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MCL coexpression mm9:742: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0000073!1.11e-26!54;UBERON:0001049!1.25e-24!52;UBERON:0005068!1.25e-24!52;UBERON:0006241!1.25e-24!52;UBERON:0007135!1.25e-24!52;UBERON:0001017!3.44e-23!73;UBERON:0001016!4.60e-23!75;UBERON:0002346!7.00e-23!64;UBERON:0003075!7.00e-23!64;UBERON:0007284!7.00e-23!64;UBERON:0002020!3.16e-22!34;UBERON:0004121!7.23e-20!95;UBERON:0000924!7.23e-20!95;UBERON:0006601!7.23e-20!95;UBERON:0000955!3.34e-19!47;UBERON:0006238!3.34e-19!47;UBERON:0010371!5.26e-19!73;UBERON:0002616!1.91e-18!46;UBERON:0003528!7.46e-17!29;UBERON:0002791!7.46e-17!29;UBERON:0001893!7.46e-17!29;UBERON:0003056!3.82e-16!49;UBERON:0003080!7.30e-16!40;UBERON:0002780!6.10e-15!39;UBERON:0001890!6.10e-15!39;UBERON:0006240!6.10e-15!39;UBERON:0010314!2.68e-13!92;UBERON:0000956!1.86e-10!21;UBERON:0001869!1.86e-10!21;UBERON:0000203!1.86e-10!21;UBERON:0002021!2.50e-10!10;UBERON:0000411!2.50e-10!10;UBERON:0001950!2.50e-10!10;UBERON:0003076!9.26e-10!12;UBERON:0003057!9.26e-10!12;UBERON:0002619!1.32e-09!17;UBERON:0002240!4.46e-08!6;UBERON:0005174!4.46e-08!6;UBERON:0001137!4.46e-08!6;UBERON:0002420!5.70e-08!8;UBERON:0007245!5.70e-08!8;UBERON:0010009!5.70e-08!8;UBERON:0010011!5.70e-08!8;UBERON:0000454!5.70e-08!8;UBERON:0001948!5.47e-07!5;UBERON:0002315!5.47e-07!5
|tfbs_overrepresentation_for_novel_motifs=0.860199,3.08026,0.807108,0.360062,0.200163,0.373426,1.16061,0.392928,0.131493,0.771958,1.071,0.447169,1.85989,0.470194,0.214197,0,0.656089,0.19356,1.209,0.451901,0.732601,0.60924,0.469335,0.198877,1.4907,4.29599,1.71373,1.01819,1.24776,0.967915,0.379806,0.754912,1.06562,0.31333,1.1554,0.6066,2.32607,0.443753,0.166348,0.442131,0.196807,0.999982,0.56316,0.215898,0.119503,1.6507,0.578773,1.05036,0.104497,0.241306,0.639101,1.29662,0.259389,0.894161,0.911367,0.47699,0.249055,1.11002,0.68053,2.07809,0.735292,0.531188,0.433822,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,1.40499,0.128829,6.50374,0.944464,2.20686,0.623453,0.0942164,0.567793,0.718494,0.268962,0.406536,0.673009,0.529804,0.119727,0.830765,4.02411,0.0697823,0.572901,0.583509,1.55487,1.11522,0.835661,0.767462,1.11849,7.34789,0.149272,0.388243,0.770215,0.57902,0.234357,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,2.11468,2.90151,0.845852,0.878738,0.26996,0.421988,1.12221,0.195318,3.9317,0.953611,0.657356,0.534159,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,0.33206,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,1.00091,0.581788,1.88287,0.331322,1.10485,0.580497,8.42698,0.895708,0.911723,0.489108,0.976367,0.523103,0.637798,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.19482
|tfbs_overrepresentation_jaspar=MA0003.1;0.51522,MA0004.1;0.946922,MA0006.1;1.78357,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;2.6738,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;0.219287,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;1.82935,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;1.60346,MA0056.1;0,MA0057.1;0.817159,MA0058.1;1.37894,MA0059.1;0.777514,MA0060.1;0.145297,MA0061.1;0.973999,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.0621035,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;0.0100778,MA0074.1;0.451832,MA0076.1;0.249619,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.14959,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;1.20057,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;4.2147,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.167085,MA0115.1;0.878749,MA0116.1;2.51573,MA0117.1;0.846964,MA0119.1;2.21661,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.121562,MA0140.1;1.12231,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;1.03071,MA0146.1;0.923066,MA0147.1;1.6106,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;0.314778,MA0035.2;1.1319,MA0039.2;0.468563,MA0138.2;0.590987,MA0002.2;0.781868,MA0137.2;0.257017,MA0104.2;1.9417,MA0047.2;0.495607,MA0112.2;0.371983,MA0065.2;0.373167,MA0150.1;0.916186,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.0498353,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;1.05,MA0160.1;0.378276,MA0161.1;0,MA0162.1;3.21731,MA0163.1;1.69351,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;1.42938,MA0079.2;2.84905,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;1.56071,MA0442.1;0
}}

