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MCL coexpression mm9:2878: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003056!2.40e-18!49;UBERON:0002346!2.49e-18!64;UBERON:0003075!2.49e-18!64;UBERON:0007284!2.49e-18!64;UBERON:0010371!4.03e-17!73;UBERON:0001049!9.01e-16!52;UBERON:0005068!9.01e-16!52;UBERON:0006241!9.01e-16!52;UBERON:0007135!9.01e-16!52;UBERON:0003080!3.25e-15!40;UBERON:0000955!7.71e-15!47;UBERON:0006238!7.71e-15!47;UBERON:0000073!7.78e-15!54;UBERON:0002780!1.23e-14!39;UBERON:0001890!1.23e-14!39;UBERON:0006240!1.23e-14!39;UBERON:0002616!2.52e-14!46;UBERON:0001017!2.24e-13!73;UBERON:0004121!4.87e-13!95;UBERON:0000924!4.87e-13!95;UBERON:0006601!4.87e-13!95;UBERON:0010314!1.62e-12!92;UBERON:0001016!2.90e-12!75;UBERON:0002020!2.90e-11!34;UBERON:0003528!5.51e-10!29;UBERON:0002791!5.51e-10!29;UBERON:0001893!5.51e-10!29;UBERON:0000956!4.05e-08!21;UBERON:0001869!4.05e-08!21;UBERON:0000203!4.05e-08!21;UBERON:0000153!1.97e-07!43
|ontology_enrichment_uberon=UBERON:0003056!2.40e-18!49;UBERON:0002346!2.49e-18!64;UBERON:0003075!2.49e-18!64;UBERON:0007284!2.49e-18!64;UBERON:0010371!4.03e-17!73;UBERON:0001049!9.01e-16!52;UBERON:0005068!9.01e-16!52;UBERON:0006241!9.01e-16!52;UBERON:0007135!9.01e-16!52;UBERON:0003080!3.25e-15!40;UBERON:0000955!7.71e-15!47;UBERON:0006238!7.71e-15!47;UBERON:0000073!7.78e-15!54;UBERON:0002780!1.23e-14!39;UBERON:0001890!1.23e-14!39;UBERON:0006240!1.23e-14!39;UBERON:0002616!2.52e-14!46;UBERON:0001017!2.24e-13!73;UBERON:0004121!4.87e-13!95;UBERON:0000924!4.87e-13!95;UBERON:0006601!4.87e-13!95;UBERON:0010314!1.62e-12!92;UBERON:0001016!2.90e-12!75;UBERON:0002020!2.90e-11!34;UBERON:0003528!5.51e-10!29;UBERON:0002791!5.51e-10!29;UBERON:0001893!5.51e-10!29;UBERON:0000956!4.05e-08!21;UBERON:0001869!4.05e-08!21;UBERON:0000203!4.05e-08!21;UBERON:0000153!1.97e-07!43
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,1.17946,0.479531,1.91723,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,1.38557,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,1.55113,0.99159,0.825437,1.24901,1.40911,0.411696,0.608816,0.872889,0.563758,2.08624,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,1.47707,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,1.882,1.83166,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,5.79199,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,1.17262,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.833542
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,1.17946,0.479531,1.91723,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,1.38557,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,1.55113,0.99159,0.825437,1.24901,1.40911,0.411696,0.608816,0.872889,0.563758,2.08624,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,1.47707,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,1.882,1.83166,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,5.79199,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,1.17262,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.833542
|tfbs_overrepresentation_jaspar=MA0003.1;0.899234,MA0004.1;0.801718,MA0006.1;1.46714,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;5.84668,MA0017.1;1.5346,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;4.34959,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;1.25521,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.680038,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.766354,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;1.83298,MA0113.1;0.986839,MA0114.1;1.3296,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;1.70419,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;2.77996,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;8.52387,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.40695,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;1.44804,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.312898,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;1.53682,MA0163.1;2.84458,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;7.3104,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}
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Revision as of 15:31, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:91600731..91600748,+p2@Ssbp2
Mm9::chr13:91600750..91600793,+p1@Ssbp2
Mm9::chr4:102887944..102887994,-p3@Slc35d1


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:0003697single-stranded DNA binding0.0361584397085411
GO:0043566structure-specific DNA binding0.0433901276502493



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)7.71e-0723
neuroblast (sensu Vertebrata)7.71e-0723

Uber Anatomy
Ontology termp-valuen
pre-chordal neural plate2.40e-1849
neurectoderm2.49e-1864
neural plate2.49e-1864
presumptive neural plate2.49e-1864
ecto-epithelium4.03e-1773
neural tube9.01e-1652
neural rod9.01e-1652
future spinal cord9.01e-1652
neural keel9.01e-1652
anterior neural tube3.25e-1540
brain7.71e-1547
future brain7.71e-1547
regional part of nervous system7.78e-1554
regional part of forebrain1.23e-1439
forebrain1.23e-1439
future forebrain1.23e-1439
regional part of brain2.52e-1446
central nervous system2.24e-1373
ectoderm-derived structure4.87e-1395
ectoderm4.87e-1395
presumptive ectoderm4.87e-1395
structure with developmental contribution from neural crest1.62e-1292
nervous system2.90e-1275
gray matter2.90e-1134
brain grey matter5.51e-1029
regional part of telencephalon5.51e-1029
telencephalon5.51e-1029
cerebral cortex4.05e-0821
cerebral hemisphere4.05e-0821
pallium4.05e-0821
anterior region of body1.97e-0743


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)
MA0003.10.899234
MA0004.10.801718
MA0006.11.46714
MA0007.10.784593
MA0009.11.27673
MA0014.15.84668
MA0017.11.5346
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.14.34959
MA0058.10.690848
MA0059.10.705317
MA0060.11.25521
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.680038
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.11.83298
MA0113.10.986839
MA0114.11.3296
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.11.70419
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.12.77996
MA0147.10.556853
MA0148.10.820161
MA0149.18.52387
MA0062.20.412742
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.21.44804
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.11.53682
MA0163.12.84458
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.27.3104
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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