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MCL coexpression mm9:1137: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002346!1.16e-36!64;UBERON:0003075!1.16e-36!64;UBERON:0007284!1.16e-36!64;UBERON:0001017!3.54e-35!73;UBERON:0001016!3.61e-35!75;UBERON:0004121!3.75e-35!95;UBERON:0000924!3.75e-35!95;UBERON:0006601!3.75e-35!95;UBERON:0010371!4.21e-31!73;UBERON:0003056!1.01e-29!49;UBERON:0000073!6.08e-29!54;UBERON:0001049!1.27e-27!52;UBERON:0005068!1.27e-27!52;UBERON:0006241!1.27e-27!52;UBERON:0007135!1.27e-27!52;UBERON:0000955!3.03e-25!47;UBERON:0006238!3.03e-25!47;UBERON:0010314!1.17e-24!92;UBERON:0002616!2.18e-24!46;UBERON:0003080!1.02e-22!40;UBERON:0002780!4.71e-22!39;UBERON:0001890!4.71e-22!39;UBERON:0006240!4.71e-22!39;UBERON:0002020!1.35e-19!34;UBERON:0003528!4.69e-17!29;UBERON:0002791!4.69e-17!29;UBERON:0001893!4.69e-17!29;UBERON:0000956!2.95e-12!21;UBERON:0001869!2.95e-12!21;UBERON:0000203!2.95e-12!21;UBERON:0002619!3.87e-09!17;UBERON:0000970!1.13e-07!9;UBERON:0000019!1.13e-07!9;UBERON:0000047!1.13e-07!9;UBERON:0010312!1.13e-07!9;UBERON:0004088!1.13e-07!9;UBERON:0002104!1.13e-07!9;UBERON:0001456!1.13e-07!9;UBERON:0003072!1.13e-07!9;UBERON:0004128!1.13e-07!9;UBERON:0003071!1.13e-07!9;UBERON:0002021!1.79e-07!10;UBERON:0000411!1.79e-07!10;UBERON:0001950!1.79e-07!10;UBERON:0000020!4.77e-07!12;UBERON:0001032!4.77e-07!12;UBERON:0004456!4.77e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,0.480627,0.810002,0.495263,0.587291,0.206208,1.15776,0.219671,0.542749,0.575086,1.12363,0.599731,0.315771,0,0.795315,0.291368,0.19222,0.112498,0.374752,0.27937,0.598814,0.29769,0.419327,1.51917,0.184473,0.516511,0.344372,0.446946,0.50223,0.897561,1.43437,0.166577,0.316253,2.47396,1.40094,0.57142,0.258564,0.652422,0.800988,0.507468,0.0742755,0.317766,0.115244,0.469348,0.714592,0.532496,0.82704,0.347313,0.777641,0.654933,0.851157,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,2.7172,1.09164,0.97874,0.159969,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.613286,0.667407,2.03326,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.668513,0.203879,0.913319,0.71485,3.25743,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.187586,2.10934,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.545091,1.04192,0.681896,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.763807,1.40533,0.0907999
|tfbs_overrepresentation_jaspar=MA0003.1;0.188259,MA0004.1;1.20906,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.222567,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;0.391504,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;0.362005,MA0056.1;0,MA0057.1;3.14169,MA0058.1;1.00014,MA0059.1;1.02718,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.385183,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;1.60783,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.598004,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;1.58083,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,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;2.30533,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;1.90582,MA0143.1;2.69964,MA0144.1;0.262477,MA0145.1;0.304732,MA0146.1;0.264322,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.790799,MA0138.2;0.727395,MA0002.2;1.11916,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;1.51738,MA0112.2;1.05549,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.397336,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;0.878466,MA0163.1;0.82914,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;5.73977,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:27, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:60996517..60996540,+p@chr14:60996517..60996540
+
Mm9::chr14:60997132..60997208,+p1@Fam123a
Mm9::chr14:65208639..65208685,+p2@ENSMUST00000164162
Mm9::chr2:181501988..181502026,+p3@Myt1
Mm9::chr2:181502048..181502090,+p@chr2:181502048..181502090
+
Mm9::chr5:117041820..117041839,-p1@Srrm4
Mm9::chr5:117041867..117041874,-p3@Srrm4


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
neurectoderm1.16e-3664
neural plate1.16e-3664
presumptive neural plate1.16e-3664
central nervous system3.54e-3573
nervous system3.61e-3575
ectoderm-derived structure3.75e-3595
ectoderm3.75e-3595
presumptive ectoderm3.75e-3595
ecto-epithelium4.21e-3173
pre-chordal neural plate1.01e-2949
regional part of nervous system6.08e-2954
neural tube1.27e-2752
neural rod1.27e-2752
future spinal cord1.27e-2752
neural keel1.27e-2752
brain3.03e-2547
future brain3.03e-2547
structure with developmental contribution from neural crest1.17e-2492
regional part of brain2.18e-2446
anterior neural tube1.02e-2240
regional part of forebrain4.71e-2239
forebrain4.71e-2239
future forebrain4.71e-2239
gray matter1.35e-1934
brain grey matter4.69e-1729
regional part of telencephalon4.69e-1729
telencephalon4.69e-1729
cerebral cortex2.95e-1221
cerebral hemisphere2.95e-1221
pallium2.95e-1221
regional part of cerebral cortex3.87e-0917
eye1.13e-079
camera-type eye1.13e-079
simple eye1.13e-079
immature eye1.13e-079
ocular region1.13e-079
visual system1.13e-079
face1.13e-079
optic cup1.13e-079
optic vesicle1.13e-079
eye primordium1.13e-079
occipital lobe1.79e-0710
visual cortex1.79e-0710
neocortex1.79e-0710
sense organ4.77e-0712
sensory system4.77e-0712
entire sense organ system4.77e-0712


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)
MA0003.10.188259
MA0004.11.20906
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.10.222567
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
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.13.14169
MA0058.11.00014
MA0059.11.02718
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.152496
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.11.60783
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.11.58083
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.12.30533
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
MA0142.11.90582
MA0143.12.69964
MA0144.10.262477
MA0145.10.304732
MA0146.10.264322
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.790799
MA0138.20.727395
MA0002.21.11916
MA0137.20.365364
MA0104.20.218974
MA0047.21.51738
MA0112.21.05549
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.102995
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.878466
MA0163.10.82914
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.25.73977
MA0102.21.65195
MA0258.10.688848
MA0259.10.26402
MA0442.10
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