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MCL coexpression mm9:1170: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002346!7.64e-20!64;UBERON:0003075!7.64e-20!64;UBERON:0007284!7.64e-20!64;UBERON:0000073!7.33e-18!54;UBERON:0010371!7.98e-18!73;UBERON:0001049!3.59e-17!52;UBERON:0005068!3.59e-17!52;UBERON:0006241!3.59e-17!52;UBERON:0007135!3.59e-17!52;UBERON:0000955!3.50e-16!47;UBERON:0006238!3.50e-16!47;UBERON:0004121!1.63e-15!95;UBERON:0000924!1.63e-15!95;UBERON:0006601!1.63e-15!95;UBERON:0001017!2.20e-15!73;UBERON:0002616!8.17e-15!46;UBERON:0001016!8.87e-15!75;UBERON:0003056!3.39e-14!49;UBERON:0010314!1.45e-13!92;UBERON:0003080!1.41e-10!40;UBERON:0002780!2.08e-09!39;UBERON:0001890!2.08e-09!39;UBERON:0006240!2.08e-09!39;UBERON:0002950!3.13e-09!4;UBERON:0001891!3.13e-09!4;UBERON:0009616!3.13e-09!4;UBERON:0010286!3.13e-09!4;UBERON:0002420!1.70e-08!8;UBERON:0007245!1.70e-08!8;UBERON:0010009!1.70e-08!8;UBERON:0010011!1.70e-08!8;UBERON:0000454!1.70e-08!8;UBERON:0002020!2.84e-08!34;UBERON:0003076!4.68e-08!12;UBERON:0003057!4.68e-08!12;UBERON:0003528!2.98e-07!29;UBERON:0002791!2.98e-07!29;UBERON:0001893!2.98e-07!29;UBERON:0002038!3.24e-07!3;UBERON:0009663!3.24e-07!3;UBERON:0009661!3.24e-07!3;UBERON:0000125!3.24e-07!3;UBERON:0002308!3.24e-07!3
|ontology_enrichment_uberon=UBERON:0002346!7.64e-20!64;UBERON:0003075!7.64e-20!64;UBERON:0007284!7.64e-20!64;UBERON:0000073!7.33e-18!54;UBERON:0010371!7.98e-18!73;UBERON:0001049!3.59e-17!52;UBERON:0005068!3.59e-17!52;UBERON:0006241!3.59e-17!52;UBERON:0007135!3.59e-17!52;UBERON:0000955!3.50e-16!47;UBERON:0006238!3.50e-16!47;UBERON:0004121!1.63e-15!95;UBERON:0000924!1.63e-15!95;UBERON:0006601!1.63e-15!95;UBERON:0001017!2.20e-15!73;UBERON:0002616!8.17e-15!46;UBERON:0001016!8.87e-15!75;UBERON:0003056!3.39e-14!49;UBERON:0010314!1.45e-13!92;UBERON:0003080!1.41e-10!40;UBERON:0002780!2.08e-09!39;UBERON:0001890!2.08e-09!39;UBERON:0006240!2.08e-09!39;UBERON:0002950!3.13e-09!4;UBERON:0001891!3.13e-09!4;UBERON:0009616!3.13e-09!4;UBERON:0010286!3.13e-09!4;UBERON:0002420!1.70e-08!8;UBERON:0007245!1.70e-08!8;UBERON:0010009!1.70e-08!8;UBERON:0010011!1.70e-08!8;UBERON:0000454!1.70e-08!8;UBERON:0002020!2.84e-08!34;UBERON:0003076!4.68e-08!12;UBERON:0003057!4.68e-08!12;UBERON:0003528!2.98e-07!29;UBERON:0002791!2.98e-07!29;UBERON:0001893!2.98e-07!29;UBERON:0002038!3.24e-07!3;UBERON:0009663!3.24e-07!3;UBERON:0009661!3.24e-07!3;UBERON:0000125!3.24e-07!3;UBERON:0002308!3.24e-07!3
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.0609112,0.542749,1.40872,1.12363,0.599731,0.315771,0,0.795315,0.792229,0.19222,0.112498,0.374752,0.586604,0.598814,0.29769,1.07577,0.62766,0.184473,0.516511,0.344372,1.41139,0.50223,0.897561,0.289148,0.166577,0.316253,0.101236,0.279977,0.57142,0.258564,0.230656,0.800988,0.507468,0.0742755,0.317766,0.115244,0.469348,0.714592,0.532496,0.0609361,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,0.936963,0.498755,0.703064,0.859987,0.98764,0.610783,0.812889,0.663039,0.200155,0.975495,0.146394,0.042613,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.823238,0.254625,0.237542,0.589174,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.187586,0.484437,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.580299,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.545091,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,1.11101,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.0907999
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.0609112,0.542749,1.40872,1.12363,0.599731,0.315771,0,0.795315,0.792229,0.19222,0.112498,0.374752,0.586604,0.598814,0.29769,1.07577,0.62766,0.184473,0.516511,0.344372,1.41139,0.50223,0.897561,0.289148,0.166577,0.316253,0.101236,0.279977,0.57142,0.258564,0.230656,0.800988,0.507468,0.0742755,0.317766,0.115244,0.469348,0.714592,0.532496,0.0609361,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,0.936963,0.498755,0.703064,0.859987,0.98764,0.610783,0.812889,0.663039,0.200155,0.975495,0.146394,0.042613,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.823238,0.254625,0.237542,0.589174,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.187586,0.484437,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.580299,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.545091,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,1.11101,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.0907999
|tfbs_overrepresentation_jaspar=MA0003.1;0.0286946,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.0886247,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,MA0029.1;3.30488,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;1.84075,MA0042.1;1.01509,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;1.29283,MA0051.1;2.60576,MA0052.1;0.945011,MA0055.1;0.157978,MA0056.1;0,MA0057.1;0.117936,MA0058.1;1.00014,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.724575,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.121435,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;1.29103,MA0072.1;0.927016,MA0073.1;0.00782298,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.285759,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.879104,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.9471,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.304732,MA0146.1;0.108739,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.113749,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.102995,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.0312493,MA0163.1;0.116706,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.0190804,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}
}}

