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MCL coexpression mm9:2665: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!6.95e-23!73;UBERON:0001016!1.00e-21!75;UBERON:0000073!1.68e-21!54;UBERON:0010314!5.16e-21!92;UBERON:0004121!9.04e-21!95;UBERON:0000924!9.04e-21!95;UBERON:0006601!9.04e-21!95;UBERON:0002346!9.44e-21!64;UBERON:0003075!9.44e-21!64;UBERON:0007284!9.44e-21!64;UBERON:0001049!2.65e-20!52;UBERON:0005068!2.65e-20!52;UBERON:0006241!2.65e-20!52;UBERON:0007135!2.65e-20!52;UBERON:0010371!1.07e-18!73;UBERON:0000955!1.02e-17!47;UBERON:0006238!1.02e-17!47;UBERON:0002616!4.67e-17!46;UBERON:0003056!3.10e-15!49;UBERON:0002020!5.53e-15!34;UBERON:0003080!1.91e-14!40;UBERON:0002780!6.42e-14!39;UBERON:0001890!6.42e-14!39;UBERON:0006240!6.42e-14!39;UBERON:0003528!1.78e-12!29;UBERON:0002791!1.78e-12!29;UBERON:0001893!1.78e-12!29;UBERON:0000956!1.61e-08!21;UBERON:0001869!1.61e-08!21;UBERON:0000203!1.61e-08!21;UBERON:0004111!5.36e-08!122;UBERON:0002619!5.67e-08!17;UBERON:0000468!6.79e-08!333;UBERON:0002021!8.38e-08!10;UBERON:0000411!8.38e-08!10;UBERON:0001950!8.38e-08!10;UBERON:0000025!2.13e-07!114
|ontology_enrichment_uberon=UBERON:0001017!6.95e-23!73;UBERON:0001016!1.00e-21!75;UBERON:0000073!1.68e-21!54;UBERON:0010314!5.16e-21!92;UBERON:0004121!9.04e-21!95;UBERON:0000924!9.04e-21!95;UBERON:0006601!9.04e-21!95;UBERON:0002346!9.44e-21!64;UBERON:0003075!9.44e-21!64;UBERON:0007284!9.44e-21!64;UBERON:0001049!2.65e-20!52;UBERON:0005068!2.65e-20!52;UBERON:0006241!2.65e-20!52;UBERON:0007135!2.65e-20!52;UBERON:0010371!1.07e-18!73;UBERON:0000955!1.02e-17!47;UBERON:0006238!1.02e-17!47;UBERON:0002616!4.67e-17!46;UBERON:0003056!3.10e-15!49;UBERON:0002020!5.53e-15!34;UBERON:0003080!1.91e-14!40;UBERON:0002780!6.42e-14!39;UBERON:0001890!6.42e-14!39;UBERON:0006240!6.42e-14!39;UBERON:0003528!1.78e-12!29;UBERON:0002791!1.78e-12!29;UBERON:0001893!1.78e-12!29;UBERON:0000956!1.61e-08!21;UBERON:0001869!1.61e-08!21;UBERON:0000203!1.61e-08!21;UBERON:0004111!5.36e-08!122;UBERON:0002619!5.67e-08!17;UBERON:0000468!6.79e-08!333;UBERON:0002021!8.38e-08!10;UBERON:0000411!8.38e-08!10;UBERON:0001950!8.38e-08!10;UBERON:0000025!2.13e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,1.40558,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,1.83166,1.05896,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,2.17757,0.562367,0.904334,0.135528
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,1.40558,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,1.83166,1.05896,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,2.17757,0.562367,0.904334,0.135528
|tfbs_overrepresentation_jaspar=MA0003.1;0.245953,MA0004.1;0.801718,MA0006.1;1.46714,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.825079,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;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;2.89013,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.896032,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,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;2.11706,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;1.40099,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;1.51475,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;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,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;1.16863,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;1.44443,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;3.25387,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;0.292912,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;0.499274,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.890297,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}
}}

Revision as of 15:12, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:3763898..3763913,-p2@Osbp2
Mm9::chr1:174259448..174259457,-p2@Kcnj9
Mm9::chr7:16715105..16715194,+p2@Slc8a2


