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MCL coexpression mm9:483: Difference between revisions

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{{MCL_coexpression_mm9
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thiolesterase activity;0.0191150467997155;236733,57775!GO:0004843;ubiquitin-specific protease activity;0.0191150467997155;236733,57775!GO:0019783;small conjugating protein-specific protease activity;0.0191150467997155;236733,57775!GO:0016790;thiolester hydrolase activity;0.0219964618309032;236733,57775!GO:0006511;ubiquitin-dependent protein catabolic process;0.0219964618309032;236733,57775!GO:0043632;modification-dependent macromolecule catabolic process;0.0219964618309032;236733,57775!GO:0019941;modification-dependent protein catabolic process;0.0219964618309032;236733,57775!GO:0051603;proteolysis involved in cellular protein catabolic process;0.0219964618309032;236733,57775!GO:0044257;cellular protein catabolic process;0.0219964618309032;236733,57775!GO:0008234;cysteine-type peptidase activity;0.0283538819435009;236733,57775!GO:0016012;sarcoglycan complex;0.0283538819435009;24052!GO:0016011;dystroglycan complex;0.0285738468227538;24052!GO:0030163;protein catabolic process;0.0285738468227538;236733,57775!GO:0044265;cellular macromolecule catabolic process;0.0398502399423991;236733,57775!GO:0016010;dystrophin-associated glycoprotein complex;0.0398502399423991;24052!GO:0043285;biopolymer catabolic 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|gostat_on_MCL_coexpression=GO:0004221;ubiquitin thiolesterase activity;0.0191150467997155;236733,57775!GO:0004843;ubiquitin-specific protease activity;0.0191150467997155;236733,57775!GO:0019783;small conjugating protein-specific protease activity;0.0191150467997155;236733,57775!GO:0016790;thiolester hydrolase activity;0.0219964618309032;236733,57775!GO:0006511;ubiquitin-dependent protein catabolic process;0.0219964618309032;236733,57775!GO:0043632;modification-dependent macromolecule catabolic process;0.0219964618309032;236733,57775!GO:0019941;modification-dependent protein catabolic process;0.0219964618309032;236733,57775!GO:0051603;proteolysis involved in cellular protein catabolic process;0.0219964618309032;236733,57775!GO:0044257;cellular protein catabolic process;0.0219964618309032;236733,57775!GO:0008234;cysteine-type peptidase activity;0.0283538819435009;236733,57775!GO:0016012;sarcoglycan complex;0.0283538819435009;24052!GO:0016011;dystroglycan complex;0.0285738468227538;24052!GO:0030163;protein catabolic process;0.0285738468227538;236733,57775!GO:0044265;cellular macromolecule catabolic process;0.0398502399423991;236733,57775!GO:0016010;dystrophin-associated glycoprotein complex;0.0398502399423991;24052!GO:0043285;biopolymer catabolic process;0.0398502399423991;236733,57775!
