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MCL coexpression mm9:608: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002346!7.67e-27!64;UBERON:0003075!7.67e-27!64;UBERON:0007284!7.67e-27!64;UBERON:0000073!2.61e-26!54;UBERON:0001016!8.98e-26!75;UBERON:0001017!3.28e-25!73;UBERON:0001049!1.25e-24!52;UBERON:0005068!1.25e-24!52;UBERON:0006241!1.25e-24!52;UBERON:0007135!1.25e-24!52;UBERON:0004121!8.03e-23!95;UBERON:0000924!8.03e-23!95;UBERON:0006601!8.03e-23!95;UBERON:0010371!2.18e-22!73;UBERON:0000955!3.13e-21!47;UBERON:0006238!3.13e-21!47;UBERON:0003056!3.51e-21!49;UBERON:0002616!2.01e-20!46;UBERON:0010314!2.21e-19!92;UBERON:0003080!4.40e-19!40;UBERON:0002780!3.35e-18!39;UBERON:0001890!3.35e-18!39;UBERON:0006240!3.35e-18!39;UBERON:0002020!2.15e-14!34;UBERON:0003528!2.04e-11!29;UBERON:0002791!2.04e-11!29;UBERON:0001893!2.04e-11!29;UBERON:0002021!3.14e-08!10;UBERON:0000411!3.14e-08!10;UBERON:0001950!3.14e-08!10;UBERON:0001894!3.31e-08!10;UBERON:0006222!3.31e-08!10;UBERON:0002420!5.08e-07!8;UBERON:0007245!5.08e-07!8;UBERON:0010009!5.08e-07!8;UBERON:0010011!5.08e-07!8;UBERON:0000454!5.08e-07!8;UBERON:0002619!5.56e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.267173,0.409645,1.27243,0.818969,0.1565,0.847245,1.02601,0.0908011,0.658686,0.336879,0.357058,0.385627,1.05446,0.407615,0.169024,0,0.587245,0.459418,0.279039,0.602977,0.215242,0.235703,0.406794,0.471175,0.701128,1.10486,0.0768517,0.334131,0.191143,0.438367,0.860721,0.683831,0.891038,0.866746,0.169391,0.406983,0.438297,0.382372,0.126724,0.347926,0.153518,0.326286,0.407596,0.508662,0.0677519,0.797213,0.512146,0.34807,0.337012,0.19345,0.570705,0.457464,1.59242,0.82076,0.837732,0.414119,0.200484,0.37415,1.89628,0.412262,0.664611,0.46618,0.104381,0.560059,0.424276,1.45782,0.970969,1.3158,0.660133,1.17005,1.21364,0.0945081,0.102623,0.870406,0.0680008,0.222652,0.233965,0.50152,0.648171,1.171,0.651601,0.60374,0.464847,0.0868537,0.758319,0.0325399,0.237482,0.43877,0.516731,1.47691,1.03946,0.763136,0.696137,0.940863,0.12392,0.11194,1.04257,0.698838,0.512384,1.04626,0.862562,0.683562,0.803823,0.571268,0.57027,1.56637,0.627019,0.344504,0.222586,0.216685,0.723377,0.805555,0.219561,0.361667,1.04639,0.152197,0.136172,0.826326,0.58848,0.43155,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,1.64843,0.969481,0.95011,0.787341,0.296885,0.940498,0.426575,1.06766,0.0212043,1.38011,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,1.38746,2.12778,0.201988,0.0825345,0.822286,0.747142,0.425729,0.901933,0.458393,0.178202,1.34621,2.11874,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.436256,0.999079,0.365903
|tfbs_overrepresentation_jaspar=MA0003.1;0.00810215,MA0004.1;0.303605,MA0006.1;0.16569,MA0007.1;0.790701,MA0009.1;0.709264,MA0014.1;0.109847,MA0017.1;0.186015,MA0019.1;0.535691,MA0024.1;0.667197,MA0025.1;0.936082,MA0027.1;2.34178,MA0028.1;0.516099,MA0029.1;0.64639,MA0030.1;0.65267,MA0031.1;0.618697,MA0038.1;0.432665,MA0040.1;0.721328,MA0041.1;1.93974,MA0042.1;0.648006,MA0043.1;0.802848,MA0046.1;0.743934,MA0048.1;0.680396,MA0050.1;0.337476,MA0051.1;0.440863,MA0052.1;0.729105,MA0055.1;0.226387,MA0056.1;0,MA0057.1;0.350222,MA0058.1;0.635024,MA0059.1;0.233271,MA0060.1;0.108526,MA0061.1;0.805149,MA0063.1;0,MA0066.1;0.422624,MA0067.1;1.04514,MA0068.1;0.361347,MA0069.1;0.729433,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;8.11254e-06,MA0074.1;0.390075,MA0076.1;0.200996,MA0077.1;0.691048,MA0078.1;0.471303,MA0081.1;0.702944,MA0083.1;0.802078,MA0084.1;1.3693,MA0087.1;0.760279,MA0088.1;0.742898,MA0089.1;0,MA0090.1;1.38006,MA0091.1;0.315003,MA0092.1;0.274547,MA0093.1;0.179936,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;0.675688,MA0103.1;0.566591,MA0105.1;0.846872,MA0106.1;0.478503,MA0107.1;1.05738,MA0108.2;0.557195,MA0109.1;0,MA0111.1;0.78079,MA0113.1;0.452439,MA0114.1;0.400482,MA0115.1;0.805567,MA0116.1;0.165534,MA0117.1;0.774259,MA0119.1;0.241106,MA0122.1;0.793507,MA0124.1;0.992825,MA0125.1;0.920215,MA0130.1;0,MA0131.1;0.531427,MA0132.1;0,MA0133.1;0,MA0135.1;0.838263,MA0136.1;0.408073,MA0139.1;0.297344,MA0140.1;0.379562,MA0141.1;0.210047,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;0.129525,MA0145.1;0.109043,MA0146.1;0.436286,MA0147.1;0.138228,MA0148.1;0.851609,MA0149.1;0.245177,MA0062.2;0.0662974,MA0035.2;0.998181,MA0039.2;0.0242909,MA0138.2;0.523978,MA0002.2;0.0901987,MA0137.2;0.207733,MA0104.2;0.099275,MA0047.2;0.431964,MA0112.2;0.494696,MA0065.2;0.4963,MA0150.1;0.790482,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;0.670722,MA0155.1;0.30272,MA0156.1;0.200311,MA0157.1;0.574484,MA0158.1;0,MA0159.1;0.145521,MA0160.1;0.320315,MA0161.1;0,MA0162.1;0.509255,MA0163.1;0.287849,MA0164.1;0.408402,MA0080.2;0.190316,MA0018.2;2.81315,MA0099.2;0.518072,MA0079.2;0.0229142,MA0102.2;1.42135,MA0258.1;0.756558,MA0259.1;0.130633,MA0442.1;0
}}

