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MCL coexpression mm9:2739: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!8.13e-21!54;UBERON:0002346!1.36e-20!64;UBERON:0003075!1.36e-20!64;UBERON:0007284!1.36e-20!64;UBERON:0010371!2.38e-19!73;UBERON:0001017!2.47e-19!73;UBERON:0010314!3.09e-19!92;UBERON:0001049!3.69e-19!52;UBERON:0005068!3.69e-19!52;UBERON:0006241!3.69e-19!52;UBERON:0007135!3.69e-19!52;UBERON:0004121!1.09e-18!95;UBERON:0000924!1.09e-18!95;UBERON:0006601!1.09e-18!95;UBERON:0001016!6.01e-18!75;UBERON:0000955!2.17e-16!47;UBERON:0006238!2.17e-16!47;UBERON:0003056!5.70e-16!49;UBERON:0002616!8.73e-16!46;UBERON:0002020!5.98e-15!34;UBERON:0003080!1.26e-13!40;UBERON:0002780!4.71e-13!39;UBERON:0001890!4.71e-13!39;UBERON:0006240!4.71e-13!39;UBERON:0003528!3.63e-12!29;UBERON:0002791!3.63e-12!29;UBERON:0001893!3.63e-12!29;UBERON:0000025!8.24e-10!114;UBERON:0000468!1.32e-09!333;UBERON:0004111!4.74e-09!122;UBERON:0000956!4.53e-08!21;UBERON:0001869!4.53e-08!21;UBERON:0000203!4.53e-08!21;UBERON:0000922!2.00e-07!320;UBERON:0002021!2.57e-07!10;UBERON:0000411!2.57e-07!10;UBERON:0001950!2.57e-07!10;UBERON:0002619!3.03e-07!17
|ontology_enrichment_uberon=UBERON:0000073!8.13e-21!54;UBERON:0002346!1.36e-20!64;UBERON:0003075!1.36e-20!64;UBERON:0007284!1.36e-20!64;UBERON:0010371!2.38e-19!73;UBERON:0001017!2.47e-19!73;UBERON:0010314!3.09e-19!92;UBERON:0001049!3.69e-19!52;UBERON:0005068!3.69e-19!52;UBERON:0006241!3.69e-19!52;UBERON:0007135!3.69e-19!52;UBERON:0004121!1.09e-18!95;UBERON:0000924!1.09e-18!95;UBERON:0006601!1.09e-18!95;UBERON:0001016!6.01e-18!75;UBERON:0000955!2.17e-16!47;UBERON:0006238!2.17e-16!47;UBERON:0003056!5.70e-16!49;UBERON:0002616!8.73e-16!46;UBERON:0002020!5.98e-15!34;UBERON:0003080!1.26e-13!40;UBERON:0002780!4.71e-13!39;UBERON:0001890!4.71e-13!39;UBERON:0006240!4.71e-13!39;UBERON:0003528!3.63e-12!29;UBERON:0002791!3.63e-12!29;UBERON:0001893!3.63e-12!29;UBERON:0000025!8.24e-10!114;UBERON:0000468!1.32e-09!333;UBERON:0004111!4.74e-09!122;UBERON:0000956!4.53e-08!21;UBERON:0001869!4.53e-08!21;UBERON:0000203!4.53e-08!21;UBERON:0000922!2.00e-07!320;UBERON:0002021!2.57e-07!10;UBERON:0000411!2.57e-07!10;UBERON:0001950!2.57e-07!10;UBERON:0002619!3.03e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,1.38481,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,1.19585,0.284975,1.44925,0.416814,1.03818,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.62246,0.568545,0.99201,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,2.50519,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,2.14021,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.721422,1.39822,1.28513,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,1.38481,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,1.19585,0.284975,1.44925,0.416814,1.03818,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.62246,0.568545,0.99201,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,2.50519,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,2.14021,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.721422,1.39822,1.28513,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
|tfbs_overrepresentation_jaspar=MA0003.1;0.526413,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;1.33691,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;0.932001,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.557057,MA0056.1;0,MA0057.1;0.896032,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;6.80885,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;0.439282,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;3.04822,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;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;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;0.46063,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.71803,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;1.39671,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.499274,MA0163.1;0.927936,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;1.4764,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}
}}

