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MCL coexpression mm9:1267: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!2.56e-08!333;UBERON:0001017!4.90e-08!73;UBERON:0004121!5.25e-08!95;UBERON:0000924!5.25e-08!95;UBERON:0006601!5.25e-08!95;UBERON:0001016!1.25e-07!75;UBERON:0000922!2.17e-07!320
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.7141,0.0835344,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.713088,0.657163,0.345236,0.472505,0.686615,0.63639,2.39973,0.394364,0.181062,0.558142,0.960397,0.892985,0.589948,0.956447,0.0363535,0.326478,0.629145,0.820134,0.27383,0.342638,0.56353,0.327433,0.959963,0.368882,0.524258,1.82546,0.589246,1.48928,0.397446,0.839084,0.714419,0.995874,1.10437,1.12205,1.59824,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,0.740068,1.156,2.50016,0.19692,1.11463,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,5.55221,0.479018,0.534643,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.769162,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,1.94583,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,2.32117,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,1.64681,1.63376,1.10885,1.10596,3.03596,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,4.68192
|tfbs_overrepresentation_jaspar=MA0003.1;5.57281,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;2.22952,MA0009.1;0.987341,MA0014.1;7.60945,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.969171,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;0.943003,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.895081,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.827788,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.911705,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;5.49771,MA0074.1;1.54084,MA0076.1;1.04996,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;1.19271,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.111145,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.988233,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;4.08411,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;2.83583,MA0114.1;0.822296,MA0115.1;1.08851,MA0116.1;0.944657,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;1.96032,MA0140.1;0.625902,MA0141.1;1.07584,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.379391,MA0146.1;3.00399,MA0147.1;1.54778,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;1.11803,MA0035.2;0.630778,MA0039.2;2.17024,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;2.05302,MA0047.2;0.685741,MA0112.2;3.15789,MA0065.2;1.81707,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;0.822245,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.70356,MA0163.1;4.40286,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;6.27804,MA0102.2;1.7182,MA0258.1;0.790457,MA0259.1;1.5079,MA0442.1;0
}}

Latest revision as of 16:39, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:102856319..102856355,-p@chr11:102856319..102856355
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Mm9::chr11:102878387..102878466,-p1@Dcakd
Mm9::chr11:102878481..102878493,-p3@Dcakd
Mm9::chr19:4615647..4615700,-p2@Lrfn4
Mm9::chr4:128483534..128483613,-p1@Zfp362
Mm9::chr4:128483731..128483757,-p4@Zfp362


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:0004140dephospho-CoA kinase activity0.00482099322332118



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
ectodermal cell3.94e-1144
neurectodermal cell3.94e-1144
neural cell4.39e-1143
neuron1.47e-0933
neuronal stem cell1.47e-0933
neuroblast1.47e-0933
electrically signaling cell1.47e-0933
non-terminally differentiated cell3.43e-0949
electrically responsive cell1.41e-0739
electrically active cell1.41e-0739

Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.56e-08333
central nervous system4.90e-0873
ectoderm-derived structure5.25e-0895
ectoderm5.25e-0895
presumptive ectoderm5.25e-0895
nervous system1.25e-0775
embryo2.17e-07320


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)
MA0003.15.57281
MA0004.10.536396
MA0006.10.359699
MA0007.12.22952
MA0009.10.987341
MA0014.17.60945
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
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
MA0048.10.943003
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.827788
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.911705
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.15.49771
MA0074.11.54084
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.11.19271
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.14.08411
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.12.83583
MA0114.10.822296
MA0115.11.08851
MA0116.10.944657
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
MA0139.11.96032
MA0140.10.625902
MA0141.11.07584
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.13.00399
MA0147.11.54778
MA0148.10.553294
MA0149.10.464445
MA0062.21.11803
MA0035.20.630778
MA0039.22.17024
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.22.05302
MA0047.20.685741
MA0112.23.15789
MA0065.21.81707
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.822245
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.70356
MA0163.14.40286
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.26.27804
MA0102.21.7182
MA0258.10.790457
MA0259.11.5079
MA0442.10
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