|ontology_enrichment_celltype=CL:0000117!3.17e-13!23;CL:0000337!3.17e-13!23;CL:0000540!1.92e-12!33;CL:0000047!1.92e-12!33;CL:0000031!1.92e-12!33;CL:0000404!1.92e-12!33;CL:0000393!2.25e-09!39;CL:0000211!2.25e-09!39;CL:0000221!8.38e-07!44;CL:0000133!8.38e-07!44
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!9.29e-26!64;UBERON:0003075!9.29e-26!64;UBERON:0007284!9.29e-26!64;UBERON:0000073!1.19e-24!54;UBERON:0001017!2.67e-24!73;UBERON:0001049!4.31e-23!52;UBERON:0005068!4.31e-23!52;UBERON:0006241!4.31e-23!52;UBERON:0007135!4.31e-23!52;UBERON:0001016!1.40e-22!75;UBERON:0010371!3.61e-22!73;UBERON:0004121!3.60e-21!95;UBERON:0000924!3.60e-21!95;UBERON:0006601!3.60e-21!95;UBERON:0003056!4.44e-21!49;UBERON:0010314!4.73e-21!92;UBERON:0000955!7.93e-20!47;UBERON:0006238!7.93e-20!47;UBERON:0002616!3.26e-19!46;UBERON:0003080!2.11e-18!40;UBERON:0002780!1.13e-17!39;UBERON:0001890!1.13e-17!39;UBERON:0006240!1.13e-17!39;UBERON:0002020!2.33e-15!34;UBERON:0003528!2.36e-12!29;UBERON:0002791!2.36e-12!29;UBERON:0001893!2.36e-12!29;UBERON:0000468!2.42e-08!333;UBERON:0000956!1.26e-07!21;UBERON:0001869!1.26e-07!21;UBERON:0000203!1.26e-07!21;UBERON:0000025!9.66e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.595185,0.236794,0.186933,0.238864,0.721878,0.250289,0.324772,0.210111,0.223561,0.563871,0.785008,0.84479,0.800979,0.335151,0.120865,0,0.505674,0.105493,0.0508204,0.670858,0.160516,0.0504052,0.888941,0.353775,0.192505,0.942903,0.401215,0.267095,0.851419,0.0305203,1.3116,0.598971,0.339783,0.352983,0.121176,0.354026,0.667121,0.311629,0.0859217,0.247011,0.710516,0.259911,0.252106,0.387037,0.0723457,2.65431,1.10719,0.766153,0.198601,0.141659,0.48979,0.381972,0.281801,0.732469,1.77173,0.904193,0.147717,0.820802,0.166653,0.339495,0.580338,0.390204,0.0681609,0.479581,0.925321,0.516415,0.880067,1.22155,0.576002,1.07689,1.57461,0.823515,0.0555827,0.781142,1.01021,0.606791,0.153229,1.08528,0.564426,0.163487,0.220193,0.521544,0.388944,0.774743,1.6106,0.106224,0.127322,1.25315,0.438181,1.38183,0.947651,0.676142,0.610915,0.365956,0.595467,0.257625,0.206664,0.613539,0.43404,0.469526,0.0985954,0.59871,0.715894,0.490329,0.489372,0.719532,0.543989,0.276621,0.499786,0.94444,0.201092,0.717588,0.164285,0.292444,0.954503,0.705468,0.964922,0.678491,0.506861,0.656773,0.786314,0.46068,1.68726,0.422901,1.00724,1.39345,0.331666,0.60459,0.8786,0.747079,0.699779,1.22651,0.850049,0.352905,0.975524,0.277782,0.212784,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,0.436593,1.7082,0.214583,2.37091,0.303478,0.249469,0.733963,0.266555,0.352111,0.81211,0.996119,0.803531,0.204546,0.60983,0.93695,1.60892,0.568261,0.199399,0.480505,1.63655,0.663991,0.841805,0.00458245
|tfbs_overrepresentation_jaspar=MA0003.1;0.0773439,MA0004.1;0.67248,MA0006.1;0.37642,MA0007.1;0.227553,MA0009.1;1.51082,MA0014.1;0.457814,MA0017.1;0.832511,MA0019.1;1.15568,MA0024.1;3.55984,MA0025.1;0.845702,MA0027.1;2.24512,MA0028.1;1.86083,MA0029.1;0.562703,MA0030.1;0.568779,MA0031.1;0.535959,MA0038.1;0.358622,MA0040.1;0.635404,MA0041.1;0.18185,MA0042.1;0.172351,MA0043.1;0.71494,MA0046.1;0.657417,MA0048.1;1.11639,MA0050.1;0.270164,MA0051.1;0.366328,MA0052.1;0.642973,MA0055.1;1.76425,MA0056.1;0,MA0057.1;0.226212,MA0058.1;0.501197,MA0059.1;0.176308,MA0060.1;3.80958