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MCL coexpression mm9:1290: Difference between revisions

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{{MCL_coexpression_mm9
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sulfotransferase activity;0.0106802490055942;54200!GO:0006791;sulfur utilization;0.0106802490055942;54200!GO:0000103;sulfate assimilation;0.0106802490055942;54200!GO:0017018;myosin phosphatase activity;0.0106802490055942;19052!GO:0000158;protein phosphatase type 2A activity;0.0106802490055942;19052!GO:0008420;CTD phosphatase activity;0.0106802490055942;19052!GO:0000163;protein phosphatase type 1 activity;0.0137294915714405;19052!GO:0015071;protein phosphatase type 2C activity;0.0253475270387853;19052!GO:0004722;protein serine/threonine phosphatase activity;0.0367371534976019;19052!GO:0008146;sulfotransferase activity;0.0452792271193379;54200!GO:0007498;mesoderm development;0.0452792271193379;19052!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0452792271193379;54200!GO:0006790;sulfur metabolic 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|gostat_on_MCL_coexpression=GO:0004027;alcohol sulfotransferase activity;0.0106802490055942;54200!GO:0006791;sulfur utilization;0.0106802490055942;54200!GO:0000103;sulfate assimilation;0.0106802490055942;54200!GO:0017018;myosin phosphatase activity;0.0106802490055942;19052!GO:0000158;protein phosphatase type 2A activity;0.0106802490055942;19052!GO:0008420;CTD phosphatase activity;0.0106802490055942;19052!GO:0000163;protein phosphatase type 1 activity;0.0137294915714405;19052!GO:0015071;protein phosphatase type 2C activity;0.0253475270387853;19052!GO:0004722;protein serine/threonine phosphatase activity;0.0367371534976019;19052!GO:0008146;sulfotransferase activity;0.0452792271193379;54200!GO:0007498;mesoderm development;0.0452792271193379;19052!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0452792271193379;54200!GO:0006790;sulfur metabolic process;0.0491477462105298;54200!
|ontology_enrichment_celltype=CL:0000117!6.93e-11!23;CL:0000337!6.93e-11!23;CL:0000540!1.69e-08!33;CL:0000047!1.69e-08!33;CL:0000031!1.69e-08!33;CL:0000404!1.69e-08!33;CL:0002319!1.02e-07!43;CL:0000221!1.74e-07!44;CL:0000133!1.74e-07!44
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!1.54e-21!75;UBERON:0001017!4.68e-21!73;UBERON:0000073!1.71e-20!54;UBERON:0001049!2.67e-19!52;UBERON:0005068!2.67e-19!52;UBERON:0006241!2.67e-19!52;UBERON:0007135!2.67e-19!52;UBERON:0004121!8.96e-18!95;UBERON:0000924!8.96e-18!95;UBERON:0006601!8.96e-18!95;UBERON:0002020!7.05e-17!34;UBERON:0000955!2.77e-16!47;UBERON:0006238!2.77e-16!47;UBERON:0002346!8.02e-16!64;UBERON:0003075!8.02e-16!64;UBERON:0007284!8.02e-16!64;UBERON:0002616!1.27e-15!46;UBERON:0003080!1.74e-14!40;UBERON:0010371!2.96e-14!73;UBERON:0002780!6.60e-14!39;UBERON:0001890!6.60e-14!39;UBERON:0006240!6.60e-14!39;UBERON:0003528!8.12e-14!29;UBERON:0002791!8.12e-14!29;UBERON:0001893!8.12e-14!29;UBERON:0003056!1.12e-11!49;UBERON:0000064!2.24e-10!99;UBERON:0000956!1.69e-09!21;UBERON:0001869!1.69e-09!21;UBERON:0000203!1.69e-09!21;UBERON:0002619!4.76e-09!17;UBERON:0002021!9.56e-09!10;UBERON:0000411!9.56e-09!10;UBERON:0001950!9.56e-09!10;UBERON:0010314!3.49e-08!92;UBERON:0011216!7.22e-07!194
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.594834,1.46067,0.632897,0.692139,1.58279,0.364314,0,0.856992,0.338549,0.232269,0.86893,0.426133,0.35122,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,1.02135,0.534301,0.558142,0.960397,0.336199,0.204204,1.70316,0.335531,1.56842,0.629145,0.820134,1.37841,0.342638,0.56353,0.0995018,0.366415,0.368882,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.995874,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.97697,0.253541,3.09546,1.156,1.13013,0.57254,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,0.768392,0.479018,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.281222,0.244935,0.976308,0.775372,0.938145,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,1.11115,1.92,0.484547,1.0885,1.10269,0.605144,1.33732,0.90315,1.35637,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,1.64681,0.183562,3.59715,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.5667
|tfbs_overrepresentation_jaspar=MA0003.1;1.39154,MA0004.1;0.536396,MA0006.1;1.68531,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.883128,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;1.50576,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.212634,MA0056.1;0,MA0057.1;0.457693,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.000157319,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.111145,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;1.03097,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.944657,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.379391,MA0146.1;0.353523,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.0271858,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.881902,MA0160.1;0.556423,MA0161.1;0,MA0162.1;1.08528,MA0163.1;0.372305,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.221916,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}

