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MCL coexpression mm9:3187: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004119!1.87e-08!118;UBERON:0000925!1.87e-08!118;UBERON:0006595!1.87e-08!118;UBERON:0009569!2.02e-08!66;UBERON:0001007!5.12e-08!116;UBERON:0001555!5.12e-08!116;UBERON:0007026!5.12e-08!116;UBERON:0000481!8.32e-08!230;UBERON:0000922!1.36e-07!320;UBERON:0004921!1.54e-07!114;UBERON:0005409!1.64e-07!47;UBERON:0005423!2.83e-07!304
|ontology_enrichment_uberon=UBERON:0004119!1.87e-08!118;UBERON:0000925!1.87e-08!118;UBERON:0006595!1.87e-08!118;UBERON:0009569!2.02e-08!66;UBERON:0001007!5.12e-08!116;UBERON:0001555!5.12e-08!116;UBERON:0007026!5.12e-08!116;UBERON:0000481!8.32e-08!230;UBERON:0000922!1.36e-07!320;UBERON:0004921!1.54e-07!114;UBERON:0005409!1.64e-07!47;UBERON:0005423!2.83e-07!304
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.99159,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,1.05896,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,1.16164,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.99159,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,1.05896,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,1.16164,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
|tfbs_overrepresentation_jaspar=MA0003.1;0.0699972,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.133574,MA0017.1;0.635031,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;1.69964,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;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;1.33581,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;0.00834468,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;0.27999,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;1.70277,MA0103.1;0.647985,MA0105.1;1.04599,MA0106.1;1.01755,MA0107.1;2.61846,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;1.3296,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,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;0.151124,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.0481552,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;1.44603,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.166722,MA0163.1;0.477233,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.00937321,MA0102.2;2.01714,MA0258.1;1.29343,MA0259.1;0.543506,MA0442.1;0
}}
}}

Revision as of 15:59, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:34723708..34723728,+p@chr19:34723708..34723728
+
Mm9::chr7:29678757..29678782,-p@chr7:29678757..29678782
-
Mm9::chr9:80129298..80129306,+p@chr9:80129298..80129306
+


