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MCL coexpression mm9:556: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!1.21e-31!54;UBERON:0001049!1.85e-29!52;UBERON:0005068!1.85e-29!52;UBERON:0006241!1.85e-29!52;UBERON:0007135!1.85e-29!52;UBERON:0001017!7.11e-29!73;UBERON:0001016!1.45e-27!75;UBERON:0002346!2.05e-27!64;UBERON:0003075!2.05e-27!64;UBERON:0007284!2.05e-27!64;UBERON:0000955!1.50e-24!47;UBERON:0006238!1.50e-24!47;UBERON:0002616!1.22e-23!46;UBERON:0010371!1.55e-23!73;UBERON:0004121!9.51e-23!95;UBERON:0000924!9.51e-23!95;UBERON:0006601!9.51e-23!95;UBERON:0003080!8.88e-22!40;UBERON:0010314!3.42e-21!92;UBERON:0002780!9.41e-21!39;UBERON:0001890!9.41e-21!39;UBERON:0006240!9.41e-21!39;UBERON:0003056!9.47e-21!49;UBERON:0002020!1.45e-17!34;UBERON:0003528!3.04e-13!29;UBERON:0002791!3.04e-13!29;UBERON:0001893!3.04e-13!29;UBERON:0002021!2.28e-09!10;UBERON:0000411!2.28e-09!10;UBERON:0001950!2.28e-09!10;UBERON:0001894!8.48e-09!10;UBERON:0006222!8.48e-09!10;UBERON:0002420!2.91e-08!8;UBERON:0007245!2.91e-08!8;UBERON:0010009!2.91e-08!8;UBERON:0010011!2.91e-08!8;UBERON:0000454!2.91e-08!8;UBERON:0003076!4.66e-08!12;UBERON:0003057!4.66e-08!12;UBERON:0002619!2.41e-07!17;UBERON:0000956!3.54e-07!21;UBERON:0001869!3.54e-07!21;UBERON:0000203!3.54e-07!21;UBERON:0002240!5.59e-07!6;UBERON:0005174!5.59e-07!6;UBERON:0001137!5.59e-07!6;UBERON:0000007!7.99e-07!8;UBERON:0003296!7.99e-07!8;UBERON:0010133!7.99e-07!8
|ontology_enrichment_uberon=UBERON:0000073!1.21e-31!54;UBERON:0001049!1.85e-29!52;UBERON:0005068!1.85e-29!52;UBERON:0006241!1.85e-29!52;UBERON:0007135!1.85e-29!52;UBERON:0001017!7.11e-29!73;UBERON:0001016!1.45e-27!75;UBERON:0002346!2.05e-27!64;UBERON:0003075!2.05e-27!64;UBERON:0007284!2.05e-27!64;UBERON:0000955!1.50e-24!47;UBERON:0006238!1.50e-24!47;UBERON:0002616!1.22e-23!46;UBERON:0010371!1.55e-23!73;UBERON:0004121!9.51e-23!95;UBERON:0000924!9.51e-23!95;UBERON:0006601!9.51e-23!95;UBERON:0003080!8.88e-22!40;UBERON:0010314!3.42e-21!92;UBERON:0002780!9.41e-21!39;UBERON:0001890!9.41e-21!39;UBERON:0006240!9.41e-21!39;UBERON:0003056!9.47e-21!49;UBERON:0002020!1.45e-17!34;UBERON:0003528!3.04e-13!29;UBERON:0002791!3.04e-13!29;UBERON:0001893!3.04e-13!29;UBERON:0002021!2.28e-09!10;UBERON:0000411!2.28e-09!10;UBERON:0001950!2.28e-09!10;UBERON:0001894!8.48e-09!10;UBERON:0006222!8.48e-09!10;UBERON:0002420!2.91e-08!8;UBERON:0007245!2.91e-08!8;UBERON:0010009!2.91e-08!8;UBERON:0010011!2.91e-08!8;UBERON:0000454!2.91e-08!8;UBERON:0003076!4.66e-08!12;UBERON:0003057!4.66e-08!12;UBERON:0002619!2.41e-07!17;UBERON:0000956!3.54e-07!21;UBERON:0001869!3.54e-07!21;UBERON:0000203!3.54e-07!21;UBERON:0002240!5.59e-07!6;UBERON:0005174!5.59e-07!6;UBERON:0001137!5.59e-07!6;UBERON:0000007!7.99e-07!8;UBERON:0003296!7.99e-07!8;UBERON:0010133!7.99e-07!8
