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MCL coexpression mm9:580: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002346!5.05e-36!64;UBERON:0003075!5.05e-36!64;UBERON:0007284!5.05e-36!64;UBERON:0000073!4.98e-32!54;UBERON:0001017!2.69e-31!73;UBERON:0010371!3.90e-31!73;UBERON:0001016!9.28e-31!75;UBERON:0001049!1.45e-30!52;UBERON:0005068!1.45e-30!52;UBERON:0006241!1.45e-30!52;UBERON:0007135!1.45e-30!52;UBERON:0004121!1.18e-29!95;UBERON:0000924!1.18e-29!95;UBERON:0006601!1.18e-29!95;UBERON:0003056!7.39e-27!49;UBERON:0002020!8.21e-27!34;UBERON:0000955!1.81e-26!47;UBERON:0006238!1.81e-26!47;UBERON:0002616!1.56e-25!46;UBERON:0003528!1.29e-22!29;UBERON:0002791!1.29e-22!29;UBERON:0001893!1.29e-22!29;UBERON:0003080!1.66e-22!40;UBERON:0010314!3.06e-22!92;UBERON:0002780!8.54e-22!39;UBERON:0001890!8.54e-22!39;UBERON:0006240!8.54e-22!39;UBERON:0000956!2.91e-16!21;UBERON:0001869!2.91e-16!21;UBERON:0000203!2.91e-16!21;UBERON:0002619!1.85e-12!17;UBERON:0002021!1.85e-09!10;UBERON:0000411!1.85e-09!10;UBERON:0001950!1.85e-09!10;UBERON:0003076!2.17e-08!12;UBERON:0003057!2.17e-08!12;UBERON:0002420!1.76e-07!8;UBERON:0007245!1.76e-07!8;UBERON:0010009!1.76e-07!8;UBERON:0010011!1.76e-07!8;UBERON:0000454!1.76e-07!8
|ontology_enrichment_uberon=UBERON:0002346!5.05e-36!64;UBERON:0003075!5.05e-36!64;UBERON:0007284!5.05e-36!64;UBERON:0000073!4.98e-32!54;UBERON:0001017!2.69e-31!73;UBERON:0010371!3.90e-31!73;UBERON:0001016!9.28e-31!75;UBERON:0001049!1.45e-30!52;UBERON:0005068!1.45e-30!52;UBERON:0006241!1.45e-30!52;UBERON:0007135!1.45e-30!52;UBERON:0004121!1.18e-29!95;UBERON:0000924!1.18e-29!95;UBERON:0006601!1.18e-29!95;UBERON:0003056!7.39e-27!49;UBERON:0002020!8.21e-27!34;UBERON:0000955!1.81e-26!47;UBERON:0006238!1.81e-26!47;UBERON:0002616!1.56e-25!46;UBERON:0003528!1.29e-22!29;UBERON:0002791!1.29e-22!29;UBERON:0001893!1.29e-22!29;UBERON:0003080!1.66e-22!40;UBERON:0010314!3.06e-22!92;UBERON:0002780!8.54e-22!39;UBERON:0001890!8.54e-22!39;UBERON:0006240!8.54e-22!39;UBERON:0000956!2.91e-16!21;UBERON:0001869!2.91e-16!21;UBERON:0000203!2.91e-16!21;UBERON:0002619!1.85e-12!17;UBERON:0002021!1.85e-09!10;UBERON:0000411!1.85e-09!10;UBERON:0001950!1.85e-09!10;UBERON:0003076!2.17e-08!12;UBERON:0003057!2.17e-08!12;UBERON:0002420!1.76e-07!8;UBERON:0007245!1.76e-07!8;UBERON:0010009!1.76e-07!8;UBERON:0010011!1.76e-07!8;UBERON:0000454!1.76e-07!8
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.341626,0.223558,0.279403,0.430128,0.291576,0.370193,0.268276,0.59395,0.484613,0.883008,0.944872,0.960432,0.992198,0.459846,0,0.557619,0.416118,0.896399,0.529269,0.194751,0.383765,0.38026,0.427399,0.64994,0.405649,0.232118,0.309422,1.56623,1.05808,0.805906,0.653099,0.817922,0.202991,0.151158,1.9793,0.125578,0.356403,0.111088,0.309817,0.136186,0.301802,0.0669139,0.152251,0.381636,0.270091,0.48361,1.55597,0.0503358,0.994443,0.541299,0.429887,0.366754,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,1.05034,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.583711,0.991331,0.838198,0.458017,0.192403,0.202885,1.192,0.617814,0.198007,0.279684,0.573903,0.437131,0.932192,0.72691,0.303892,1.44513,2.55287,1.22406,1.44275,1.0064,0.731688,0.665283,0.143149,6.2319,0.661488,0.948949,0.667958,0.483845,1.80811,0.396021,0.652833,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,2.45503,0.570648,0.671624,0.773781,0.19888,0.336214,1.01331,0.41985,0.404932,0.772215,0.558838,0.389429,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,0.445937,0.755703,0.273302,0.907893,1.03283,1.03449,0.932479,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,1.22055,1.76978,0.253405,0.140226,0.173337,1.60376,0.790393,0.331601,0.398786,0.869538,0.430798,0.159498,0.242603,0.251242,0.995609,0.726089,1.50676,0.237049,0.531751,1.01654,0.12482,0.358185,0.085942
