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MCL coexpression mm9:1083: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000055!2.56e-19!49;CL:0002319!2.85e-17!43;CL:0000221!8.78e-17!44;CL:0000133!8.78e-17!44;CL:0000393!1.67e-15!39;CL:0000211!1.67e-15!39;CL:0000540!1.42e-13!33;CL:0000047!1.42e-13!33;CL:0000031!1.42e-13!33;CL:0000404!1.42e-13!33;CL:0000117!1.40e-12!23;CL:0000337!1.40e-12!23;CL:0002321!2.21e-10!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.10e-31!73;UBERON:0001016!1.32e-31!75;UBERON:0004121!4.11e-29!95;UBERON:0000924!4.11e-29!95;UBERON:0006601!4.11e-29!95;UBERON:0000073!1.29e-24!54;UBERON:0001049!3.31e-23!52;UBERON:0005068!3.31e-23!52;UBERON:0006241!3.31e-23!52;UBERON:0007135!3.31e-23!52;UBERON:0002346!1.23e-22!64;UBERON:0003075!1.23e-22!64;UBERON:0007284!1.23e-22!64;UBERON:0010371!4.41e-21!73;UBERON:0010314!9.91e-21!92;UBERON:0000955!3.05e-20!47;UBERON:0006238!3.05e-20!47;UBERON:0002616!1.11e-19!46;UBERON:0002020!1.48e-19!34;UBERON:0003528!6.73e-17!29;UBERON:0002791!6.73e-17!29;UBERON:0001893!6.73e-17!29;UBERON:0003080!2.46e-16!40;UBERON:0002780!8.37e-16!39;UBERON:0001890!8.37e-16!39;UBERON:0006240!8.37e-16!39;UBERON:0003056!1.91e-15!49;UBERON:0000025!8.82e-15!114;UBERON:0004111!1.01e-14!122;UBERON:0000956!1.68e-12!21;UBERON:0001869!1.68e-12!21;UBERON:0000203!1.68e-12!21;UBERON:0002619!8.81e-11!17;UBERON:0002021!8.20e-08!10;UBERON:0000411!8.20e-08!10;UBERON:0001950!8.20e-08!10;UBERON:0003076!1.38e-07!12;UBERON:0003057!1.38e-07!12;UBERON:0000468!1.64e-07!333
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.161863,0.411716,0.480627,0.810002,0.495263,1.43443,0.594722,0.616096,0.478312,1.34037,0.575086,1.12363,0.599731,0.315771,0,0.795315,0.291368,1.68259,1.20169,0.374752,0.586604,1.45867,0.29769,1.07577,0.62766,0.184473,0.516511,0.344372,0.876948,0.50223,0.897561,0.289148,0.498917,0.316253,0.0235321,0.766323,0.57142,0.717242,0.230656,0.295233,0.507468,0.258106,0.317766,1.19315,0.469348,1.70029,1.31862,0.219744,0.347313,0.777641,0.654933,0.851157,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,1.89163,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,4.13143,1.09164,0.17012,0.936963,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,1.84334,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,3.69772,0.237542,0.203879,0.913319,1.70082,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,1.59063,0.484437,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,6.19177,1.04192,1.26486,1.5029,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,1.86859
}}

Latest revision as of 16:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:6100148..6100213,-p1@Nudcd3
Mm9::chr11:61393124..61393131,-p2@Epn2
Mm9::chr11:61393139..61393209,-p1@Epn2
Mm9::chr2:34681707..34681760,-p1@Fbxw2
Mm9::chr4:125933470..125933614,-p1@Mtap7d1
Mm9::chr7:112782039..112782115,-p1@Trim3
Mm9::chr9:45646655..45646675,+p1@Bace1


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:0009049aspartic-type signal peptidase activity0.0120528132361804
GO:0009003signal peptidase activity0.0321223493874419
GO:0004194pepsin A activity0.0321223493874419



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
central nervous system1.10e-3173
nervous system1.32e-3175
ectoderm-derived structure4.11e-2995
ectoderm4.11e-2995
presumptive ectoderm4.11e-2995
regional part of nervous system1.29e-2454
neural tube3.31e-2352
neural rod3.31e-2352
future spinal cord3.31e-2352
neural keel3.31e-2352
neurectoderm1.23e-2264
neural plate1.23e-2264
presumptive neural plate1.23e-2264
ecto-epithelium4.41e-2173
structure with developmental contribution from neural crest9.91e-2192
brain3.05e-2047
future brain3.05e-2047
regional part of brain1.11e-1946
gray matter1.48e-1934
brain grey matter6.73e-1729
regional part of telencephalon6.73e-1729
telencephalon6.73e-1729
anterior neural tube2.46e-1640
regional part of forebrain8.37e-1639
forebrain8.37e-1639
future forebrain8.37e-1639
pre-chordal neural plate1.91e-1549
tube8.82e-15114
anatomical conduit1.01e-14122
cerebral cortex1.68e-1221
cerebral hemisphere1.68e-1221
pallium1.68e-1221
regional part of cerebral cortex8.81e-1117
occipital lobe8.20e-0810
visual cortex8.20e-0810
neocortex8.20e-0810
posterior neural tube1.38e-0712
chordal neural plate1.38e-0712
multi-cellular organism1.64e-07333


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)
MA0003.13.14246
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.11.41063
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.12.35736
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.12.75483
MA0042.11.79544
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.11.23731
MA0058.10.384683
MA0059.10.397033
MA0060.10.656954
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
MA0073.10.490396
MA0074.10.580087
MA0076.12.5281
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.11.00582
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
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
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
MA0139.11.10833
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.11.05551
MA0146.14.34422
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.22.93496
MA0035.20.573016
MA0039.22.09945
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.304722
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.102995
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.11.26636
MA0163.11.20194
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.705112
MA0102.21.65195
MA0258.10.246285
MA0259.11.34223
MA0442.10
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