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.543805,0.635766,0.279403,0.430128,0.291576,0.370193,0.959416,0.59395,0.282547,0.331725,0.35958,0.960432,0.381063,0.15081,0,1.37184,0.824658,0.069633,1.21947,0.194751,0.197405,0.38026,0.137915,0.229596,0.405649,0.861345,0.833023,0.511682,0.169823,0.297405,0.653099,0.817922,0.779896,0.460714,0.510932,0.125578,0.937845,0.358188,0.309817,0.42301,0.301802,0.580776,0.152251,0.816299,0.270091,0.48361,0.322976,0.282668,0.173974,0.541299,0.429887,0.655868,0.788877,1.88857,0.387424,1.02153,0.348382,0.218496,0.385607,0.634076,0.438439,0.628157,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.0812872,0.408053,0.838198,0.796075,0.192403,1.18951,1.192,0.617814,0.198007,0.587166,0.573903,0.437131,0.0742829,0.72691,0.723377,0.00535506,0.170021,0.488122,1.44275,1.0064,0.731688,0.665283,0.440626,0.351307,0.0973538,0.559699,0.667958,0.483845,1.34415,0.396021,0.652833,0.772062,0.541854,1.33639,0.301427,1.45465,0.319507,0.584153,1.08317,0.671624,0.773781,0.577235,0.893019,1.01331,0.134943,0.910117,1.41039,0.558838,0.779038,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,0.145259,0.755703,0.751079,0.907893,0.399614,1.03449,0.0163629,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,0.486482,1.76978,0.705335,0.433248,1.07238,0.173908,0.790393,0.101059,0.398786,0.869538,0.430798,0.159498,0.680297,0.251242,0.995609,0.726089,1.50676,0.237049,0.531751,0.392164,0.786757,0.358185,0.171655
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.543805,0.635766,0.279403,0.430128,0.291576,0.370193,0.959416,0.59395,0.282547,0.331725,0.35958,0.960432,0.381063,0.15081,0,1.37184,0.824658,0.069633,1.21947,0.194751,0.197405,0.38026,0.137915,0.229596,0.405649,0.861345,0.833023,0.511682,0.169823,0.297405,0.653099,0.817922,0.779896,0.460714,0.510932,0.125578,0.937845,0.358188,0.309817,0.42301,0.301802,0.580776,0.152251,0.816299,0.270091,0.48361,0.322976,0.282668,0.173974,0.541299,0.429887,0.655868,0.788877,1.88857,0.387424,1.02153,0.348382,0.218496,0.385607,0.634076,0.438439,0.628157,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.0812872,0.408053,0.838198,0.796075,0.192403,1.18951,1.192,0.617814,0.198007,0.587166,0.573903,0.437131,0.0742829,0.72691,0.723377,0.00535506,0.170021,0.488122,1.44275,1.0064,0.731688,0.665283,0.440626,0.351307,0.0973538,0.559699,0.667958,0.483845,1.34415,0.396021,0.652833,0.772062,0.541854,1.33639,0.301427,1.45465,0.319507,0.584153,1.08317,0.671624,0.773781,0.577235,0.893019,1.01331,0.134943,0.910117,1.41039,0.558838,0.779038,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,0.145259,0.755703,0.751079,0.907893,0.399614,1.03449,0.0163629,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,0.486482,1.76978,0.705335,0.433248,1.07238,0.173908,0.790393,0.101059,0.398786,0.869538,0.430798,0.159498,0.680297,0.251242,0.995609,0.726089,1.50676,0.237049,0.531751,0.392164,0.786757,0.358185,0.171655