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:0051015actin filament binding0.000275044175098539
GO:0010324membrane invagination0.00259839869767005
GO:0006897endocytosis0.00259839869767005
GO:0015629actin cytoskeleton0.00259839869767005
GO:0048549positive regulation of pinocytosis0.00259839869767005
GO:0031143pseudopodium0.00259839869767005
GO:0048548regulation of pinocytosis0.00259839869767005
GO:0016044membrane organization and biogenesis0.00322889017312741
GO:0003779actin binding0.00322889017312741
GO:0006907pinocytosis0.00503803742470515
GO:0008092cytoskeletal protein binding0.00503803742470515
GO:0042995cell projection0.00548643371740944
GO:0014047glutamate secretion0.00559609110104334
GO:0016192vesicle-mediated transport0.00570873261979886
GO:0007010cytoskeleton organization and biogenesis0.00662238609130374
GO:0044430cytoskeletal part0.00840454279614965
GO:0051017actin filament bundle formation0.0136341191362705
GO:0051272positive regulation of cell motility0.0136341191362705
GO:0040017positive regulation of locomotion0.0136341191362705
GO:0030863cortical cytoskeleton0.0136341191362705
GO:0051271negative regulation of cell motility0.0136341191362705
GO:0007416synaptogenesis0.0136341191362705
GO:0040013negative regulation of locomotion0.0136341191362705
GO:0001725stress fiber0.0136341191362705
GO:0032432actin filament bundle0.0136341191362705
GO:0005856cytoskeleton0.0136341191362705
GO:0045807positive regulation of endocytosis0.0136341191362705
GO:0048167regulation of synaptic plasticity0.0136341191362705
GO:0042491auditory receptor cell differentiation0.0139363355499235
GO:0050803regulation of synapse structure and activity0.0139363355499235
GO:0060113inner ear receptor cell differentiation0.0158305667554699
GO:0044448cell cortex part0.0159034204314959
GO:0005905coated pit0.0166989144017156
GO:0042490mechanoreceptor differentiation0.0166989144017156
GO:0051050positive regulation of transport0.0166989144017156
GO:0006996organelle organization and biogenesis0.0166989144017156
GO:0030100regulation of endocytosis0.0166989144017156
GO:0048471perinuclear region of cytoplasm0.0167372300393083
GO:0016358dendrite development0.0181693584147975
GO:0007015actin filament organization0.0181693584147975
GO:0050808synapse organization and biogenesis0.0194966847562648
GO:0005938cell cortex0.0203284741709756
GO:0007269neurotransmitter secretion0.0213639918189818
GO:0042472inner ear morphogenesis0.0213639918189818
GO:0012506vesicle membrane0.0213639918189818
GO:0016459myosin complex0.0213639918189818
GO:0043025cell soma0.0213639918189818
GO:0043232intracellular non-membrane-bound organelle0.0213639918189818
GO:0043228non-membrane-bound organelle0.0213639918189818
GO:0051270regulation of cell motility0.0213639918189818
GO:0042471ear morphogenesis0.0213639918189818
GO:0030424axon0.0215198814487726
GO:0040012regulation of locomotion0.0215198814487726
GO:0045055regulated secretory pathway0.0215198814487726
GO:0048839inner ear development0.0231056131877493
GO:0043583ear development0.0246340710194913
GO:0051049regulation of transport0.026743587837089
GO:0003001generation of a signal involved in cell-cell signaling0.0270643873667891
GO:0001505regulation of neurotransmitter levels0.0270643873667891
GO:0007605sensory perception of sound0.0278199542996197
GO:0050954sensory perception of mechanical stimulus0.0288470957388275
GO:0043062extracellular structure organization and biogenesis0.0289654209217246
GO:0042803protein homodimerization activity0.0290799264774273
GO:0005516calmodulin binding0.0303210822497826
GO:0043005neuron projection0.0323577360247671
GO:0006810transport0.0382960575974159
GO:0044446intracellular organelle part0.0382960575974159
GO:0044422organelle part0.0382960575974159
GO:0016043cellular component organization and biogenesis0.0382960575974159
GO:0051234establishment of localization0.0382960575974159
GO:0030036actin cytoskeleton organization and biogenesis0.0392863886657246
GO:0030029actin filament-based process0.0414953798889983
GO:0042802identical protein binding0.0426550268608075
GO:0045045secretory pathway0.0428090017683298
GO:0007423sensory organ development0.0440229525732857
GO:0006605protein targeting0.0440229525732857
GO:0051179localization0.0440229525732857
GO:0007268synaptic transmission0.0440229525732857
GO:0031988membrane-bound vesicle0.0440229525732857
GO:0031175neurite development0.0440229525732857
GO:0046983protein dimerization activity0.0440229525732857
GO:0048598embryonic morphogenesis0.0440229525732857
GO:0007626locomotory behavior0.0440229525732857
GO:0032940secretion by cell0.0443553457870037
GO:0048666neuron development0.0463715920723049
GO:0019226transmission of nerve impulse0.0472949444162742



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.87e-08118
endoderm1.87e-08118
presumptive endoderm1.87e-08118
subdivision of trunk2.02e-0866
digestive system5.12e-08116
digestive tract5.12e-08116
primitive gut5.12e-08116
multi-tissue structure8.32e-08230
embryo1.36e-07320
subdivision of digestive tract1.54e-07114
gastrointestinal system1.64e-0747
developing anatomical structure2.83e-07304


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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.133574
MA0017.10.635031
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
MA0041.11.69964
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
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.11.33581
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.11.70277
MA0103.10.647985
MA0105.11.04599
MA0106.11.01755
MA0107.12.61846
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.11.3296
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
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
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.0481552
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.21.44603
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.00937321
MA0102.22.01714
MA0258.11.29343
MA0259.10.543506
MA0442.10
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