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.341626,0.223558,0.279403,0.430128,0.291576,0.370193,0.268276,0.59395,0.484613,0.883008,0.944872,0.960432,0.992198,0.459846,0,0.557619,0.416118,0.896399,0.529269,0.194751,0.383765,0.38026,0.427399,0.64994,0.405649,0.232118,0.309422,1.56623,1.05808,0.805906,0.653099,0.817922,0.202991,0.151158,1.9793,0.125578,0.356403,0.111088,0.309817,0.136186,0.301802,0.0669139,0.152251,0.381636,0.270091,0.48361,1.55597,0.0503358,0.994443,0.541299,0.429887,0.366754,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,1.05034,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.583711,0.991331,0.838198,0.458017,0.192403,0.202885,1.192,0.617814,0.198007,0.279684,0.573903,0.437131,0.932192,0.72691,0.303892,1.44513,2.55287,1.22406,1.44275,1.0064,0.731688,0.665283,0.143149,6.2319,0.661488,0.948949,0.667958,0.483845,1.80811,0.396021,0.652833,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,2.45503,0.570648,0.671624,0.773781,0.19888,0.336214,1.01331,0.41985,0.404932,0.772215,0.558838,0.389429,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,0.445937,0.755703,0.273302,0.907893,1.03283,1.03449,0.932479,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,1.22055,1.76978,0.253405,0.140226,0.173337,1.60376,0.790393,0.331601,0.398786,0.869538,0.430798,0.159498,0.242603,0.251242,0.995609,0.726089,1.50676,0.237049,0.531751,1.01654,0.12482,0.358185,0.085942
|tfbs_overrepresentation_jaspar=MA0003.1;0.353731,MA0004.1;0.279808,MA0006.1;0.451962,MA0007.1;0.267314,MA0009.1;0.678286,MA0014.1;0.650706,MA0017.1;0.166909,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;0.155127,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.622762,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.0358824,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.0835619,MA0056.1;0,MA0057.1;3.96596,MA0058.1;0.585652,MA0059.1;0.212009,MA0060.1;0.0941959,MA0061.1;0.363764,MA0063.1;0,MA0066.1;1.02437,MA0067.1;1.01206,MA0068.1;2.80508,MA0069.1;0.698271,MA0070.1;0.688999,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;6.13352,MA0074.1;0.363923,MA0076.1;0.181159,MA0077.1;0.660245,MA0078.1;0.443468,MA0081.1;0.230351,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.965806,MA0089.1;0,MA0090.1;0.251458,MA0091.1;0.290854,MA0092.1;0.251716,MA0093.1;0.485518,MA0095.1;0,MA0098.1;0,MA0100.1;0.353762,MA0101.1;0.625174,MA0103.1;0.174916,MA0105.1;0.0530438,MA0106.1;0.450539,MA0107.1;0.170338,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.727672,MA0113.1;0.424958,MA0114.1;0.111687,MA0115.1;0.773793,MA0116.1;0.451594,MA0117.1;0.742722,MA0119.1;0.626271,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.262087,MA0140.1;0.353662,MA0141.1;0.18979,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.365041,MA0145.1;0.223975,MA0146.1;0.11048,MA0147.1;0.386218,MA0148.1;0.796977,MA0149.1;0.635479,MA0062.2;0.0556611,MA0035.2;0.357786,MA0039.2;0.728142,MA0138.2;0.495254,MA0002.2;0.0773396,MA0137.2;0.187581,MA0104.2;0.289861,MA0047.2;0.404891,MA0112.2;0.223965,MA0065.2;1.41974,MA0150.1;0.267221,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.593208,MA0155.1;2.52589,MA0156.1;0.180505,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.128669,MA0160.1;0.296006,MA0161.1;0,MA0162.1;0.0597766,MA0163.1;0.386747,MA0164.1;0.381832,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;3.71771,MA0102.2;1.38728,MA0258.1;0.336791,MA0259.1;0.114734,MA0442.1;0
}}
}}

Revision as of 11:59, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:165705099..165705145,-p3@Zmynd8
Mm9::chr2:94104870..94104891,-p1@ENSMUST00000129661
