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MCL coexpression mm9:538: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002346!9.61e-26!64;UBERON:0003075!9.61e-26!64;UBERON:0007284!9.61e-26!64;UBERON:0010371!1.46e-22!73;UBERON:0001049!3.14e-21!52;UBERON:0005068!3.14e-21!52;UBERON:0006241!3.14e-21!52;UBERON:0007135!3.14e-21!52;UBERON:0000073!4.73e-21!54;UBERON:0003056!5.72e-21!49;UBERON:0001017!2.79e-20!73;UBERON:0004121!3.34e-20!95;UBERON:0000924!3.34e-20!95;UBERON:0006601!3.34e-20!95;UBERON:0001016!3.60e-19!75;UBERON:0000955!4.35e-19!47;UBERON:0006238!4.35e-19!47;UBERON:0002616!3.41e-18!46;UBERON:0002020!9.50e-18!34;UBERON:0003080!9.08e-17!40;UBERON:0010314!1.44e-16!92;UBERON:0002780!4.97e-16!39;UBERON:0001890!4.97e-16!39;UBERON:0006240!4.97e-16!39;UBERON:0003528!1.35e-15!29;UBERON:0002791!1.35e-15!29;UBERON:0001893!1.35e-15!29;UBERON:0000956!5.72e-12!21;UBERON:0001869!5.72e-12!21;UBERON:0000203!5.72e-12!21;UBERON:0002619!1.06e-10!17;UBERON:0002021!2.21e-10!10;UBERON:0000411!2.21e-10!10;UBERON:0001950!2.21e-10!10;UBERON:0000025!4.10e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.00367872,0.204219,0.716126,0.123731,0.743234,0.346405,0.237242,0.0719629,0.0394224,0.308886,0.336042,0.237599,0.357027,0.134875,0,0.530547,0.377686,0.0594359,0.100162,2.27104,0.0622339,0.356242,0.388504,0.210021,0.381085,0.0554034,0.287195,0.154744,0.145734,0.275529,0.624931,0.117091,0.397142,0.135203,0.0302663,0.111136,0.332941,0.322338,0.0808072,0.121091,0.279796,0.295897,0.136236,0.0109479,0.24907,0.457618,0.300372,0.237017,0.156829,0.514446,0.404841,0.137142,0.759566,0.776306,0.363247,0.950326,0.325117,0.744745,0.36147,0.606104,0.413233,0.0784106,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.189925,0.0700673,0.0681764,0.808562,0.0481979,0.0433214,0.702638,0.447339,0.590017,0.531085,0.247973,0.546623,1.05972,0.849185,0.69807,0.0177525,0.0697055,0.145915,0.462057,1.41118,0.975915,0.702809,0.636995,0.401201,0.0951738,0.601346,0.503836,0.639644,0.457849,0.0288834,0.725622,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,0.177945,0.218949,0.744577,0.180573,0.313258,0.982794,0.119923,0.0290103,0.26114,0.53175,0.352143,0.813766,1.21719,0.382687,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.406303,0.726634,0.252176,0.877862,0.375176,1.0039,0.0607709,0.65343,0.280962,0.955897,1.77738,1.3796,0.91261,1.01903,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,0.124893,0.0377782,0.0106906,0.761071,0.0882878,0.374365,0.839715,0.405736,0.143092,0.222538,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.110426,0.33468,0.000933345
|tfbs_overrepresentation_jaspar=MA0003.1;0.000592671,MA0004.1;0.258473,MA0006.1;0.412095,MA0007.1;0.246385,MA0009.1;0.649874,MA0014.1;0.00638392,MA0017.1;0.150118,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;0.588275,MA0030.1;1.44943,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;1.59033,MA0041.1;1.09418,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.0293065,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.0206669,MA0056.1;0,MA0057.1;0.107353,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;0.0819399,MA0061.1;0.32765,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.807617,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;0.000323235,MA0074.1;0.340281,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.0136969,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;0.231323,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;0.199903,MA0103.1;0.157724,MA0105.1;0.0444807,MA0106.1;0.425111,MA0107.1;0.153373,MA0108.2;0.50131,MA0109.1;0,MA0111.1;0.242308,MA0113.1;0.400008,MA0114.1;0.0981613,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;1.99553,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.0649474,MA0140.1;0.879752,MA0141.1;0.171891,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.100037,MA0145.1;0.0158349,MA0146.1;0.00972339,MA0147.1;0.107632,MA0148.1;0.271704,MA0149.1;0.204102,MA0062.2;0.046824,MA0035.2;0.33429,MA0039.2;0.00306976,MA0138.2;0.469076,MA0002.2;0.235791,MA0137.2;0.169785,MA0104.2;0.0740839,MA0047.2;0.380343,MA0112.2;0.0158338,MA0065.2;0.0735294,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.990823,MA0153.1;0.792819,MA0154.1;0.525346,MA0155.1;0.0198039,MA0156.1;0.163042,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.365914,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.00209837,MA0163.1;0.00169705,MA0164.1;0.940888,MA0080.2;0.153997,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;8.76579e-06,MA0102.2;1.35579,MA0258.1;0.0900907,MA0259.1;0.101001,MA0442.1;0
}}

