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MCL coexpression mm9:3299: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002346!1.01e-27!64;UBERON:0003075!1.01e-27!64;UBERON:0007284!1.01e-27!64;UBERON:0003056!1.22e-24!49;UBERON:0010371!8.90e-23!73;UBERON:0004121!8.28e-21!95;UBERON:0000924!8.28e-21!95;UBERON:0006601!8.28e-21!95;UBERON:0002020!7.96e-20!34;UBERON:0001049!5.42e-19!52;UBERON:0005068!5.42e-19!52;UBERON:0006241!5.42e-19!52;UBERON:0007135!5.42e-19!52;UBERON:0000073!3.49e-18!54;UBERON:0001017!1.07e-16!73;UBERON:0003528!1.15e-16!29;UBERON:0002791!1.15e-16!29;UBERON:0001893!1.15e-16!29;UBERON:0000955!2.77e-16!47;UBERON:0006238!2.77e-16!47;UBERON:0001016!5.79e-16!75;UBERON:0010314!1.40e-15!92;UBERON:0002616!3.32e-15!46;UBERON:0003080!2.49e-14!40;UBERON:0002780!1.66e-13!39;UBERON:0001890!1.66e-13!39;UBERON:0006240!1.66e-13!39;UBERON:0000970!2.12e-13!9;UBERON:0000019!2.12e-13!9;UBERON:0000047!2.12e-13!9;UBERON:0010312!2.12e-13!9;UBERON:0004088!2.12e-13!9;UBERON:0002104!2.12e-13!9;UBERON:0001456!2.12e-13!9;UBERON:0003072!2.12e-13!9;UBERON:0004128!2.12e-13!9;UBERON:0003071!2.12e-13!9;UBERON:0000956!2.63e-11!21;UBERON:0001869!2.63e-11!21;UBERON:0000203!2.63e-11!21;UBERON:0001444!1.63e-10!11;UBERON:0002619!1.84e-09!17;UBERON:0000020!1.94e-09!12;UBERON:0001032!1.94e-09!12;UBERON:0004456!1.94e-09!12;UBERON:0002021!9.11e-09!10;UBERON:0000411!9.11e-09!10;UBERON:0001950!9.11e-09!10;UBERON:0000033!1.57e-08!13;UBERON:0005085!1.57e-08!13;UBERON:0000369!3.34e-08!5;UBERON:0002435!3.34e-08!5;UBERON:0000204!3.34e-08!5;UBERON:0010082!3.34e-08!5
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,1.43553,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,1.96186,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,1.47967,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.971403,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,2.74819,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,1.862,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.833542
|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;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;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;0.557057,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;0.439282,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;1.91105,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;1.44443,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;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;0.840842,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;0.927936,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.166764,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;1.34197,MA0442.1;0
}}

Latest revision as of 19:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:105921082..105921087,+p@chr2:105921082..105921087
+
Mm9::chr3:17686834..17686845,-p1@ENSMUST00000099198
Mm9::chr3:17693908..17693926,+p@chr3:17693908..17693926
+


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)1.35e-1123
neuroblast (sensu Vertebrata)1.35e-1123
neuron8.50e-0733
neuronal stem cell8.50e-0733
neuroblast8.50e-0733
electrically signaling cell8.50e-0733

Uber Anatomy
Ontology termp-valuen
neurectoderm1.01e-2764
neural plate1.01e-2764
presumptive neural plate1.01e-2764
pre-chordal neural plate1.22e-2449
ecto-epithelium8.90e-2373
ectoderm-derived structure8.28e-2195
ectoderm8.28e-2195
presumptive ectoderm8.28e-2195
gray matter7.96e-2034
neural tube5.42e-1952
neural rod5.42e-1952
future spinal cord5.42e-1952
neural keel5.42e-1952
regional part of nervous system3.49e-1854
central nervous system1.07e-1673
brain grey matter1.15e-1629
regional part of telencephalon1.15e-1629
telencephalon1.15e-1629
brain2.77e-1647
future brain2.77e-1647
nervous system5.79e-1675
structure with developmental contribution from neural crest1.40e-1592
regional part of brain3.32e-1546
anterior neural tube2.49e-1440
regional part of forebrain1.66e-1339
forebrain1.66e-1339
future forebrain1.66e-1339
eye2.12e-139
camera-type eye2.12e-139
simple eye2.12e-139
immature eye2.12e-139
ocular region2.12e-139
visual system2.12e-139
face2.12e-139
optic cup2.12e-139
optic vesicle2.12e-139
eye primordium2.12e-139
cerebral cortex2.63e-1121
cerebral hemisphere2.63e-1121
pallium2.63e-1121
subdivision of head1.63e-1011
regional part of cerebral cortex1.84e-0917
sense organ1.94e-0912
sensory system1.94e-0912
entire sense organ system1.94e-0912
occipital lobe9.11e-0910
visual cortex9.11e-0910
neocortex9.11e-0910
head1.57e-0813
ectodermal placode1.57e-0813
corpus striatum3.34e-085
striatum3.34e-085
ventral part of telencephalon3.34e-085
future corpus striatum3.34e-085


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
MA0014.10.133574
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
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
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
MA0073.10.439282
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
MA0091.11.91105
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
MA0146.11.44443
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.181475
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
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.927936
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.166764
MA0102.22.01714
MA0258.10.520639
MA0259.11.34197
MA0442.10
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