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MCL coexpression mm9:664: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0001017!2.72e-31!73;UBERON:0001016!6.51e-31!75;UBERON:0004121!7.02e-28!95;UBERON:0000924!7.02e-28!95;UBERON:0006601!7.02e-28!95;UBERON:0000073!6.20e-25!54;UBERON:0001049!3.07e-23!52;UBERON:0005068!3.07e-23!52;UBERON:0006241!3.07e-23!52;UBERON:0007135!3.07e-23!52;UBERON:0002346!3.65e-23!64;UBERON:0003075!3.65e-23!64;UBERON:0007284!3.65e-23!64;UBERON:0010371!2.32e-22!73;UBERON:0000955!5.64e-19!47;UBERON:0006238!5.64e-19!47;UBERON:0002616!3.12e-18!46;UBERON:0010314!5.61e-18!92;UBERON:0002020!7.51e-17!34;UBERON:0003080!2.61e-13!40;UBERON:0003528!5.54e-13!29;UBERON:0002791!5.54e-13!29;UBERON:0001893!5.54e-13!29;UBERON:0003056!1.62e-12!49;UBERON:0002780!1.71e-12!39;UBERON:0001890!1.71e-12!39;UBERON:0006240!1.71e-12!39;UBERON:0003076!8.82e-12!12;UBERON:0003057!8.82e-12!12;UBERON:0002619!9.95e-11!17;UBERON:0002021!6.21e-10!10;UBERON:0000411!6.21e-10!10;UBERON:0001950!6.21e-10!10;UBERON:0000956!4.45e-09!21;UBERON:0001869!4.45e-09!21;UBERON:0000203!4.45e-09!21;UBERON:0004111!3.58e-07!122;UBERON:0004733!7.48e-07!6;UBERON:0004732!7.48e-07!6;UBERON:0002028!7.48e-07!6;UBERON:0007277!7.48e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.750994,0.269904,0.878892,0.52369,0.342839,1.08973,1.15922,0.732132,0.208174,0.385334,1.06556,0.106288,1.11437,0.555819,0,0.619876,0.170475,1.60971,0.387499,0.238546,0.281622,0.436294,0.520732,0.758244,0.4628,0.630402,0.361771,0.213277,0.500344,1.648,0.717576,0.168723,0.965283,0.556756,0.075793,0.486454,0.411296,0.445168,0.123934,0.173534,0.353696,1.53671,0.191571,0.557517,0.319944,0.543674,0.376103,0.401883,0.215702,0.603113,1.22385,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.0851299,1.12465,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.355763,0.0307733,0.905636,0.0810502,0.258161,0.270351,0.532872,0.681539,0.679143,0.724739,0.636582,0.495545,0.333618,0.792744,0.123451,0.143445,0.500771,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.340672,0.732731,0.543917,0.0534645,0.943642,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.67437,0.781068,0.840348,0.243062,0.390066,1.0825,0.172131,0.337757,0.333247,0.621127,0.158673,0.910937,0.572279,1.17341,0.532013,1.13603,0.685116,0.433317,0.723425,2.29674,0.183744,0.821997,0.323373,0.976125,2.99438,1.10385,3.19188,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.93276,0.546641,1.84176,0.302077,0.527071,1.31443,0.765699,0.857198,0.133365,0.455644,0.93735,0.488969,0.57908,0.290467,0.299755,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.160658,1.86958,0.935682
|tfbs_overrepresentation_jaspar=MA0003.1;0.570495,MA0004.1;0.330313,MA0006.1;1.04465,MA0007.1;0.850001,MA0009.1;0.743257,MA0014.1;0.270116,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;2.03691,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;3.40691,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.0494654,MA0056.1;0,MA0057.1;0.181039,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.12537,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.0500842,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.00168399,MA0074.1;0.419185,MA0076.1;0.223625,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.760108,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;1.22895,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;1.47462,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.619698,MA0105.1;0.556739,MA0106.1;0.509454,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.446898,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;0.265536,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;1.14144,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.88666,MA0145.1;0.903527,MA0146.1;0.775515,MA0147.1;0.925698,MA0148.1;0.912216,MA0149.1;0.269772,MA0062.2;0.0791588,MA0035.2;0.412747,MA0039.2;0.143896,MA0138.2;0.555696,MA0002.2;1.69388,MA0137.2;0.652494,MA0104.2;0.369356,MA0047.2;0.46201,MA0112.2;0.57262,MA0065.2;0.574339,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.0529077,MA0155.1;0.99367,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;2.18339,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.609924,MA0163.1;1.8528,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;0.0743239,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;0.455671,MA0442.1;0
}}