,MA0061.1;0.295622,MA0063.1;0,MA0066.1;0.349199,MA0067.1;0.953264,MA0068.1;0.446117,MA0069.1;0.643292,MA0070.1;0.634186,MA0071.1;0.269487,MA0072.1;0.626238,MA0073.1;0.468292,MA0074.1;0.318792,MA0076.1;1.42655,MA0077.1;0.605975,MA0078.1;0.395048,MA0081.1;0.193203,MA0083.1;0.714187,MA0084.1;1.27474,MA0087.1;0.673355,MA0088.1;0.292366,MA0089.1;0,MA0090.1;0.212772,MA0091.1;0.24961,MA0092.1;0.610874,MA0093.1;0.809981,MA0095.1;0,MA0098.1;0,MA0100.1;0.309116,MA0101.1;0.182791,MA0103.1;0.14251,MA0105.1;0.147614,MA0106.1;0.401864,MA0107.1;0.138378,MA0108.2;0.476838,MA0109.1;0,MA0111.1;0.635898,MA0113.1;0.377232,MA0114.1;0.291992,MA0115.1;0.717599,MA0116.1;1.80308,MA0117.1;0.686999,MA0119.1;0.183219,MA0122.1;0.705806,MA0124.1;0.901619,MA0125.1;0.830088,MA0130.1;0,MA0131.1;0.452196,MA0132.1;0,MA0133.1;0,MA0135.1;0.749615,MA0136.1;0.335579,MA0139.1;0.20466,MA0140.1;0.30902,MA0141.1;0.155997,MA0142.1;0.522654,MA0143.1;0.391481,MA0144.1;0.617592,MA0145.1;1.15108,MA0146.1;0.383608,MA0147.1;1.08486,MA0148.1;0.252062,MA0149.1;0.18682,MA0062.2;1.41609,MA0035.2;0.312946,MA0039.2;0.466859,MA0138.2;0.445088,MA0002.2;0.208749,MA0137.2;1.4616,MA0104.2;0.85335,MA0047.2;0.357963,MA0112.2;0.819738,MA0065.2;0.321967,MA0150.1;0.227466,MA0151.1;0,MA0152.1;0.358055,MA0153.1;0.765498,MA0154.1;0.247047,MA0155.1;0.916876,MA0156.1;0.885026,MA0157.1;0.493416,MA0158.1;0,MA0159.1;0.679844,MA0160.1;0.254455,MA0161.1;0,MA0162.1;2.62387,MA0163.1;0.605183,MA0164.1;0.335886,MA0080.2;0.13897,MA0018.2;1.6308,MA0099.2;0.439458,MA0079.2;2.10326,MA0102.2;1.32652,MA0258.1;0.0789466,MA0259.1;0.299239,MA0442.1;0
}}

Latest revision as of 15:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:91627958..91627984,-p2@Rmst
Mm9::chr11:47802464..47802482,-p7@Sgcd
Mm9::chr18:59222142..59222192,+p1@A730017C20Rik
Mm9::chr7:13365956..13366028,-p@chr7:13365956..13366028
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Mm9::chr7:6683274..6683357,+p1@Usp29
Mm9::chr7:6683398..6683427,+p2@Usp29
Mm9::chr8:114535292..114535347,+p1@Terf2ip
Mm9::chr9:111174336..111174418,+p1@Epm2aip1
Mm9::chr9:111174424..111174447,+p2@Epm2aip1
Mm9::chr9:45792860..45792891,-p2@Pafah1b2
Mm9::chrX:132330652..132330703,+p2@Gprasp1
Mm9::chrX:132373579..132373614,+p1@Gprasp2
Mm9::chrX:132373618..132373625,+p2@Gprasp2
Mm9::chrX:20281048..20281077,+p1@Usp11
Mm9::chrX:7151370..7151438,-p2@Ppp1r3f


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:0004221ubiquitin thiolesterase activity0.0191150467997155
GO:0004843ubiquitin-specific protease activity0.0191150467997155
GO:0019783small conjugating protein-specific protease activity0.0191150467997155
GO:0016790thiolester hydrolase activity0.0219964618309032
GO:0006511ubiquitin-dependent protein catabolic process0.0219964618309032
GO:0043632modification-dependent macromolecule catabolic process0.0219964618309032
GO:0019941modification-dependent protein catabolic process0.0219964618309032
GO:0051603proteolysis involved in cellular protein catabolic process0.0219964618309032
GO:0044257cellular protein catabolic process0.0219964618309032
GO:0008234cysteine-type peptidase activity0.0283538819435009
GO:0016012sarcoglycan complex0.0283538819435009
GO:0016011dystroglycan complex0.0285738468227538
GO:0030163protein catabolic process0.0285738468227538
