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MCL coexpression mm9:2757: Difference between revisions

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{{MCL_coexpression_mm9
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part morphogenesis;0.00383725525219653;76260,67378!GO:0030030;cell projection organization and biogenesis;0.00383725525219653;76260,67378!GO:0048858;cell projection morphogenesis;0.00383725525219653;76260,67378!GO:0035084;flagellum axoneme biogenesis;0.00394401676804148;67378!GO:0007288;sperm axoneme assembly;0.00394401676804148;67378!GO:0035082;axoneme biogenesis;0.00394401676804148;67378!GO:0032989;cellular structure morphogenesis;0.00394401676804148;76260,67378!GO:0000902;cell morphogenesis;0.00394401676804148;76260,67378!GO:0009296;flagellum biogenesis;0.00394401676804148;67378!GO:0043064;flagellum organization and biogenesis;0.00414110414531841;67378!GO:0040015;negative regulation of multicellular organism growth;0.004436654167573;67378!GO:0001578;microtubule bundle formation;0.004436654167573;67378!GO:0045494;photoreceptor cell maintenance;0.004550289848289;67378!GO:0045926;negative regulation of growth;0.0105588312374131;67378!GO:0009653;anatomical structure morphogenesis;0.0132778908246798;76260,67378!GO:0007286;spermatid development;0.0152961233346457;67378!GO:0048515;spermatid differentiation;0.0152961233346457;67378!GO:0030031;cell projection biogenesis;0.0157579132921437;67378!GO:0040014;regulation of multicellular organism growth;0.0161708207912581;67378!GO:0035264;multicellular organism growth;0.0171587491100827;67378!GO:0030534;adult behavior;0.0171587491100827;67378!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0171829064360956;67378!GO:0048856;anatomical structure development;0.0255344755434262;76260,67378!GO:0007601;visual perception;0.0261915865658138;67378!GO:0050953;sensory perception of light stimulus;0.0261915865658138;67378!GO:0016043;cellular component organization and biogenesis;0.0323024183464406;76260,67378!GO:0040008;regulation of growth;0.0323024183464406;67378!GO:0007017;microtubule-based process;0.0370132419321383;67378!GO:0007283;spermatogenesis;0.0382550392137857;67378!GO:0048232;male gamete 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|gostat_on_MCL_coexpression=GO:0032990;cell part morphogenesis;0.00383725525219653;76260,67378!GO:0030030;cell projection organization and biogenesis;0.00383725525219653;76260,67378!GO:0048858;cell projection morphogenesis;0.00383725525219653;76260,67378!GO:0035084;flagellum axoneme biogenesis;0.00394401676804148;67378!GO:0007288;sperm axoneme assembly;0.00394401676804148;67378!GO:0035082;axoneme biogenesis;0.00394401676804148;67378!GO:0032989;cellular structure morphogenesis;0.00394401676804148;76260,67378!GO:0000902;cell morphogenesis;0.00394401676804148;76260,67378!GO:0009296;flagellum biogenesis;0.00394401676804148;67378!GO:0043064;flagellum organization and biogenesis;0.00414110414531841;67378!GO:0040015;negative regulation of multicellular organism growth;0.004436654167573;67378!GO:0001578;microtubule bundle formation;0.004436654167573;67378!GO:0045494;photoreceptor cell maintenance;0.004550289848289;67378!GO:0045926;negative regulation of growth;0.0105588312374131;67378!GO:0009653;anatomical structure morphogenesis;0.0132778908246798;76260,67378!GO:0007286;spermatid development;0.0152961233346457;67378!GO:0048515;spermatid differentiation;0.0152961233346457;67378!GO:0030031;cell projection biogenesis;0.0157579132921437;67378!GO:0040014;regulation of multicellular organism growth;0.0161708207912581;67378!GO:0035264;multicellular organism growth;0.0171587491100827;67378!GO:0030534;adult behavior;0.0171587491100827;67378!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0171829064360956;67378!GO:0048856;anatomical structure development;0.0255344755434262;76260,67378!GO:0007601;visual perception;0.0261915865658138;67378!GO:0050953;sensory perception of light stimulus;0.0261915865658138;67378!GO:0016043;cellular component organization and biogenesis;0.0323024183464406;76260,67378!GO:0040008;regulation of growth;0.0323024183464406;67378!GO:0007017;microtubule-based process;0.0370132419321383;67378!GO:0007283;spermatogenesis;0.0382550392137857;67378!GO:0048232;male gamete generation;0.0382550392137857;67378!GO:0019725;cellular homeostasis;0.039810733065846;67378!GO:0032502;developmental process;0.039810733065846;76260,67378!GO:0007276;gamete generation;0.0445187564059488;67378!
|ontology_enrichment_celltype=CL:0000117!3.69e-08!23;CL:0000337!3.69e-08!23;CL:0000540!5.39e-08!33;CL:0000047!5.39e-08!33;CL:0000031!5.39e-08!33;CL:0000404!5.39e-08!33;CL:0000393!8.69e-07!39;CL:0000211!8.69e-07!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!6.38e-26!64;UBERON:0003075!6.38e-26!64;UBERON:0007284!6.38e-26!64;UBERON:0004121!9.39e-24!95;UBERON:0000924!9.39e-24!95;UBERON:0006601!9.39e-24!95;UBERON:0001017!1.43e-23!73;UBERON:0010371!2.29e-23!73;UBERON:0001016!2.45e-22!75;UBERON:0003056!3.26e-22!49;UBERON:0000073!4.62e-22!54;UBERON:0001049!6.28e-21!52;UBERON:0005068!6.28e-21!52;UBERON:0006241!6.28e-21!52;UBERON:0007135!6.28e-21!52;UBERON:0000955!5.67e-20!47;UBERON:0006238!5.67e-20!47;UBERON:0010314!1.07e-19!92;UBERON:0002616!2.93e-19!46;UBERON:0003080!6.06e-18!40;UBERON:0002780!2.87e-17!39;UBERON:0001890!2.87e-17!39;UBERON:0006240!2.87e-17!39;UBERON:0002020!5.80e-13!34;UBERON:0003528!5.75e-12!29;UBERON:0002791!5.75e-12!29;UBERON:0001893!5.75e-12!29;UBERON:0000956!5.76e-09!21;UBERON:0001869!5.76e-09!21;UBERON:0000203!5.76e-09!21;UBERON:0004111!1.34e-08!122;UBERON:0002619!4.83e-08!17;UBERON:0000468!1.23e-07!333;UBERON:0000025!1.33e-07!114;UBERON:0002021!4.02e-07!10;UBERON:0000411!4.02e-07!10;UBERON:0001950!4.02e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,1.38557,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,2.0549,0.610669,0.474221,1.85291,1.05665,0.859154,1.23487,1.55852,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,1.03818,0.411601,1.04436,1.20986,1.63704,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,2.51458,0.94678,0.562367,0.904334,2.62466
|tfbs_overrepresentation_jaspar=MA0003.1;0.245953,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;1.49373,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;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;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;0.0430758,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;1.80015,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;1.16863,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;2.29555,MA0144.1;0.541532,MA0145.1;0.794492,MA0146.1;0.900029,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.181475,MA0138.2;2.42889,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;0.166722,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.0332569,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:100158741..100158763,+p2@Ttc8
Mm9::chr12:100158777..100158829,+p1@Ttc8
Mm9::chr8:96622242..96622288,-p1@Bbs2