Mm9::chr2:94104902..94104921,-p1@Mir670
Mm9::chr3:120589646..120589664,-p1@uc008rdn.1
Mm9::chr3:88011230..88011250,+p3@uc008pug.1
Mm9::chr3:88019594..88019602,+p1@Mir9-1
Mm9::chr3:88031356..88031360,+p@chr3:88031356..88031360
+
Mm9::chr4:34011611..34011626,+p1@Cnr1
Mm9::chr4:34012007..34012022,+p4@Cnr1
Mm9::chr4:34013350..34013359,+p6@Cnr1
Mm9::chr4:34032489..34032494,+p@chr4:34032489..34032494
+
Mm9::chr9:21828864..21828867,-p@chr9:21828864..21828867
-
Mm9::chr9:34296406..34296420,+p2@Kirrel3


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>

Uber Anatomy
Ontology termp-valuen
neurectoderm5.05e-3664
neural plate5.05e-3664
presumptive neural plate5.05e-3664
regional part of nervous system4.98e-3254
central nervous system2.69e-3173
ecto-epithelium3.90e-3173
nervous system9.28e-3175
neural tube1.45e-3052
neural rod1.45e-3052
future spinal cord1.45e-3052
neural keel1.45e-3052
ectoderm-derived structure1.18e-2995
ectoderm1.18e-2995
presumptive ectoderm1.18e-2995
pre-chordal neural plate7.39e-2749
gray matter8.21e-2734
brain1.81e-2647
future brain1.81e-2647
regional part of brain1.56e-2546
brain grey matter1.29e-2229
regional part of telencephalon1.29e-2229
telencephalon1.29e-2229
anterior neural tube1.66e-2240
structure with developmental contribution from neural crest3.06e-2292
regional part of forebrain8.54e-2239
forebrain8.54e-2239
future forebrain8.54e-2239
cerebral cortex2.91e-1621
cerebral hemisphere2.91e-1621
pallium2.91e-1621
regional part of cerebral cortex1.85e-1217
occipital lobe1.85e-0910
visual cortex1.85e-0910
neocortex1.85e-0910
posterior neural tube2.17e-0812
chordal neural plate2.17e-0812
basal ganglion1.76e-078
nuclear complex of neuraxis1.76e-078
aggregate regional part of brain1.76e-078
collection of basal ganglia1.76e-078
cerebral subcortex1.76e-078


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)
MA0003.10.353731
MA0004.10.279808
MA0006.10.451962
MA0007.10.267314
MA0009.10.678286
MA0014.10.650706
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.622762
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.0358824
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.0835619
MA0056.10
MA0057.13.96596
MA0058.10.585652
MA0059.10.212009
MA0060.10.0941959
MA0061.10.363764
MA0063.10
MA0066.11.02437
MA0067.11.01206
MA0068.12.80508
MA0069.10.698271
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.16.13352
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.230351
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.965806
MA0089.10
MA0090.10.251458
MA0091.10.290854
MA0092.10.251716
MA0093.10.485518
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.10.625174
MA0103.10.174916
MA0105.10.0530438
MA0106.10.450539
MA0107.10.170338
MA0108.20.527977
MA0109.10
MA0111.10.727672
MA0113.10.424958
MA0114.10.111687
MA0115.10.773793
MA0116.10.451594
MA0117.10.742722
MA0119.10.626271
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.262087
MA0140.10.353662
MA0141.10.18979
MA0142.10.575041
MA0143.10.439766
MA0144.10.365041
MA0145.10.223975
MA0146.10.11048
MA0147.10.386218
MA0148.10.796977
MA0149.10.635479
MA0062.20.0556611
MA0035.20.357786
MA0039.20.728142
MA0138.20.495254
MA0002.20.0773396
MA0137.20.187581
MA0104.20.289861
MA0047.20.404891
MA0112.20.223965
MA0065.21.41974
MA0150.10.267221
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.593208
MA0155.12.52589
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.128669
MA0160.10.296006
MA0161.10
MA0162.10.0597766
MA0163.10.386747
MA0164.10.381832
MA0080.20.170995
MA0018.20.390455
MA0099.20.489441
MA0079.23.71771
MA0102.21.38728
MA0258.10.336791
MA0259.10.114734
MA0442.10
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