Latest revision as of 15:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:136605836..136605866,+p2@Syt2
Mm9::chr1:136605870..136605895,+p4@Syt2
Mm9::chr1:136605938..136605946,+p8@Syt2
Mm9::chr2:25174713..25174724,-p2@Grin1
Mm9::chr6:115201825..115201836,-p6@Timp4
Mm9::chr6:115201857..115201885,-p1@Timp4
Mm9::chr6:39369941..39369957,-p6@Mkrn1
Mm9::chr7:134164719..134164730,-p6@Prrt2
Mm9::chr8:24085395..24085404,+p18@Ank1
Mm9::chr8:74031641..74031665,-p@chr8:74031641..74031665
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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)2.16e-1623
neuroblast (sensu Vertebrata)2.16e-1623
neuron2.93e-0933
neuronal stem cell2.93e-0933
neuroblast2.93e-0933
electrically signaling cell2.93e-0933
ectodermal cell3.14e-0744
neurectodermal cell3.14e-0744
neural cell6.30e-0743
electrically responsive cell7.55e-0739
electrically active cell7.55e-0739

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.11e-2654
neural tube1.25e-2452
neural rod1.25e-2452
future spinal cord1.25e-2452
neural keel1.25e-2452
central nervous system3.44e-2373
nervous system4.60e-2375
neurectoderm7.00e-2364
neural plate7.00e-2364
presumptive neural plate7.00e-2364
gray matter3.16e-2234
ectoderm-derived structure7.23e-2095
ectoderm7.23e-2095
presumptive ectoderm7.23e-2095
brain3.34e-1947
future brain3.34e-1947
ecto-epithelium5.26e-1973
regional part of brain1.91e-1846
brain grey matter7.46e-1729
regional part of telencephalon7.46e-1729
telencephalon7.46e-1729
pre-chordal neural plate3.82e-1649
anterior neural tube7.30e-1640
regional part of forebrain6.10e-1539
forebrain6.10e-1539
future forebrain6.10e-1539
structure with developmental contribution from neural crest2.68e-1392
cerebral cortex1.86e-1021
cerebral hemisphere1.86e-1021
pallium1.86e-1021
occipital lobe2.50e-1010
visual cortex2.50e-1010
neocortex2.50e-1010
posterior neural tube9.26e-1012
chordal neural plate9.26e-1012
regional part of cerebral cortex1.32e-0917
spinal cord4.46e-086
dorsal region element4.46e-086
dorsum4.46e-086
basal ganglion5.70e-088
nuclear complex of neuraxis5.70e-088
aggregate regional part of brain5.70e-088
collection of basal ganglia5.70e-088
cerebral subcortex5.70e-088
regional part of spinal cord5.47e-075
gray matter of spinal cord5.47e-075


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)
MA0003.10.51522
MA0004.10.946922
MA0006.11.78357
MA0007.10.346734
MA0009.10.780842
MA0014.12.6738
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.11.82935
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.11.60346
MA0056.10
MA0057.10.817159
MA0058.11.37894
MA0059.10.777514
MA0060.10.145297
MA0061.10.973999
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.0621035
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.0100778
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.14959
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.11.20057
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.14.2147
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.167085
MA0115.10.878749
MA0116.12.51573
MA0117.10.846964
MA0119.12.21661
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.121562
MA0140.11.12231
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.11.03071
MA0146.10.923066
MA0147.11.6106
MA0148.10.375491
MA0149.10.2978
MA0062.20.314778
MA0035.21.1319
MA0039.20.468563
MA0138.20.590987
MA0002.20.781868
MA0137.20.257017
MA0104.21.9417
MA0047.20.495607
MA0112.20.371983
MA0065.20.373167
MA0150.10.916186
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.0498353
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.11.05
MA0160.10.378276
MA0161.10
MA0162.13.21731
MA0163.11.69351
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.21.42938
MA0079.22.84905
MA0102.21.49914
MA0258.10.156336
MA0259.11.56071
MA0442.10
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