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MCL coexpression mm9:986: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.82e-21!54;UBERON:0001016!6.78e-21!75;UBERON:0001017!1.64e-20!73;UBERON:0001049!2.98e-20!52;UBERON:0005068!2.98e-20!52;UBERON:0006241!2.98e-20!52;UBERON:0007135!2.98e-20!52;UBERON:0000955!7.30e-18!47;UBERON:0006238!7.30e-18!47;UBERON:0002616!2.37e-17!46;UBERON:0002346!2.98e-17!64;UBERON:0003075!2.98e-17!64;UBERON:0007284!2.98e-17!64;UBERON:0004121!2.14e-16!95;UBERON:0000924!2.14e-16!95;UBERON:0006601!2.14e-16!95;UBERON:0002020!5.03e-15!34;UBERON:0010371!1.00e-14!73;UBERON:0003080!1.05e-14!40;UBERON:0002780!2.32e-14!39;UBERON:0001890!2.32e-14!39;UBERON:0006240!2.32e-14!39;UBERON:0003056!1.14e-13!49;UBERON:0003528!1.16e-12!29;UBERON:0002791!1.16e-12!29;UBERON:0001893!1.16e-12!29;UBERON:0010314!1.06e-10!92;UBERON:0000956!3.03e-09!21;UBERON:0001869!3.03e-09!21;UBERON:0000203!3.03e-09!21;UBERON:0001264!1.10e-08!12;UBERON:0002619!2.46e-08!17;UBERON:0002021!8.39e-07!10;UBERON:0000411!8.39e-07!10;UBERON:0001950!8.39e-07!10
|tfbs_overrepresentation_for_novel_motifs=1.01838,3.26486,0.367606,0.434198,0.260188,0.448401,1.33049,0.173246,0.535519,0.0447303,0.494602,0.526159,7.53946,0.550255,0.275867,0,0.742571,0.252772,0.160384,1.03863,0.332107,0.223663,0.549359,0.258745,0.374936,2.41525,0.909128,0.469052,0.303071,1.23861,0.455168,0.843667,1.99811,0.136998,0.276324,6.25975,1.26012,0.522578,0.221921,4.04451,0.256422,0.460258,0.0558565,0.27776,1.7835,0.423266,0.662995,0.484612,0.687215,1.49483,1.72213,0.604356,0.112729,2.25604,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,1.067,1.6988,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.50864,1.03623,1.98853,0.131016,0.839631,0.651651,0.806481,0.336166,3.04829,0.759925,0.612313,0.167672,0.920903,4.33535,0.293679,0.118251,1.60318,1.65055,1.20871,0.925879,0.856465,0.265734,3.39227,1.73859,0.1711,0.859272,3.90961,2.26041,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,1.61924,0.333829,0.386136,0.96962,0.337254,3.19041,1.21576,0.254749,0.603195,0.437894,1.76093,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,1.35892,0.950857,0.427043,1.10792,0.570914,1.23736,0.479867,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,1.33415,0.120154,3.43703,0.986833,1.12835,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,2.72853,0.524587,1.99758
}}

Latest revision as of 16:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:164286731..164286784,+p3@Sys1
Mm9::chr9:95307527..95307538,-p9@Chst2
Mm9::chr9:95307603..95307610,-p8@Chst2
Mm9::chr9:95307620..95307631,-p6@Chst2
Mm9::chr9:95307646..95307658,-p4@Chst2
Mm9::chr9:95307659..95307695,-p1@Chst2
Mm9::chr9:95307700..95307718,-p3@Chst2
Mm9::chr9:95307769..95307780,-p5@Chst2


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:0005794Golgi apparatus0.0275945020412737
GO:0006041glucosamine metabolic process0.0275945020412737
GO:0006044N-acetylglucosamine metabolic process0.0275945020412737
GO:0006040amino sugar metabolic process0.0275945020412737
GO:0008146sulfotransferase activity0.0390632786382272
GO:0016782transferase activity, transferring sulfur-containing groups0.0390632786382272



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
ectodermal cell6.99e-0944
neurectodermal cell6.99e-0944
neural cell2.10e-0843
CNS neuron (sensu Vertebrata)8.88e-0823
neuroblast (sensu Vertebrata)8.88e-0823
non-terminally differentiated cell2.52e-0749

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.82e-2154
nervous system6.78e-2175
central nervous system1.64e-2073
neural tube2.98e-2052
neural rod2.98e-2052
future spinal cord2.98e-2052
neural keel2.98e-2052
brain7.30e-1847
future brain7.30e-1847
regional part of brain2.37e-1746
neurectoderm2.98e-1764
neural plate2.98e-1764
presumptive neural plate2.98e-1764
ectoderm-derived structure2.14e-1695
ectoderm2.14e-1695
presumptive ectoderm2.14e-1695
gray matter5.03e-1534
ecto-epithelium1.00e-1473
anterior neural tube1.05e-1440
regional part of forebrain2.32e-1439
forebrain2.32e-1439
future forebrain2.32e-1439
pre-chordal neural plate1.14e-1349
brain grey matter1.16e-1229
regional part of telencephalon1.16e-1229
telencephalon1.16e-1229
structure with developmental contribution from neural crest1.06e-1092
cerebral cortex3.03e-0921
cerebral hemisphere3.03e-0921
pallium3.03e-0921
pancreas1.10e-0812
regional part of cerebral cortex2.46e-0817
occipital lobe8.39e-0710
visual cortex8.39e-0710
neocortex8.39e-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)
MA0003.11.81836
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.11.54572
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.2091
MA0056.10
MA0057.12.81184
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.12.61807
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.319589
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.214367
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.11.74144
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.11.29043
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.11.69377
MA0103.10.307078
MA0105.17.72134
MA0106.10.626997
MA0107.11.47808
MA0108.20.710846
MA0109.10
MA0111.14.92036
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.951747
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.11.87609
MA0146.11.31232
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.402847
MA0138.20.675599
MA0002.20.172399
MA0137.20.863775
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.11.4435
MA0163.10.0186439
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.24.92979
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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