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MCL coexpression mm9:1330: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.75e-37!73;UBERON:0001016!3.55e-37!75;UBERON:0004121!9.72e-34!95;UBERON:0000924!9.72e-34!95;UBERON:0006601!9.72e-34!95;UBERON:0002346!6.73e-30!64;UBERON:0003075!6.73e-30!64;UBERON:0007284!6.73e-30!64;UBERON:0000073!3.79e-28!54;UBERON:0010371!6.74e-27!73;UBERON:0001049!7.53e-27!52;UBERON:0005068!7.53e-27!52;UBERON:0006241!7.53e-27!52;UBERON:0007135!7.53e-27!52;UBERON:0000955!8.75e-24!47;UBERON:0006238!8.75e-24!47;UBERON:0002616!3.67e-23!46;UBERON:0003056!4.71e-21!49;UBERON:0010314!1.39e-19!92;UBERON:0002020!1.92e-19!34;UBERON:0003080!6.14e-19!40;UBERON:0002780!2.34e-18!39;UBERON:0001890!2.34e-18!39;UBERON:0006240!2.34e-18!39;UBERON:0003528!9.07e-17!29;UBERON:0002791!9.07e-17!29;UBERON:0001893!9.07e-17!29;UBERON:0000956!1.51e-12!21;UBERON:0001869!1.51e-12!21;UBERON:0000203!1.51e-12!21;UBERON:0002619!1.14e-10!17;UBERON:0003076!1.83e-08!12;UBERON:0003057!1.83e-08!12;UBERON:0002021!3.60e-07!10;UBERON:0000411!3.60e-07!10;UBERON:0001950!3.60e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,1.32583,0.916672,0.550971,0.645383,0.247459,0.257202,0.0835344,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,1.72037,1.58083,0.345236,1.19059,0.686615,0.63639,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.204204,0.364821,2.34972,0.326478,0.629145,0.303703,1.37841,0.907317,0.56353,0.0995018,0.366415,0.161543,0.524258,0.77511,0.589246,0.594982,1.02809,0.839084,0.714419,3.00063,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,1.36208,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,0.19692,0.589776,1.80128,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,0.0539203,0.220054,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.9304,0.2995,1.40549,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,1.67199,0.971067,0.831964,0.564002,1.83209,2.10357,0.503174,0.348692,0.540361,0.0987301,1.10596,1.42796,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.30995
|tfbs_overrepresentation_jaspar=MA0003.1;0.476238,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.12867,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;2.13766,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;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.212634,MA0056.1;0,MA0057.1;1.43735,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;1.38604,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;9.20738,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.562383,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;1.74419,MA0089.1;0,MA0090.1;1.25093,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;0.199622,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;1.16221,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;0.119202,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;0.181031,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;1.64036,MA0112.2;0.37938,MA0065.2;0.763394,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;1.08528,MA0163.1;0.372305,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;7.21796,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:73509649..73509660,-p5@Rtn1
Mm9::chr15:88809388..88809422,-p4@Mlc1
Mm9::chr7:31076790..31076798,+p5@Clip3
Mm9::chr7:31076822..31076826,+p7@Clip3
Mm9::chr7:31076935..31076958,+p2@Clip3
Mm9::chr7:31076960..31076987,+p4@Clip3


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:0000299integral to membrane of membrane fraction0.0394336841875496



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>

Uber Anatomy
Ontology termp-valuen
central nervous system2.75e-3773
nervous system3.55e-3775
ectoderm-derived structure9.72e-3495
ectoderm9.72e-3495
presumptive ectoderm9.72e-3495
neurectoderm6.73e-3064
neural plate6.73e-3064
presumptive neural plate6.73e-3064
regional part of nervous system3.79e-2854
ecto-epithelium6.74e-2773
neural tube7.53e-2752
neural rod7.53e-2752
future spinal cord7.53e-2752
neural keel7.53e-2752
brain8.75e-2447
future brain8.75e-2447
regional part of brain3.67e-2346
pre-chordal neural plate4.71e-2149
structure with developmental contribution from neural crest1.39e-1992
gray matter1.92e-1934
anterior neural tube6.14e-1940
regional part of forebrain2.34e-1839
forebrain2.34e-1839
future forebrain2.34e-1839
brain grey matter9.07e-1729
regional part of telencephalon9.07e-1729
telencephalon9.07e-1729
cerebral cortex1.51e-1221
cerebral hemisphere1.51e-1221
pallium1.51e-1221
regional part of cerebral cortex1.14e-1017
posterior neural tube1.83e-0812
chordal neural plate1.83e-0812
occipital lobe3.60e-0710
visual cortex3.60e-0710
neocortex3.60e-0710


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
MA0007.10.52077
MA0009.10.987341
MA0014.10.12867
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.12.13766
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.11.43735
MA0058.10.436487
MA0059.10.449345
MA0060.11.38604
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.19.20738
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.562383
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.11.74419
MA0089.10
MA0090.11.25093
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.11.16221
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
MA0145.10.119202
MA0146.11.89206
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.181031
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.21.64036
MA0112.20.37938
MA0065.20.763394
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.10.372305
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.27.21796
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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