|tfbs_overrepresentation_jaspar=MA0003.1;0.882307,MA0004.1;0.279808,MA0006.1;0.14766,MA0007.1;0.737361,MA0009.1;0.678286,MA0014.1;0.288351,MA0017.1;0.499735,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;0.218039,MA0042.1;0.598261,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;1.81898,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;1.06788,MA0056.1;0,MA0057.1;0.878515,MA0058.1;0.202403,MA0059.1;0.212009,MA0060.1;1.07734,MA0061.1;0.113212,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;0.312793,MA0069.1;0.698271,MA0070.1;0.688999,MA0071.1;0.838726,MA0072.1;0.680902,MA0073.1;0.0201813,MA0074.1;1.70003,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;0.204026,MA0089.1;0,MA0090.1;0.251458,MA0091.1;0.290854,MA0092.1;0.70143,MA0093.1;0.161141,MA0095.1;0,MA0098.1;0,MA0100.1;0.931999,MA0101.1;0.219061,MA0103.1;0.174916,MA0105.1;0.196316,MA0106.1;0.450539,MA0107.1;0.170338,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.263095,MA0113.1;0.424958,MA0114.1;1.19632,MA0115.1;0.773793,MA0116.1;0.147513,MA0117.1;0.742722,MA0119.1;0.219527,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;0.0756871,MA0140.1;0.353662,MA0141.1;0.555407,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.1137,MA0145.1;0.0201868,MA0146.1;0.358872,MA0147.1;0.121834,MA0148.1;0.293462,MA0149.1;0.223436,MA0062.2;0.0556611,MA0035.2;0.940904,MA0039.2;0.728142,MA0138.2;0.495254,MA0002.2;0.0773396,MA0137.2;0.187581,MA0104.2;0.0856657,MA0047.2;0.404891,MA0112.2;0.427883,MA0065.2;2.86769,MA0150.1;0.267221,MA0151.1;0,MA0152.1;1.04455,MA0153.1;0.822355,MA0154.1;0.326723,MA0155.1;0.778998,MA0156.1;0.180505,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.403827,MA0160.1;0.296006,MA0161.1;0,MA0162.1;0.137604,MA0163.1;2.58612,MA0164.1;0.381832,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;2.94567,MA0102.2;1.38728,MA0258.1;0.336791,MA0259.1;0.367748,MA0442.1;0
}}
}}

Revision as of 11:56, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:101329495..101329506,+p7@Rnd2
Mm9::chr13:25034764..25034799,+p6@Gpld1
Mm9::chr17:25393219..25393238,-p1@Baiap3
Mm9::chr18:31476613..31476624,-p4@Rit2
Mm9::chr1:75274920..75275015,-p1@Resp18
Mm9::chr1:75275016..75275030,-p2@Resp18
Mm9::chr3:31106988..31106998,-p@chr3:31106988..31106998
-
Mm9::chrX:46838265..46838299,+p@chrX:46838265..46838299
+
Mm9::chrX:47141381..47141413,-p2@Igsf1
Mm9::chrX:7497036..7497046,+p2@Pcsk1n
Mm9::chrX:7499517..7499528,-p@chrX:7499517..7499528
-
Mm9::chrX:7500293..7500317,-p@chrX:7500293..7500317
-
Mm9::chrX:93908798..93908814,+p1@Gpr165


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:0004621glycosylphosphatidylinositol phospholipase D activity0.0170656878321372
GO:0006507GPI anchor release0.0170656878321372



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)1.58e-1223
neuroblast (sensu Vertebrata)1.58e-1223
neuron4.07e-0933
neuronal stem cell4.07e-0933
neuroblast4.07e-0933
electrically signaling cell4.07e-0933

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.21e-3154
neural tube1.85e-2952
neural rod1.85e-2952
future spinal cord1.85e-2952
neural keel1.85e-2952
central nervous system7.11e-2973
nervous system1.45e-2775
neurectoderm2.05e-2764
neural plate2.05e-2764
presumptive neural plate2.05e-2764
brain1.50e-2447
future brain1.50e-2447
