955!2.73e-15!47;UBERON:0006238!2.73e-15!47;UBERON:0002616!1.28e-14!46;UBERON:0001017!1.71e-14!73;UBERON:0003056!1.95e-14!49;UBERON:0001016!5.36e-14!75;UBERON:0003528!7.02e-14!29;UBERON:0002791!7.02e-14!29;UBERON:0001893!7.02e-14!29;UBERON:0003080!7.60e-14!40;UBERON:0010371!1.35e-13!73;UBERON:0002780!2.10e-13!39;UBERON:0001890!2.10e-13!39;UBERON:0006240!2.10e-13!39;UBERON:0004121!9.84e-13!95;UBERON:0000924!9.84e-13!95;UBERON:0006601!9.84e-13!95;UBERON:0000956!4.96e-10!21;UBERON:0001869!4.96e-10!21;UBERON:0000203!4.96e-10!21;UBERON:0010314!6.44e-10!92;UBERON:0002619!8.68e-08!17
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,1.17362,0.535892,0.346849,1.35778,0.645383,0.247459,0.257202,0.0835344,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,0.108444,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,1.0231,0.558142,0.960397,0.336199,0.589948,0.364821,0.335531,0.871288,0.629145,1.48701,1.37841,0.342638,0.56353,0.0995018,0.366415,0.368882,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,1.59383,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,1.21401,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,2.01946,0.874787,0.722675,0.676326,1.03903,0.198949,0.0610418,1.02367,1.83587,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.769162,1.27104,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.937314,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,1.25097,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.540361,0.667976,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,1.93554,0.671017,0.325308,0.63125,0.131395
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,1.17362,0.535892,0.346849,1.35778,0.645383,0.247459,0.257202,0.0835344,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,0.108444,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,1.0231,0.558142,0.960397,0.336199,0.589948,0.364821,0.335531,0.871288,0.629145,1.48701,1.37841,0.342638,0.56353,0.0995018,0.366415,0.368882,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,1.59383,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,1.21401,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,2.01946,0.874787,0.722675,0.676326,1.03903,0.198949,0.0610418,1.02367,1.83587,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.769162,1.27104,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.937314,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,1.25097,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.540361,0.667976,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,1.93554,0.671017,0.325308,0.63125,0.131395
|tfbs_overrepresentation_jaspar=MA0003.1;0.00973143,MA0004.1;0.536396,MA0006.1;0.945134,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.304529,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.161427,MA0050.1;1.41229,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.212634,MA0056.1;0,MA0057.1;0.457693,MA0058.1;0.436487,MA0059.1;1.14076,MA0060.1;1.38604,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;1.41046,MA0072.1;0.990133,MA0073.1;0.169297,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;2.36749,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;1.25163,MA0093.1;0.988233,MA0095.1;0,MA0098.1;0,MA0100.1;1.51574,MA0101.1;1.16089,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.822296,MA0115.1;2.46592,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;0.353523,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.525037,MA0138.2;0.788113,MA0002.2;0.689262,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;1.24784,MA0150.1;1.29346,MA0151.1;0,MA0152.1;1.64059,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;0.822245,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.881902,MA0160.1;0.556423,MA0161.1;0,MA0162.1;1.53386,MA0163.1;0.372305,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.911432,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}
}}

Revision as of 13:04, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:115489574..115489612,-p3@Slc25a19
Mm9::chr8:124967535..124967559,+p1@9330133O14Rik
Mm9::chr8:75072293..75072323,+p@chr8:75072293..75072323
+
Mm9::chr9:112136737..112136755,+p2@2900079G21Rik
Mm9::chr9:112136761..112136817,+p1@2900079G21Rik
Mm9::chrX:156065014..156065035,+p25@Sh3kbp1


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

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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
CNS neuron (sensu Vertebrata)1.05e-1123
neuroblast (sensu Vertebrata)1.05e-1123

Uber Anatomy
Ontology termp-valuen
regional part of nervous system7.54e-1854
neural tube1.46e-1752
neural rod1.46e-1752
future spinal cord1.46e-1752
neural keel1.46e-1752
gray matter2.39e-1634
neurectoderm1.08e-1564
neural plate1.08e-1564
presumptive neural plate1.08e-1564
brain2.73e-1547
future brain2.73e-1547
regional part of brain1.28e-1446
central nervous system1.71e-1473
pre-chordal neural plate1.95e-1449
nervous system5.36e-1475
brain grey matter7.02e-1429
regional part of telencephalon7.02e-1429
telencephalon7.02e-1429
anterior neural tube7.60e-1440
ecto-epithelium1.35e-1373
regional part of forebrain2.10e-1339
forebrain2.10e-1339
future forebrain2.10e-1339
ectoderm-derived structure9.84e-1395
ectoderm9.84e-1395
presumptive ectoderm9.84e-1395
cerebral cortex4.96e-1021
cerebral hemisphere4.96e-1021
pallium4.96e-1021
structure with developmental contribution from neural crest6.44e-1092
regional part of cerebral cortex8.68e-0817


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)
MA0003.10.00973143
MA0004.10.536396
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.304529
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.11.41229
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.11.14076
MA0060.11.38604
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.11.41046
MA0072.10.990133
MA0073.10.169297
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.12.36749
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.11.25163
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.11.51574
MA0101.11.16089
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.822296
MA0115.12.46592
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.353523
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.525037
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.119197
MA0065.21.24784
MA0150.11.29346
MA0151.10
MA0152.11.64059
MA0153.11.13945
MA0154.10.480757
MA0155.10.822245
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.881902
MA0160.10.556423
MA0161.10
MA0162.11.53386
MA0163.10.372305
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.911432
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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