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:0032990cell part morphogenesis0.00383725525219653
GO:0030030cell projection organization and biogenesis0.00383725525219653
GO:0048858cell projection morphogenesis0.00383725525219653
GO:0035084flagellum axoneme biogenesis0.00394401676804148
GO:0007288sperm axoneme assembly0.00394401676804148
GO:0035082axoneme biogenesis0.00394401676804148
GO:0032989cellular structure morphogenesis0.00394401676804148
GO:0000902cell morphogenesis0.00394401676804148
GO:0009296flagellum biogenesis0.00394401676804148
GO:0043064flagellum organization and biogenesis0.00414110414531841
GO:0040015negative regulation of multicellular organism growth0.004436654167573
GO:0001578microtubule bundle formation0.004436654167573
GO:0045494photoreceptor cell maintenance0.004550289848289
GO:0045926negative regulation of growth0.0105588312374131
GO:0009653anatomical structure morphogenesis0.0132778908246798
GO:0007286spermatid development0.0152961233346457
GO:0048515spermatid differentiation0.0152961233346457
GO:0030031cell projection biogenesis0.0157579132921437
GO:0040014regulation of multicellular organism growth0.0161708207912581
GO:0035264multicellular organism growth0.0171587491100827
GO:0030534adult behavior0.0171587491100827
GO:0000226microtubule cytoskeleton organization and biogenesis0.0171829064360956
GO:0048856anatomical structure development0.0255344755434262
GO:0007601visual perception0.0261915865658138
GO:0050953sensory perception of light stimulus0.0261915865658138
GO:0016043cellular component organization and biogenesis0.0323024183464406
GO:0040008regulation of growth0.0323024183464406
GO:0007017microtubule-based process0.0370132419321383
GO:0007283spermatogenesis0.0382550392137857
GO:0048232male gamete generation0.0382550392137857
GO:0019725cellular homeostasis0.039810733065846
GO:0032502developmental process0.039810733065846
GO:0007276gamete generation0.0445187564059488



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)3.69e-0823
neuroblast (sensu Vertebrata)3.69e-0823
neuron5.39e-0833
neuronal stem cell5.39e-0833
neuroblast5.39e-0833
electrically signaling cell5.39e-0833
electrically responsive cell8.69e-0739
electrically active cell8.69e-0739

Uber Anatomy
Ontology termp-valuen
neurectoderm6.38e-2664
neural plate6.38e-2664
presumptive neural plate6.38e-2664
ectoderm-derived structure9.39e-2495
ectoderm9.39e-2495
presumptive ectoderm9.39e-2495
central nervous system1.43e-2373
ecto-epithelium2.29e-2373
nervous system2.45e-2275
pre-chordal neural plate3.26e-2249
regional part of nervous system4.62e-2254
neural tube6.28e-2152
neural rod6.28e-2152
future spinal cord6.28e-2152
neural keel6.28e-2152
brain5.67e-2047
future brain5.67e-2047
structure with developmental contribution from neural crest1.07e-1992
regional part of brain2.93e-1946
anterior neural tube6.06e-1840
regional part of forebrain2.87e-1739
forebrain2.87e-1739
future forebrain2.87e-1739
gray matter5.80e-1334
brain grey matter5.75e-1229
regional part of telencephalon5.75e-1229
telencephalon5.75e-1229
cerebral cortex5.76e-0921
cerebral hemisphere5.76e-0921
pallium5.76e-0921
anatomical conduit1.34e-08122
regional part of cerebral cortex4.83e-0817
multi-cellular organism1.23e-07333
tube1.33e-07114
occipital lobe4.02e-0710
visual cortex4.02e-0710
neocortex4.02e-0710


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
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.133574
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.11.49373
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
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
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
MA0073.10.0430758
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
MA0092.11.80015
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
MA0139.11.16863
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.12.29555
MA0144.10.541532
MA0145.10.794492
MA0146.10.900029
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.181475
MA0138.22.42889
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
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.0332569
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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