regional part of brain1.22e-2346
ecto-epithelium1.55e-2373
ectoderm-derived structure9.51e-2395
ectoderm9.51e-2395
presumptive ectoderm9.51e-2395
anterior neural tube8.88e-2240
structure with developmental contribution from neural crest3.42e-2192
regional part of forebrain9.41e-2139
forebrain9.41e-2139
future forebrain9.41e-2139
pre-chordal neural plate9.47e-2149
gray matter1.45e-1734
brain grey matter3.04e-1329
regional part of telencephalon3.04e-1329
telencephalon3.04e-1329
occipital lobe2.28e-0910
visual cortex2.28e-0910
neocortex2.28e-0910
diencephalon8.48e-0910
future diencephalon8.48e-0910
basal ganglion2.91e-088
nuclear complex of neuraxis2.91e-088
aggregate regional part of brain2.91e-088
collection of basal ganglia2.91e-088
cerebral subcortex2.91e-088
posterior neural tube4.66e-0812
chordal neural plate4.66e-0812
regional part of cerebral cortex2.41e-0717
cerebral cortex3.54e-0721
cerebral hemisphere3.54e-0721
pallium3.54e-0721
spinal cord5.59e-076
dorsal region element5.59e-076
dorsum5.59e-076
pituitary gland7.99e-078
gland of diencephalon7.99e-078
neuroendocrine gland7.99e-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)
MA0003.10.882307
MA0004.10.279808
MA0006.10.14766
MA0007.10.737361
MA0009.10.678286
MA0014.10.288351
MA0017.10.499735
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
MA0041.10.218039
MA0042.10.598261
MA0043.10.771094
MA0046.10.712646
MA0048.11.81898
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.11.06788
MA0056.10
MA0057.10.878515
MA0058.10.202403
MA0059.10.212009
MA0060.11.07734
MA0061.10.113212
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.10.312793
MA0069.10.698271
MA0070.10.688999
MA0071.10.838726
MA0072.10.680902
MA0073.10.0201813
MA0074.11.70003
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.230351
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.204026
MA0089.10
MA0090.10.251458
MA0091.10.290854
MA0092.10.70143
MA0093.10.161141
MA0095.10
MA0098.10
MA0100.10.931999
MA0101.10.219061
MA0103.10.174916
MA0105.10.196316
MA0106.10.450539
MA0107.10.170338
MA0108.20.527977
MA0109.10
MA0111.10.263095
MA0113.10.424958
MA0114.11.19632
MA0115.10.773793
MA0116.10.147513
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.0756871
MA0140.10.353662
MA0141.10.555407
MA0142.10.575041
MA0143.10.439766
MA0144.10.1137
MA0145.10.0201868
MA0146.10.358872
MA0147.10.121834
MA0148.10.293462
MA0149.10.223436
MA0062.20.0556611
MA0035.20.940904
MA0039.20.728142
MA0138.20.495254
MA0002.20.0773396
MA0137.20.187581
MA0104.20.0856657
MA0047.20.404891
MA0112.20.427883
MA0065.22.86769
MA0150.10.267221
MA0151.10
MA0152.11.04455
MA0153.10.822355
MA0154.10.326723
MA0155.10.778998
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.403827
MA0160.10.296006
MA0161.10
MA0162.10.137604
MA0163.12.58612
MA0164.10.381832
MA0080.20.170995
MA0018.20.390455
MA0099.20.489441
MA0079.22.94567
MA0102.21.38728
MA0258.10.336791
MA0259.10.367748
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:556&oldid=2573951"