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MCL coexpression mm9:2539: Difference between revisions

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{{MCL_coexpression_mm9
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part;0.0202373801242691;15273,26896!GO:0005654;nucleoplasm;0.0202373801242691;15273,26896!GO:0031981;nuclear lumen;0.0202373801242691;15273,26896!GO:0031974;membrane-enclosed lumen;0.0202373801242691;15273,26896!GO:0043233;organelle lumen;0.0202373801242691;15273,26896!GO:0000119;mediator complex;0.0241471748558044;26896!GO:0044428;nuclear part;0.0255491761587703;15273,26896!GO:0016591;DNA-directed RNA polymerase II, holoenzyme;0.0414820964828024;26896!GO:0043234;protein complex;0.0414820964828024;15273,26896!GO:0003713;transcription coactivator activity;0.0414820964828024;26896!GO:0006355;regulation of transcription, DNA-dependent;0.0414820964828024;15273,26896!GO:0006351;transcription, DNA-dependent;0.0414820964828024;15273,26896!GO:0032774;RNA biosynthetic process;0.0414820964828024;15273,26896!GO:0045449;regulation of transcription;0.0414820964828024;15273,26896!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0414820964828024;15273,26896!GO:0006350;transcription;0.0414820964828024;15273,26896!GO:0032991;macromolecular complex;0.0414820964828024;15273,26896!GO:0010468;regulation of gene expression;0.0414820964828024;15273,26896!GO:0031323;regulation of cellular metabolic process;0.0414820964828024;15273,26896!GO:0019222;regulation of metabolic process;0.0414820964828024;15273,26896!GO:0016070;RNA metabolic process;0.0414820964828024;15273,26896!GO:0003712;transcription cofactor activity;0.0414820964828024;26896!GO:0044446;intracellular organelle part;0.0414820964828024;15273,26896!GO:0044422;organelle part;0.0414820964828024;15273,26896!GO:0016563;transcription activator activity;0.0483065873043917;26896!GO:0008134;transcription factor binding;0.0483065873043917;26896!GO:0010467;gene expression;0.0483065873043917;15273,26896!GO:0045944;positive regulation of transcription from RNA polymerase II 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|gostat_on_MCL_coexpression=GO:0044451;nucleoplasm part;0.0202373801242691;15273,26896!GO:0005654;nucleoplasm;0.0202373801242691;15273,26896!GO:0031981;nuclear lumen;0.0202373801242691;15273,26896!GO:0031974;membrane-enclosed lumen;0.0202373801242691;15273,26896!GO:0043233;organelle lumen;0.0202373801242691;15273,26896!GO:0000119;mediator complex;0.0241471748558044;26896!GO:0044428;nuclear part;0.0255491761587703;15273,26896!GO:0016591;DNA-directed RNA polymerase II, holoenzyme;0.0414820964828024;26896!GO:0043234;protein complex;0.0414820964828024;15273,26896!GO:0003713;transcription coactivator activity;0.0414820964828024;26896!GO:0006355;regulation of transcription, DNA-dependent;0.0414820964828024;15273,26896!GO:0006351;transcription, DNA-dependent;0.0414820964828024;15273,26896!GO:0032774;RNA biosynthetic process;0.0414820964828024;15273,26896!GO:0045449;regulation of transcription;0.0414820964828024;15273,26896!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0414820964828024;15273,26896!GO:0006350;transcription;0.0414820964828024;15273,26896!GO:0032991;macromolecular complex;0.0414820964828024;15273,26896!GO:0010468;regulation of gene expression;0.0414820964828024;15273,26896!GO:0031323;regulation of cellular metabolic process;0.0414820964828024;15273,26896!GO:0019222;regulation of metabolic process;0.0414820964828024;15273,26896!GO:0016070;RNA metabolic process;0.0414820964828024;15273,26896!GO:0003712;transcription cofactor activity;0.0414820964828024;26896!GO:0044446;intracellular organelle part;0.0414820964828024;15273,26896!GO:0044422;organelle part;0.0414820964828024;15273,26896!GO:0016563;transcription activator activity;0.0483065873043917;26896!GO:0008134;transcription factor binding;0.0483065873043917;26896!GO:0010467;gene expression;0.0483065873043917;15273,26896!GO:0045944;positive regulation of transcription from RNA polymerase II promoter;0.0483065873043917;26896!
|ontology_enrichment_celltype=CL:0000540!3.12e-07!33;CL:0000047!3.12e-07!33;CL:0000031!3.12e-07!33;CL:0000404!3.12e-07!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002020!2.94e-13!34;UBERON:0000064!1.86e-12!99;UBERON:0003528!1.12e-11!29;UBERON:0002791!1.12e-11!29;UBERON:0001893!1.12e-11!29;UBERON:0000956!6.12e-11!21;UBERON:0001869!6.12e-11!21;UBERON:0000203!6.12e-11!21;UBERON:0001016!1.26e-10!75;UBERON:0000073!1.40e-10!54;UBERON:0001017!1.96e-10!73;UBERON:0001049!4.30e-10!52;UBERON:0005068!4.30e-10!52;UBERON:0006241!4.30e-10!52;UBERON:0007135!4.30e-10!52;UBERON:0004121!1.57e-09!95;UBERON:0000924!1.57e-09!95;UBERON:0006601!1.57e-09!95;UBERON:0000955!4.29e-09!47;UBERON:0006238!4.29e-09!47;UBERON:0002780!1.05e-08!39;UBERON:0001890!1.05e-08!39;UBERON:0006240!1.05e-08!39;UBERON:0002619!1.07e-08!17;UBERON:0003080!1.22e-08!40;UBERON:0010371!1.24e-08!73;UBERON:0002616!1.44e-08!46;UBERON:0002021!4.47e-08!10;UBERON:0000411!4.47e-08!10;UBERON:0001950!4.47e-08!10;UBERON:0002346!4.80e-08!64;UBERON:0003075!4.80e-08!64;UBERON:0007284!4.80e-08!64
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,1.138,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,2.02463,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,1.83166,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.62246,0.195254,1.75916,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,1.38502,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,2.74838,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.609576,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,1.79943,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.421338
}}

