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MCL coexpression mm9:3355: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!1.42e-08!23;CL:0000337!1.42e-08!23;CL:0000540!2.07e-08!33;CL:0000047!2.07e-08!33;CL:0000031!2.07e-08!33;CL:0000404!2.07e-08!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!1.12e-28!92;UBERON:0000073!1.94e-23!54;UBERON:0001017!1.12e-21!73;UBERON:0001049!1.86e-21!52;UBERON:0005068!1.86e-21!52;UBERON:0006241!1.86e-21!52;UBERON:0007135!1.86e-21!52;UBERON:0002346!2.44e-21!64;UBERON:0003075!2.44e-21!64;UBERON:0007284!2.44e-21!64;UBERON:0001016!1.33e-20!75;UBERON:0004121!1.58e-18!95;UBERON:0000924!1.58e-18!95;UBERON:0006601!1.58e-18!95;UBERON:0000955!1.87e-18!47;UBERON:0006238!1.87e-18!47;UBERON:0002020!6.38e-18!34;UBERON:0002616!1.47e-17!46;UBERON:0010371!2.37e-17!73;UBERON:0003056!2.59e-16!49;UBERON:0003080!1.01e-15!40;UBERON:0002780!5.43e-15!39;UBERON:0001890!5.43e-15!39;UBERON:0006240!5.43e-15!39;UBERON:0000025!6.99e-15!114;UBERON:0003528!7.47e-15!29;UBERON:0002791!7.47e-15!29;UBERON:0001893!7.47e-15!29;UBERON:0004111!2.92e-13!122;UBERON:0002021!1.69e-11!10;UBERON:0000411!1.69e-11!10;UBERON:0001950!1.69e-11!10;UBERON:0000956!1.90e-11!21;UBERON:0001869!1.90e-11!21;UBERON:0000203!1.90e-11!21;UBERON:0007100!9.32e-10!18;UBERON:0000948!9.32e-10!18;UBERON:0005498!9.32e-10!18;UBERON:0004140!9.32e-10!18;UBERON:0009881!9.32e-10!18;UBERON:0004141!9.32e-10!18;UBERON:0003084!9.32e-10!18;UBERON:0007005!9.32e-10!18;UBERON:0004139!9.32e-10!18;UBERON:0004291!9.32e-10!18;UBERON:0002619!5.78e-09!17;UBERON:0000483!7.43e-07!174
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,1.23487,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,2.71163,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,1.26911,0.464141,1.26539,1.05692,0.928366,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
|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;2.87313,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;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;0.00834468,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;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;0.151124,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;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;0.00137444,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:58, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:55304110..55304114,+p@chr2:55304110..55304114
+
Mm9::chr2:55449703..55449718,+p@chr2:55449703..55449718
+
Mm9::chr2:55449728..55449754,+p@chr2:55449728..55449754
+


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

no results for this coexpression

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)1.42e-0823
neuroblast (sensu Vertebrata)1.42e-0823
neuron2.07e-0833
neuronal stem cell2.07e-0833
neuroblast2.07e-0833
electrically signaling cell2.07e-0833

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest1.12e-2892
regional part of nervous system1.94e-2354
central nervous system1.12e-2173
neural tube1.86e-2152
neural rod1.86e-2152
future spinal cord1.86e-2152
neural keel1.86e-2152
neurectoderm2.44e-2164
neural plate2.44e-2164
presumptive neural plate2.44e-2164
nervous system1.33e-2075
ectoderm-derived structure1.58e-1895
ectoderm1.58e-1895
presumptive ectoderm1.58e-1895
brain1.87e-1847
future brain1.87e-1847
gray matter6.38e-1834
regional part of brain1.47e-1746
ecto-epithelium2.37e-1773
pre-chordal neural plate2.59e-1649
anterior neural tube1.01e-1540
regional part of forebrain5.43e-1539
forebrain5.43e-1539
future forebrain5.43e-1539
tube6.99e-15114
brain grey matter7.47e-1529
regional part of telencephalon7.47e-1529
telencephalon7.47e-1529
anatomical conduit2.92e-13122
occipital lobe1.69e-1110
visual cortex1.69e-1110
neocortex1.69e-1110
cerebral cortex1.90e-1121
cerebral hemisphere1.90e-1121
pallium1.90e-1121
primary circulatory organ9.32e-1018
heart9.32e-1018
primitive heart tube9.32e-1018
primary heart field9.32e-1018
anterior lateral plate mesoderm9.32e-1018
heart tube9.32e-1018
heart primordium9.32e-1018
cardiac mesoderm9.32e-1018
cardiogenic plate9.32e-1018
heart rudiment9.32e-1018
regional part of cerebral cortex5.78e-0917
epithelium7.43e-07174


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
MA0040.12.87313
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
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
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
MA0101.10.71579
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
MA0146.10.151124
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
MA0112.20.29236
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
MA0079.20.00137444
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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