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MCL coexpression mm9:1316: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0000073!1.27e-25!54;UBERON:0002346!1.99e-24!64;UBERON:0003075!1.99e-24!64;UBERON:0007284!1.99e-24!64;UBERON:0001049!7.55e-24!52;UBERON:0005068!7.55e-24!52;UBERON:0006241!7.55e-24!52;UBERON:0007135!7.55e-24!52;UBERON:0001017!3.90e-23!73;UBERON:0001016!7.06e-22!75;UBERON:0000955!6.03e-21!47;UBERON:0006238!6.03e-21!47;UBERON:0002616!2.78e-20!46;UBERON:0003056!1.03e-19!49;UBERON:0010371!2.22e-19!73;UBERON:0003080!2.74e-19!40;UBERON:0010314!8.08e-19!92;UBERON:0002780!1.28e-18!39;UBERON:0001890!1.28e-18!39;UBERON:0006240!1.28e-18!39;UBERON:0004121!3.49e-18!95;UBERON:0000924!3.49e-18!95;UBERON:0006601!3.49e-18!95;UBERON:0002020!6.69e-16!34;UBERON:0003528!2.99e-13!29;UBERON:0002791!2.99e-13!29;UBERON:0001893!2.99e-13!29;UBERON:0002021!5.66e-10!10;UBERON:0000411!5.66e-10!10;UBERON:0001950!5.66e-10!10;UBERON:0000956!5.36e-09!21;UBERON:0001869!5.36e-09!21;UBERON:0000203!5.36e-09!21;UBERON:0002619!7.81e-08!17;UBERON:0002369!7.67e-07!7;UBERON:0006858!7.67e-07!7
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,1.98257,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,1.91365,0.713088,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,1.02135,0.534301,0.558142,0.960397,0.336199,0.589948,0.364821,0.951637,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,1.04848,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.11437,1.156,0.599223,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.439832,0.0610418,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.769162,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.706252,1.25097,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.540361,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,1.74506,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.131395
|tfbs_overrepresentation_jaspar=MA0003.1;0.476238,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;1.29371,MA0009.1;0.987341,MA0014.1;0.304529,MA0017.1;1.7816,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;4.07114,MA0042.1;3.99113,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.465302,MA0056.1;0,MA0057.1;0.149949,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,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;0.0477423,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;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.57901,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;0.682297,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.379391,MA0146.1;1.89206,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.00481054,MA0138.2;0.788113,MA0002.2;0.689262,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;1.24784,MA0150.1;0.520653,MA0151.1;0,MA0152.1;2.76297,MA0153.1;1.13945,MA0154.1;1.49271,MA0155.1;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;1.58527,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.397553,MA0163.1;0.163321,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;1.60558,MA0099.2;0.781628,MA0079.2;0.00144739,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:44, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:103800037..103800050,+p@chr12:103800037..103800050
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Mm9::chr18:25911757..25911774,+p@chr18:25911757..25911774
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Mm9::chr2:132607437..132607452,+p4@Chgb
Mm9::chr2:132611711..132611724,+p@chr2:132611711..132611724
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Mm9::chr2:132618170..132618205,+p@chr2:132618170..132618205
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Mm9::chr2:132618264..132618278,+p@chr2:132618264..132618278
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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)3.83e-0923
neuroblast (sensu Vertebrata)3.83e-0923
neuron3.98e-0833
neuronal stem cell3.98e-0833
neuroblast3.98e-0833
electrically signaling cell3.98e-0833

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.27e-2554
neurectoderm1.99e-2464
neural plate1.99e-2464
presumptive neural plate1.99e-2464
neural tube7.55e-2452
neural rod7.55e-2452
future spinal cord7.55e-2452
neural keel7.55e-2452
central nervous system3.90e-2373
nervous system7.06e-2275
brain6.03e-2147
future brain6.03e-2147
regional part of brain2.78e-2046
pre-chordal neural plate1.03e-1949
ecto-epithelium2.22e-1973
anterior neural tube2.74e-1940
structure with developmental contribution from neural crest8.08e-1992
regional part of forebrain1.28e-1839
forebrain1.28e-1839
future forebrain1.28e-1839
ectoderm-derived structure3.49e-1895
ectoderm3.49e-1895
presumptive ectoderm3.49e-1895
gray matter6.69e-1634
brain grey matter2.99e-1329
regional part of telencephalon2.99e-1329
telencephalon2.99e-1329
occipital lobe5.66e-1010
visual cortex5.66e-1010
neocortex5.66e-1010
cerebral cortex5.36e-0921
cerebral hemisphere5.36e-0921
pallium5.36e-0921
regional part of cerebral cortex7.81e-0817
adrenal gland7.67e-077
adrenal/interrenal gland7.67e-077


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)
MA0003.10.476238
MA0004.10.536396
MA0006.10.359699
MA0007.11.29371
MA0009.10.987341
MA0014.10.304529
MA0017.11.7816
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
MA0041.14.07114
MA0042.13.99113
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.465302
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
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
MA0073.10.0477423
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.57901
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
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.11.89206
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.00481054
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.21.24784
MA0150.10.520653
MA0151.10
MA0152.12.76297
MA0153.11.13945
MA0154.11.49271
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.11.58527
MA0160.10.556423
MA0161.10
MA0162.10.397553
MA0163.10.163321
MA0164.10.658997
MA0080.20.393257
MA0018.21.60558
MA0099.20.781628
MA0079.20.00144739
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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