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:0015467G-protein activated inward rectifier potassium channel activity0.0136734947147237
GO:0005432calcium:sodium antiporter activity0.0136734947147237
GO:0015368calcium:cation antiporter activity0.0136734947147237
GO:0030001metal ion transport0.0136734947147237
GO:0008324cation transmembrane transporter activity0.0136734947147237
GO:0006812cation transport0.0136734947147237
GO:0006810transport0.0136734947147237
GO:0015491cation:cation antiporter activity0.0136734947147237
GO:0051234establishment of localization0.0136734947147237
GO:0005242inward rectifier potassium channel activity0.0137961185645107
GO:0051179localization0.0147758858641532
GO:0015298solute:cation antiporter activity0.0147758858641532
GO:0015075ion transmembrane transporter activity0.0147758858641532
GO:0015300solute:solute antiporter activity0.0147758858641532
GO:0006811ion transport0.0167436859806347
GO:0022891substrate-specific transmembrane transporter activity0.0167436859806347
GO:0005887integral to plasma membrane0.018698688541823
GO:0031226intrinsic to plasma membrane0.018698688541823
GO:0022857transmembrane transporter activity0.018698688541823
GO:0015297antiporter activity0.018698688541823
GO:0022892substrate-specific transporter activity0.0203986913227776
GO:0006869lipid transport0.033037647344639
GO:0005249voltage-gated potassium channel activity0.0354271221175463
GO:0006816calcium ion transport0.0404093888106348
GO:0005516calmodulin binding0.0404093888106348
GO:0030955potassium ion binding0.0404093888106348
GO:0044459plasma membrane part0.0404093888106348
GO:0022843voltage-gated cation channel activity0.0405974668135945
GO:0005267potassium channel activity0.0412114347041476
GO:0015674di-, tri-valent inorganic cation transport0.0434034188796974
GO:0008202steroid metabolic process0.0441970131025135
GO:0006813potassium ion transport0.0467582099443818
GO:0005244voltage-gated ion channel activity0.0479976399891441
GO:0022832voltage-gated channel activity0.0479976399891441
GO:0015291secondary active transmembrane transporter activity0.0480191429561284
GO:0031420alkali metal ion binding0.0480191429561284
GO:0005886plasma membrane0.0486374730126832



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)2.56e-0923
neuroblast (sensu Vertebrata)2.56e-0923
neuron9.53e-0933
neuronal stem cell9.53e-0933
neuroblast9.53e-0933
electrically signaling cell9.53e-0933
ectodermal cell2.20e-0744
neurectodermal cell2.20e-0744
neural cell2.67e-0743

Uber Anatomy
Ontology termp-valuen
central nervous system6.95e-2373
nervous system1.00e-2175
regional part of nervous system1.68e-2154
structure with developmental contribution from neural crest5.16e-2192
ectoderm-derived structure9.04e-2195
ectoderm9.04e-2195
presumptive ectoderm9.04e-2195
neurectoderm9.44e-2164
neural plate9.44e-2164
presumptive neural plate9.44e-2164
neural tube2.65e-2052
neural rod2.65e-2052
future spinal cord2.65e-2052
neural keel2.65e-2052
ecto-epithelium1.07e-1873
brain1.02e-1747
future brain1.02e-1747
regional part of brain4.67e-1746
pre-chordal neural plate3.10e-1549
gray matter5.53e-1534
anterior neural tube1.91e-1440
regional part of forebrain6.42e-1439
forebrain6.42e-1439
future forebrain6.42e-1439
brain grey matter1.78e-1229
regional part of telencephalon1.78e-1229
telencephalon1.78e-1229
cerebral cortex1.61e-0821
cerebral hemisphere1.61e-0821
pallium1.61e-0821
anatomical conduit5.36e-08122
regional part of cerebral cortex5.67e-0817
multi-cellular organism6.79e-08333
occipital lobe8.38e-0810
visual cortex8.38e-0810
neocortex8.38e-0810
tube2.13e-07114


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)
MA0003.10.245953
MA0004.10.801718
MA0006.11.46714
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
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
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.12.89013
MA0055.10.190475
MA0056.10
MA0057.10.896032
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
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
MA0073.12.11706
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.11.40099
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.11.51475
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
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
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
MA0139.11.16863
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.11.44443
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.23.25387
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
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
MA0162.10.499274
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.890297
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:2665&oldid=2576060"