Revision as of 15:19, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:94335638..94335661,-p6@Cacna1g
Mm9::chr11:94335672..94335699,-p1@Cacna1g
Mm9::chr16:91729681..91729719,+p4@Itsn1


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:0005891voltage-gated calcium channel complex0.0488632521975829
GO:0005509calcium ion binding0.0488632521975829
GO:0005245voltage-gated calcium channel activity0.0488632521975829
GO:0030027lamellipodium0.0488632521975829
GO:0019717synaptosome0.0488632521975829
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0488632521975829
GO:0035023regulation of Rho protein signal transduction0.0488632521975829
GO:0044459plasma membrane part0.0488632521975829
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0488632521975829
GO:0005262calcium channel activity0.0488632521975829
GO:0031252leading edge0.0488632521975829
GO:0007266Rho protein signal transduction0.0488632521975829
GO:0005886plasma membrane0.0488632521975829
GO:0046578regulation of Ras protein signal transduction0.0488632521975829
GO:0006816calcium ion transport0.0488632521975829
GO:0022843voltage-gated cation channel activity0.0488632521975829
GO:0005085guanyl-nucleotide exchange factor activity0.0488632521975829
GO:0051056regulation of small GTPase mediated signal transduction0.0488632521975829
GO:0015674di-, tri-valent inorganic cation transport0.0488632521975829
GO:0006810transport0.0488632521975829
GO:0051234establishment of localization0.0488632521975829
GO:0007265Ras protein signal transduction0.0488632521975829
GO:0005083small GTPase regulator activity0.0488632521975829
GO:0022832voltage-gated channel activity0.0488632521975829
GO:0005244voltage-gated ion channel activity0.0488632521975829
GO:0010324membrane invagination0.0488632521975829
GO:0006897endocytosis0.0488632521975829



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)7.29e-1123
neuroblast (sensu Vertebrata)7.29e-1123
neuron3.19e-0833
neuronal stem cell3.19e-0833
neuroblast3.19e-0833
electrically signaling cell3.19e-0833

Uber Anatomy
Ontology termp-valuen
regional part of nervous system8.13e-2154
neurectoderm1.36e-2064
neural plate1.36e-2064
presumptive neural plate1.36e-2064
ecto-epithelium2.38e-1973
central nervous system2.47e-1973
structure with developmental contribution from neural crest3.09e-1992
neural tube3.69e-1952
neural rod3.69e-1952
future spinal cord3.69e-1952
neural keel3.69e-1952
ectoderm-derived structure1.09e-1895
ectoderm1.09e-1895
presumptive ectoderm1.09e-1895
nervous system6.01e-1875
brain2.17e-1647
future brain2.17e-1647
pre-chordal neural plate5.70e-1649
regional part of brain8.73e-1646
gray matter5.98e-1534
anterior neural tube1.26e-1340
regional part of forebrain4.71e-1339
forebrain4.71e-1339
future forebrain4.71e-1339
brain grey matter3.63e-1229
regional part of telencephalon3.63e-1229
telencephalon3.63e-1229
tube8.24e-10114
multi-cellular organism1.32e-09333
anatomical conduit4.74e-09122
cerebral cortex4.53e-0821
cerebral hemisphere4.53e-0821
pallium4.53e-0821
embryo2.00e-07320
occipital lobe2.57e-0710
visual cortex2.57e-0710
neocortex2.57e-0710
regional part of cerebral cortex3.03e-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)
MA0003.10.526413
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.33691
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
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
MA0056.10
MA0057.10.896032
MA0058.10.690848
MA0059.10.705317
MA0060.16.80885
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
MA0073.10.439282
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.13.04822
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
MA0101.10.71579
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
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.71803
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
MA0159.11.39671
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.927936
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.21.4764
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_mm9:2739&oldid=2576134"