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MCL coexpression mm9:1087: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!2.82e-23!75;UBERON:0001017!1.31e-22!73;UBERON:0000073!1.92e-17!54;UBERON:0004121!1.78e-16!95;UBERON:0000924!1.78e-16!95;UBERON:0006601!1.78e-16!95;UBERON:0001049!3.04e-16!52;UBERON:0005068!3.04e-16!52;UBERON:0006241!3.04e-16!52;UBERON:0007135!3.04e-16!52;UBERON:0002020!2.54e-15!34;UBERON:0002346!3.41e-15!64;UBERON:0003075!3.41e-15!64;UBERON:0007284!3.41e-15!64;UBERON:0010314!2.72e-14!92;UBERON:0000955!2.82e-13!47;UBERON:0006238!2.82e-13!47;UBERON:0002616!6.70e-13!46;UBERON:0003528!3.18e-12!29;UBERON:0002791!3.18e-12!29;UBERON:0001893!3.18e-12!29;UBERON:0003080!3.90e-11!40;UBERON:0002780!7.38e-11!39;UBERON:0001890!7.38e-11!39;UBERON:0006240!7.38e-11!39;UBERON:0010371!1.53e-10!73;UBERON:0000025!1.02e-09!114;UBERON:0003056!1.48e-09!49;UBERON:0000956!3.28e-08!21;UBERON:0001869!3.28e-08!21;UBERON:0000203!3.28e-08!21;UBERON:0004111!9.59e-08!122;UBERON:0002619!5.22e-07!17;UBERON:0002021!8.23e-07!10;UBERON:0000411!8.23e-07!10;UBERON:0001950!8.23e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,0.480627,0.299217,0.495263,0.587291,1.12275,1.80944,0.478312,0.542749,0.575086,0.59526,1.46059,0.315771,0,0.795315,0.291368,0.561256,0.112498,0.978328,0.586604,0.598814,0.29769,0.419327,0.62766,0.542568,0.516511,0.344372,0.446946,0.50223,0.897561,0.78719,0.166577,0.316253,0.0235321,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.932136,0.317766,0.515031,0.469348,0.714592,0.532496,1.25414,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.608073,0.293368,1.09164,0.17012,0.482617,0.166511,0.703064,2.00003,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.0369809,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.823238,0.708155,0.237542,0.589174,0.913319,0.71485,0.127063,1.40122,0.897279,1.02279,0.778243,1.82972,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.0501572,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,2.07207,1.16374,1.50487,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,1.54859,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.813943,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.0206035
}}

Latest revision as of 16:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:70053209..70053214,-p3@Rnasek
Mm9::chr4:130372788..130372826,+p4@Sdc3
Mm9::chr4:130374681..130374703,+p@chr4:130374681..130374703
+
Mm9::chr4:130374873..130374885,+p@chr4:130374873..130374885
+
Mm9::chr4:130379298..130379314,+p@chr4:130379298..130379314
+
Mm9::chr4:130379365..130379381,+p@chr4:130379365..130379381
+
Mm9::chr5:115940335..115940338,+p@chr5:115940335..115940338
+


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:0004182carboxypeptidase A activity0.0346005779385539
GO:0004181metallocarboxypeptidase activity0.0346005779385539
GO:0004180carboxypeptidase activity0.0346005779385539
GO:0008235metalloexopeptidase activity0.0346005779385539
GO:0008238exopeptidase activity0.0472578084936854



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
nervous system2.82e-2375
central nervous system1.31e-2273
regional part of nervous system1.92e-1754
ectoderm-derived structure1.78e-1695
ectoderm1.78e-1695
presumptive ectoderm1.78e-1695
neural tube3.04e-1652
neural rod3.04e-1652
future spinal cord3.04e-1652
neural keel3.04e-1652
gray matter2.54e-1534
neurectoderm3.41e-1564
neural plate3.41e-1564
presumptive neural plate3.41e-1564
structure with developmental contribution from neural crest2.72e-1492
brain2.82e-1347
future brain2.82e-1347
regional part of brain6.70e-1346
brain grey matter3.18e-1229
regional part of telencephalon3.18e-1229
telencephalon3.18e-1229
anterior neural tube3.90e-1140
regional part of forebrain7.38e-1139
forebrain7.38e-1139
future forebrain7.38e-1139
ecto-epithelium1.53e-1073
tube1.02e-09114
pre-chordal neural plate1.48e-0949
cerebral cortex3.28e-0821
cerebral hemisphere3.28e-0821
pallium3.28e-0821
anatomical conduit9.59e-08122
regional part of cerebral cortex5.22e-0717
occipital lobe8.23e-0710
visual cortex8.23e-0710
neocortex8.23e-0710


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)
MA0003.10.0861444
MA0004.10.481116
MA0006.10.311391
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
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.12.54082
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.14.00719
MA0074.11.41926
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
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
MA0093.10.879104
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.836994
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
MA0140.11.3943
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
MA0039.20.0478878
MA0138.20.727395
MA0002.21.75516
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.21.05549
MA0065.21.0577
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.792589
MA0155.12.2767
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.12.17158
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.11.20194
MA0164.11.46244
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.23.13697
MA0102.21.65195
MA0258.11.27611
MA0259.10.26402
MA0442.10
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