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MCL coexpression mm9:1098: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!2.98e-09!23;CL:0000337!2.98e-09!23;CL:0000540!7.01e-09!33;CL:0000047!7.01e-09!33;CL:0000031!7.01e-09!33;CL:0000404!7.01e-09!33;CL:0000393!1.10e-08!39;CL:0000211!1.10e-08!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.95e-15!54;UBERON:0001016!8.85e-15!75;UBERON:0001017!1.63e-14!73;UBERON:0001049!4.26e-14!52;UBERON:0005068!4.26e-14!52;UBERON:0006241!4.26e-14!52;UBERON:0007135!4.26e-14!52;UBERON:0002020!1.26e-13!34;UBERON:0011216!4.24e-12!194;UBERON:0002346!7.30e-12!64;UBERON:0003075!7.30e-12!64;UBERON:0007284!7.30e-12!64;UBERON:0000955!1.88e-11!47;UBERON:0006238!1.88e-11!47;UBERON:0003080!1.96e-11!40;UBERON:0002616!4.07e-11!46;UBERON:0003528!4.83e-11!29;UBERON:0002791!4.83e-11!29;UBERON:0001893!4.83e-11!29;UBERON:0002780!5.76e-11!39;UBERON:0001890!5.76e-11!39;UBERON:0006240!5.76e-11!39;UBERON:0003056!3.59e-09!49;UBERON:0004121!4.15e-09!95;UBERON:0000924!4.15e-09!95;UBERON:0006601!4.15e-09!95;UBERON:0010371!1.30e-08!73;UBERON:0000956!2.26e-08!21;UBERON:0001869!2.26e-08!21;UBERON:0000203!2.26e-08!21;UBERON:0002021!3.93e-08!10;UBERON:0000411!3.93e-08!10;UBERON:0001950!3.93e-08!10;UBERON:0002619!2.38e-07!17;UBERON:0000477!5.63e-07!244;UBERON:0010314!9.86e-07!92
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,0.480627,0.810002,0.495263,0.587291,0.206208,0.215218,0.0609112,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.792229,0.561256,0.361892,0.374752,0.27937,1.45867,0.80655,0.419327,0.62766,0.184473,0.516511,0.344372,0.446946,0.50223,0.897561,0.289148,0.166577,0.316253,0.101236,0.279977,0.57142,0.258564,0.230656,1.45644,0.507468,0.258106,0.317766,0.115244,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,0.159969,0.166511,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,1.09903,0.975495,0.0369809,0.164297,0.877485,0.719558,1.70793,1.26498,0.980512,0.910485,0.823238,0.254625,1.24315,0.203879,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,1.9541,1.30996,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.0501572,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.829907,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,1.26636,0.717753,2.03691,0.448938,0.300961,0.452587,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,1.40533,0.433127
|tfbs_overrepresentation_jaspar=MA0003.1;0.00513025,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;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;1.01509,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.40238,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.0406078,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;1.33382,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.771749,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.152496,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;2.32874,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;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.0468,MA0103.1;0.348572,MA0105.1;0.488671,MA0106.1;0.677988,MA0107.1;0.906859,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;0.72625,MA0145.1;0.631666,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;0.00226251,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;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.687925,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;0.0280055,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.00878868,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:101441843..101441883,+p@chr12:101441843..101441883
+
Mm9::chr12:101443818..101443871,+p4@Calm2
p5@Calm3
p6@Calm1
Mm9::chr12:101444302..101444319,+p@chr12:101444302..101444319
+
Mm9::chr12:101444324..101444349,+p@chr12:101444324..101444349
+
Mm9::chr12:101444921..101444976,+p@chr12:101444921..101444976
+
Mm9::chr18:36955683..36955696,+p@chr18:36955683..36955696
+
Mm9::chr19:7501312..7501325,-p@chr19:7501312..7501325
-


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:0043388positive regulation of DNA binding0.0246413268465401
GO:0051099positive regulation of binding0.0246413268465401
GO:0051101regulation of DNA binding0.0246413268465401
GO:0051098regulation of binding0.0369417393457434
GO:0007049cell cycle0.0383171664200432
GO:0005509calcium ion binding0.0398702616799364



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)2.98e-0923
neuroblast (sensu Vertebrata)2.98e-0923
neuron7.01e-0933
neuronal stem cell7.01e-0933
neuroblast7.01e-0933
electrically signaling cell7.01e-0933
electrically responsive cell1.10e-0839
electrically active cell1.10e-0839

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.95e-1554
nervous system8.85e-1575
central nervous system1.63e-1473
neural tube4.26e-1452
neural rod4.26e-1452
future spinal cord4.26e-1452
neural keel4.26e-1452
gray matter1.26e-1334
organ system subdivision4.24e-12194
neurectoderm7.30e-1264
neural plate7.30e-1264
presumptive neural plate7.30e-1264
brain1.88e-1147
future brain1.88e-1147
anterior neural tube1.96e-1140
regional part of brain4.07e-1146
brain grey matter4.83e-1129
regional part of telencephalon4.83e-1129
telencephalon4.83e-1129
regional part of forebrain5.76e-1139
forebrain5.76e-1139
future forebrain5.76e-1139
pre-chordal neural plate3.59e-0949
ectoderm-derived structure4.15e-0995
ectoderm4.15e-0995
presumptive ectoderm4.15e-0995
ecto-epithelium1.30e-0873
cerebral cortex2.26e-0821
cerebral hemisphere2.26e-0821
pallium2.26e-0821
occipital lobe3.93e-0810
visual cortex3.93e-0810
neocortex3.93e-0810
regional part of cerebral cortex2.38e-0717
anatomical cluster5.63e-07244
structure with developmental contribution from neural crest9.86e-0792


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)
MA0003.10.00513025
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
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.11.01509
MA0043.11.02178
MA0046.10.960497
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.11.33382
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.152496
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.12.32874
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.10.906859
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
MA0144.10.72625
MA0145.10.631666
MA0146.10.108739
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.00226251
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.687925
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.0312493
MA0163.10.0280055
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.20.00878868
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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