Latest revision as of 16:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:51912354..51912377,+p2@Ppp2ca
Mm9::chr7:121559997..121560046,-p@chr7:121559997..121560046
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Mm9::chr7:52997694..52997711,-p@chr7:52997694..52997711
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Mm9::chr7:52997716..52997737,-p3@Sult2b1
Mm9::chr7:89078700..89078758,-p@chr7:89078700..89078758
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Mm9::chr8:15011209..15011235,+p1@Kbtbd11


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:0004027alcohol sulfotransferase activity0.0106802490055942
GO:0006791sulfur utilization0.0106802490055942
GO:0000103sulfate assimilation0.0106802490055942
GO:0017018myosin phosphatase activity0.0106802490055942
GO:0000158protein phosphatase type 2A activity0.0106802490055942
GO:0008420CTD phosphatase activity0.0106802490055942
GO:0000163protein phosphatase type 1 activity0.0137294915714405
GO:0015071protein phosphatase type 2C activity0.0253475270387853
GO:0004722protein serine/threonine phosphatase activity0.0367371534976019
GO:0008146sulfotransferase activity0.0452792271193379
GO:0007498mesoderm development0.0452792271193379
GO:0016782transferase activity, transferring sulfur-containing groups0.0452792271193379
GO:0006790sulfur metabolic process0.0491477462105298



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
CNS neuron (sensu Vertebrata)6.93e-1123
neuroblast (sensu Vertebrata)6.93e-1123
neuron1.69e-0833
neuronal stem cell1.69e-0833
neuroblast1.69e-0833
electrically signaling cell1.69e-0833
neural cell1.02e-0743
ectodermal cell1.74e-0744
neurectodermal cell1.74e-0744

Uber Anatomy
Ontology termp-valuen
nervous system1.54e-2175
central nervous system4.68e-2173
regional part of nervous system1.71e-2054
neural tube2.67e-1952
neural rod2.67e-1952
future spinal cord2.67e-1952
neural keel2.67e-1952
ectoderm-derived structure8.96e-1895
ectoderm8.96e-1895
presumptive ectoderm8.96e-1895
gray matter7.05e-1734
brain2.77e-1647
future brain2.77e-1647
neurectoderm8.02e-1664
neural plate8.02e-1664
presumptive neural plate8.02e-1664
regional part of brain1.27e-1546
anterior neural tube1.74e-1440
ecto-epithelium2.96e-1473
regional part of forebrain6.60e-1439
forebrain6.60e-1439
future forebrain6.60e-1439
brain grey matter8.12e-1429
regional part of telencephalon8.12e-1429
telencephalon8.12e-1429
pre-chordal neural plate1.12e-1149
organ part2.24e-1099
cerebral cortex1.69e-0921
cerebral hemisphere1.69e-0921
pallium1.69e-0921
regional part of cerebral cortex4.76e-0917
occipital lobe9.56e-0910
visual cortex9.56e-0910
neocortex9.56e-0910
structure with developmental contribution from neural crest3.49e-0892
organ system subdivision7.22e-07194


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)
MA0003.11.39154
MA0004.10.536396
MA0006.11.68531
MA0007.10.52077
MA0009.10.987341
MA0014.10.883128
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.11.50576
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.000157319
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.11.03097
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.944657
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.10.353523
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.0271858
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.881902
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.10.372305
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.221916
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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