Latest revision as of 15:28, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:71370224..71370227,-p@chr12:71370224..71370227
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Mm9::chr12:89961310..89961337,+p1@LOC100505240
p1@Nrxn3
Mm9::chr12:90101490..90101498,+p@chr12:90101490..90101498
+
Mm9::chr12:90195865..90195874,+p@chr12:90195865..90195874
+
Mm9::chr12:90284364..90284369,+p@chr12:90284364..90284369
+
Mm9::chr12:90327898..90327900,+p@chr12:90327898..90327900
+
Mm9::chr12:90529035..90529036,+p@chr12:90529035..90529036
+
Mm9::chr12:90642180..90642186,+p@chr12:90642180..90642186
+
Mm9::chr12:90692461..90692464,+p@chr12:90692461..90692464
+
Mm9::chr12:90840435..90840439,+p@chr12:90840435..90840439
+
Mm9::chr12:90880825..90880838,+p@chr12:90880825..90880838
+
Mm9::chr19:46400679..46400701,-p@chr19:46400679..46400701
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Mm9::chr6:37095977..37095979,-p@chr6:37095977..37095979
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Mm9::chr8:60736612..60736623,-p@chr8:60736612..60736623
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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
neuron8.41e-0833
neuronal stem cell8.41e-0833
neuroblast8.41e-0833
electrically signaling cell8.41e-0833
CNS neuron (sensu Vertebrata)1.12e-0723
neuroblast (sensu Vertebrata)1.12e-0723

Uber Anatomy
Ontology termp-valuen
neurectoderm9.61e-2664
neural plate9.61e-2664
presumptive neural plate9.61e-2664
ecto-epithelium1.46e-2273
neural tube3.14e-2152
neural rod3.14e-2152
future spinal cord3.14e-2152
neural keel3.14e-2152
regional part of nervous system4.73e-2154
pre-chordal neural plate5.72e-2149
central nervous system2.79e-2073
ectoderm-derived structure3.34e-2095
ectoderm3.34e-2095
presumptive ectoderm3.34e-2095
nervous system3.60e-1975
brain4.35e-1947
future brain4.35e-1947
regional part of brain3.41e-1846
gray matter9.50e-1834
anterior neural tube9.08e-1740
structure with developmental contribution from neural crest1.44e-1692
regional part of forebrain4.97e-1639
forebrain4.97e-1639
future forebrain4.97e-1639
brain grey matter1.35e-1529
regional part of telencephalon1.35e-1529
telencephalon1.35e-1529
cerebral cortex5.72e-1221
cerebral hemisphere5.72e-1221
pallium5.72e-1221
regional part of cerebral cortex1.06e-1017
occipital lobe2.21e-1010
visual cortex2.21e-1010
neocortex2.21e-1010
tube4.10e-07114


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)
MA0003.10.000592671
MA0004.10.258473
MA0006.10.412095
MA0007.10.246385
MA0009.10.649874
MA0014.10.00638392
MA0017.10.150118
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.10.588275
MA0030.11.44943
MA0031.10.561217
MA0038.10.381016
MA0040.11.59033
MA0041.11.09418
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.0293065
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.0206669
MA0056.10
MA0057.10.107353
MA0058.10.183941
MA0059.10.19314
MA0060.10.0819399
MA0061.10.32765
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.807617
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.10.000323235
MA0074.10.340281
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.0136969
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.231323
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.157724
MA0105.10.0444807
MA0106.10.425111
MA0107.10.153373
MA0108.20.50131
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.0981613
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.11.99553
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.0649474
MA0140.10.879752
MA0141.10.171891
MA0142.10.547747
MA0143.10.414534
MA0144.10.100037
MA0145.10.0158349
MA0146.10.00972339
MA0147.10.107632
MA0148.10.271704
MA0149.10.204102
MA0062.20.046824
MA0035.20.33429
MA0039.20.00306976
MA0138.20.469076
MA0002.20.235791
MA0137.20.169785
MA0104.20.0740839
MA0047.20.380343
MA0112.20.0158338
MA0065.20.0735294
MA0150.10.246295
MA0151.10
MA0152.10.990823
MA0153.10.792819
MA0154.10.525346
MA0155.10.0198039
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.365914
MA0160.10.274172
MA0161.10
MA0162.10.00209837
MA0163.10.00169705
MA0164.10.940888
MA0080.20.153997
MA0018.20.366212
MA0099.20.463355
MA0079.28.76579e-06
MA0102.21.35579
MA0258.10.0900907
MA0259.10.101001
MA0442.10
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