Latest revision as of 18:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13685585..13685645,+p2@Hivep2
Mm9::chr10:13685899..13685916,+p1@Hivep2
Mm9::chrX:12339216..12339239,-p4@Med14


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:0044451nucleoplasm part0.0202373801242691
GO:0005654nucleoplasm0.0202373801242691
GO:0031981nuclear lumen0.0202373801242691
GO:0031974membrane-enclosed lumen0.0202373801242691
GO:0043233organelle lumen0.0202373801242691
GO:0000119mediator complex0.0241471748558044
GO:0044428nuclear part0.0255491761587703
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.0414820964828024
GO:0043234protein complex0.0414820964828024
GO:0003713transcription coactivator activity0.0414820964828024
GO:0006355regulation of transcription, DNA-dependent0.0414820964828024
GO:0006351transcription, DNA-dependent0.0414820964828024
GO:0032774RNA biosynthetic process0.0414820964828024
GO:0045449regulation of transcription0.0414820964828024
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0414820964828024
GO:0006350transcription0.0414820964828024
GO:0032991macromolecular complex0.0414820964828024
GO:0010468regulation of gene expression0.0414820964828024
GO:0031323regulation of cellular metabolic process0.0414820964828024
GO:0019222regulation of metabolic process0.0414820964828024
GO:0016070RNA metabolic process0.0414820964828024
GO:0003712transcription cofactor activity0.0414820964828024
GO:0044446intracellular organelle part0.0414820964828024
GO:0044422organelle part0.0414820964828024
GO:0016563transcription activator activity0.0483065873043917
GO:0008134transcription factor binding0.0483065873043917
GO:0010467gene expression0.0483065873043917
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0483065873043917



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
neuron3.12e-0733
neuronal stem cell3.12e-0733
neuroblast3.12e-0733
electrically signaling cell3.12e-0733

Uber Anatomy
Ontology termp-valuen
gray matter2.94e-1334
organ part1.86e-1299
brain grey matter1.12e-1129
regional part of telencephalon1.12e-1129
telencephalon1.12e-1129
cerebral cortex6.12e-1121
cerebral hemisphere6.12e-1121
pallium6.12e-1121
nervous system1.26e-1075
regional part of nervous system1.40e-1054
central nervous system1.96e-1073
neural tube4.30e-1052
neural rod4.30e-1052
future spinal cord4.30e-1052
neural keel4.30e-1052
ectoderm-derived structure1.57e-0995
ectoderm1.57e-0995
presumptive ectoderm1.57e-0995
brain4.29e-0947
future brain4.29e-0947
regional part of forebrain1.05e-0839
forebrain1.05e-0839
future forebrain1.05e-0839
regional part of cerebral cortex1.07e-0817
anterior neural tube1.22e-0840
ecto-epithelium1.24e-0873
regional part of brain1.44e-0846
occipital lobe4.47e-0810
visual cortex4.47e-0810
neocortex4.47e-0810
neurectoderm4.80e-0864
neural plate4.80e-0864
presumptive neural plate4.80e-0864


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
MA0006.11.46714
MA0007.10.784593
MA0009.11.27673
MA0014.12.60474
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
MA0052.11.29825
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
MA0068.10.908538
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.680038
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
MA0101.10.71579
MA0103.10.647985
MA0105.11.04599
MA0106.11.01755
MA0107.11.54626
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
MA0144.11.33779
MA0145.10.794492
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.11.71612
MA0062.21.06145
MA0035.20.903829
MA0039.20.71803
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.79573
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
MA0162.10.964824
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.23.96489
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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