Revision as of 12:55, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:17211323..17211328,+p10@Prune2
Mm9::chr5:27208073..27208074,+p@chr5:27208073..27208074
+
Mm9::chr5:27384379..27384387,+p@chr5:27384379..27384387
+
Mm9::chr5:27507996..27507999,+p@chr5:27507996..27507999
+
Mm9::chr6:140439585..140439594,+p@chr6:140439585..140439594
+
Mm9::chr8:112685265..112685266,-p@chr8:112685265..112685266
-
Mm9::chr9:107242924..107242979,+p1@6430571L13Rik


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
neuron of the substantia nigra3.24e-073

Uber Anatomy
Ontology termp-valuen
neurectoderm7.64e-2064
neural plate7.64e-2064
presumptive neural plate7.64e-2064
regional part of nervous system7.33e-1854
ecto-epithelium7.98e-1873
neural tube3.59e-1752
neural rod3.59e-1752
future spinal cord3.59e-1752
neural keel3.59e-1752
brain3.50e-1647
future brain3.50e-1647
ectoderm-derived structure1.63e-1595
ectoderm1.63e-1595
presumptive ectoderm1.63e-1595
central nervous system2.20e-1573
regional part of brain8.17e-1546
nervous system8.87e-1575
pre-chordal neural plate3.39e-1449
structure with developmental contribution from neural crest1.45e-1392
anterior neural tube1.41e-1040
regional part of forebrain2.08e-0939
forebrain2.08e-0939
future forebrain2.08e-0939
regional part of midbrain3.13e-094
midbrain3.13e-094
presumptive midbrain3.13e-094
midbrain neural tube3.13e-094
basal ganglion1.70e-088
nuclear complex of neuraxis1.70e-088
aggregate regional part of brain1.70e-088
collection of basal ganglia1.70e-088
cerebral subcortex1.70e-088
gray matter2.84e-0834
posterior neural tube4.68e-0812
chordal neural plate4.68e-0812
brain grey matter2.98e-0729
regional part of telencephalon2.98e-0729
telencephalon2.98e-0729
substantia nigra3.24e-073
telencephalic nucleus3.24e-073
midbrain nucleus3.24e-073
neural nucleus3.24e-073
nucleus of brain3.24e-073


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)
MA0003.10.0286946
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.0886247
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.13.30488
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.11.84075
MA0042.11.01509
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.11.29283
MA0051.12.60576
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.10.117936
MA0058.11.00014
MA0059.10.397033
MA0060.10.232592
MA0061.10.724575
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.11.29103
MA0072.10.927016
MA0073.10.00782298
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.879104
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.9471
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.304732
MA0146.10.108739
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.113749
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.102995
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.0312493
MA0163.10.116706
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.0190804
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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