GO:0044265cellular macromolecule catabolic process0.0398502399423991
GO:0016010dystrophin-associated glycoprotein complex0.0398502399423991
GO:0043285biopolymer catabolic process0.0398502399423991



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
neurectoderm9.29e-2664
neural plate9.29e-2664
presumptive neural plate9.29e-2664
regional part of nervous system1.19e-2454
central nervous system2.67e-2473
neural tube4.31e-2352
neural rod4.31e-2352
future spinal cord4.31e-2352
neural keel4.31e-2352
nervous system1.40e-2275
ecto-epithelium3.61e-2273
ectoderm-derived structure3.60e-2195
ectoderm3.60e-2195
presumptive ectoderm3.60e-2195
pre-chordal neural plate4.44e-2149
structure with developmental contribution from neural crest4.73e-2192
brain7.93e-2047
future brain7.93e-2047
regional part of brain3.26e-1946
anterior neural tube2.11e-1840
regional part of forebrain1.13e-1739
forebrain1.13e-1739
future forebrain1.13e-1739
gray matter2.33e-1534
brain grey matter2.36e-1229
regional part of telencephalon2.36e-1229
telencephalon2.36e-1229
multi-cellular organism2.42e-08333
cerebral cortex1.26e-0721
cerebral hemisphere1.26e-0721
pallium1.26e-0721
tube9.66e-07114


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)
MA0003.10.0773439
MA0004.10.67248
MA0006.10.37642
MA0007.10.227553
MA0009.11.51082
MA0014.10.457814
MA0017.10.832511
MA0019.11.15568
MA0024.13.55984
MA0025.10.845702
MA0027.12.24512
MA0028.11.86083
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.10.358622
MA0040.10.635404
MA0041.10.18185
MA0042.10.172351
MA0043.10.71494
MA0046.10.657417
MA0048.11.11639
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.11.76425
MA0056.10
MA0057.10.226212
MA0058.10.501197
MA0059.10.176308
MA0060.13.80958
MA0061.10.295622
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.446117
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.10.468292
MA0074.10.318792
MA0076.11.42655
MA0077.10.605975
MA0078.10.395048
MA0081.10.193203
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.292366
MA0089.10
MA0090.10.212772
MA0091.10.24961
MA0092.10.610874
MA0093.10.809981
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.182791
MA0103.10.14251
MA0105.10.147614
MA0106.10.401864
MA0107.10.138378
MA0108.20.476838
MA0109.10
MA0111.10.635898
MA0113.10.377232
MA0114.10.291992
MA0115.10.717599
MA0116.11.80308
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.10.452196
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.335579
MA0139.10.20466
MA0140.10.30902
MA0141.10.155997
MA0142.10.522654
MA0143.10.391481
MA0144.10.617592
MA0145.11.15108
MA0146.10.383608
MA0147.11.08486
MA0148.10.252062
MA0149.10.18682
MA0062.21.41609
MA0035.20.312946
MA0039.20.466859
MA0138.20.445088
MA0002.20.208749
MA0137.21.4616
MA0104.20.85335
MA0047.20.357963
MA0112.20.819738
MA0065.20.321967
MA0150.10.227466
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.247047
MA0155.10.916876
MA0156.10.885026
MA0157.10.493416
MA0158.10
MA0159.10.679844
MA0160.10.254455
MA0161.10
MA0162.12.62387
MA0163.10.605183
MA0164.10.335886
MA0080.20.13897
MA0018.21.6308
MA0099.20.439458
MA0079.22.10326
MA0102.21.32652
MA0258.10.0789466
MA0259.10.299239
MA0442.10
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