Latest revision as of 15:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:87578204..87578234,+p2@Bzrap1
Mm9::chr17:8717717..8717743,-p@chr17:8717717..8717743
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Mm9::chr1:79432827..79432840,-p@chr1:79432827..79432840
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Mm9::chr1:79432904..79432923,-p@chr1:79432904..79432923
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Mm9::chr1:79436578..79436589,-p3@Scg2
Mm9::chr1:79436590..79436610,-p1@Scg2
Mm9::chr1:79436614..79436655,-p2@Scg2
Mm9::chr3:154327125..154327176,+p1@4922501L14Rik
Mm9::chr3:65106677..65106687,-p3@uc008pkk.1
Mm9::chr8:71080916..71080951,-p@chr8:71080916..71080951
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Mm9::chrX:100551830..100551852,+p2@Chic1
Mm9::chrX:70656436..70656464,+p1@Zfp92


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)1.36e-0823
neuroblast (sensu Vertebrata)1.36e-0823
neuron1.43e-0833
neuronal stem cell1.43e-0833
neuroblast1.43e-0833
electrically signaling cell1.43e-0833
electrically responsive cell7.28e-0739
electrically active cell7.28e-0739

Uber Anatomy
Ontology termp-valuen
neurectoderm7.67e-2764
neural plate7.67e-2764
presumptive neural plate7.67e-2764
regional part of nervous system2.61e-2654
nervous system8.98e-2675
central nervous system3.28e-2573
neural tube1.25e-2452
neural rod1.25e-2452
future spinal cord1.25e-2452
neural keel1.25e-2452
ectoderm-derived structure8.03e-2395
ectoderm8.03e-2395
presumptive ectoderm8.03e-2395
ecto-epithelium2.18e-2273
brain3.13e-2147
future brain3.13e-2147
pre-chordal neural plate3.51e-2149
regional part of brain2.01e-2046
structure with developmental contribution from neural crest2.21e-1992
anterior neural tube4.40e-1940
regional part of forebrain3.35e-1839
forebrain3.35e-1839
future forebrain3.35e-1839
gray matter2.15e-1434
brain grey matter2.04e-1129
regional part of telencephalon2.04e-1129
telencephalon2.04e-1129
occipital lobe3.14e-0810
visual cortex3.14e-0810
neocortex3.14e-0810
diencephalon3.31e-0810
future diencephalon3.31e-0810
basal ganglion5.08e-078
nuclear complex of neuraxis5.08e-078
aggregate regional part of brain5.08e-078
collection of basal ganglia5.08e-078
cerebral subcortex5.08e-078
regional part of cerebral cortex5.56e-0717


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)
MA0003.10.00810215
MA0004.10.303605
MA0006.10.16569
MA0007.10.790701
MA0009.10.709264
MA0014.10.109847
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.516099
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.11.93974
MA0042.10.648006
MA0043.10.802848
MA0046.10.743934
MA0048.10.680396
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.226387
MA0056.10
MA0057.10.350222
MA0058.10.635024
MA0059.10.233271
MA0060.10.108526
MA0061.10.805149
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.361347
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.18.11254e-06
MA0074.10.390075
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.702944
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.742898
MA0089.10
MA0090.11.38006
MA0091.10.315003
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.675688
MA0103.10.566591
MA0105.10.846872
MA0106.10.478503
MA0107.11.05738
MA0108.20.557195
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.10.400482
MA0115.10.805567
MA0116.10.165534
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.297344
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.109043
MA0146.10.436286
MA0147.10.138228
MA0148.10.851609
MA0149.10.245177
MA0062.20.0662974
MA0035.20.998181
MA0039.20.0242909
MA0138.20.523978
MA0002.20.0901987
MA0137.20.207733
MA0104.20.099275
MA0047.20.431964
MA0112.20.494696
MA0065.20.4963
MA0150.10.790482
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.670722
MA0155.10.30272
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.320315
MA0161.10
MA0162.10.509255
MA0163.10.287849
MA0164.10.408402
MA0080.20.190316
MA0018.22.81315
MA0099.20.518072
MA0079.20.0229142
MA0102.21.42135
MA0258.10.756558
MA0259.10.130633
MA0442.10
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