Latest revision as of 15:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:16660281..16660292,+p1@Ntsr2
Mm9::chr14:19725890..19725934,-p3@Ube2e2
Mm9::chr16:45724884..45724895,-p5@Tagln3
Mm9::chr18:15562013..15562040,-p@chr18:15562013..15562040
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Mm9::chr1:137064115..137064131,-p1@Gpr37l1
Mm9::chr1:137064144..137064164,-p2@Gpr37l1
Mm9::chr1:137064183..137064206,-p3@Gpr37l1
Mm9::chr3:90345180..90345198,+p9@S100a16
Mm9::chr5:36100600..36100615,+p4@Ablim2
Mm9::chr6:115202081..115202090,-p5@Timp4
Mm9::chr6:85283406..85283435,-p1@Sfxn5


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
ectodermal cell3.06e-1344
neurectodermal cell3.06e-1344
neural cell1.33e-1243
non-terminally differentiated cell8.09e-1049
neuron1.00e-0733
neuronal stem cell1.00e-0733
neuroblast1.00e-0733
electrically signaling cell1.00e-0733
oligodendrocyte precursor cell1.51e-078

Uber Anatomy
Ontology termp-valuen
central nervous system2.72e-3173
nervous system6.51e-3175
ectoderm-derived structure7.02e-2895
ectoderm7.02e-2895
presumptive ectoderm7.02e-2895
regional part of nervous system6.20e-2554
neural tube3.07e-2352
neural rod3.07e-2352
future spinal cord3.07e-2352
neural keel3.07e-2352
neurectoderm3.65e-2364
neural plate3.65e-2364
presumptive neural plate3.65e-2364
ecto-epithelium2.32e-2273
brain5.64e-1947
future brain5.64e-1947
regional part of brain3.12e-1846
structure with developmental contribution from neural crest5.61e-1892
gray matter7.51e-1734
anterior neural tube2.61e-1340
brain grey matter5.54e-1329
regional part of telencephalon5.54e-1329
telencephalon5.54e-1329
pre-chordal neural plate1.62e-1249
regional part of forebrain1.71e-1239
forebrain1.71e-1239
future forebrain1.71e-1239
posterior neural tube8.82e-1212
chordal neural plate8.82e-1212
regional part of cerebral cortex9.95e-1117
occipital lobe6.21e-1010
visual cortex6.21e-1010
neocortex6.21e-1010
cerebral cortex4.45e-0921
cerebral hemisphere4.45e-0921
pallium4.45e-0921
anatomical conduit3.58e-07122
segmental subdivision of hindbrain7.48e-076
segmental subdivision of nervous system7.48e-076
hindbrain7.48e-076
presumptive hindbrain7.48e-076


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)
MA0003.10.570495
MA0004.10.330313
MA0006.11.04465
MA0007.10.850001
MA0009.10.743257
MA0014.10.270116
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.12.03691
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.13.40691
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.0494654
MA0056.10
MA0057.10.181039
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.0500842
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.00168399
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.11.22895
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.11.47462
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.619698
MA0105.10.556739
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.446898
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.11.14144
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.88666
MA0145.10.903527
MA0146.10.775515
MA0147.10.925698
MA0148.10.912216
MA0149.10.269772
MA0062.20.0791588
MA0035.20.412747
MA0039.20.143896
MA0138.20.555696
MA0002.21.69388
MA0137.20.652494
MA0104.20.369356
MA0047.20.46201
MA0112.20.57262
MA0065.20.574339
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.0529077
MA0155.10.99367
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.12.18339
MA0160.10.347545
MA0161.10
MA0162.10.609924
MA0163.11.8528
MA0164.10.437937
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.20.0743239
MA0102.21.45844
MA0258.10.135621
MA0259.10.455671
MA0442.10
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