Personal tools

MCL coexpression mm9:1280: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0001016!3.86e-30!75;UBERON:0001017!2.72e-29!73;UBERON:0000073!3.87e-22!54;UBERON:0001049!8.56e-21!52;UBERON:0005068!8.56e-21!52;UBERON:0006241!8.56e-21!52;UBERON:0007135!8.56e-21!52;UBERON:0004121!3.88e-18!95;UBERON:0000924!3.88e-18!95;UBERON:0006601!3.88e-18!95;UBERON:0000955!5.28e-18!47;UBERON:0006238!5.28e-18!47;UBERON:0002616!6.79e-18!46;UBERON:0002346!7.65e-17!64;UBERON:0003075!7.65e-17!64;UBERON:0007284!7.65e-17!64;UBERON:0003080!1.63e-16!40;UBERON:0002020!2.74e-16!34;UBERON:0002780!3.37e-16!39;UBERON:0001890!3.37e-16!39;UBERON:0006240!3.37e-16!39;UBERON:0003528!1.51e-13!29;UBERON:0002791!1.51e-13!29;UBERON:0001893!1.51e-13!29;UBERON:0010314!6.01e-13!92;UBERON:0003056!7.42e-12!49;UBERON:0010371!9.24e-12!73;UBERON:0000956!7.38e-10!21;UBERON:0001869!7.38e-10!21;UBERON:0000203!7.38e-10!21;UBERON:0002619!2.23e-08!17
|ontology_enrichment_uberon=UBERON:0001016!3.86e-30!75;UBERON:0001017!2.72e-29!73;UBERON:0000073!3.87e-22!54;UBERON:0001049!8.56e-21!52;UBERON:0005068!8.56e-21!52;UBERON:0006241!8.56e-21!52;UBERON:0007135!8.56e-21!52;UBERON:0004121!3.88e-18!95;UBERON:0000924!3.88e-18!95;UBERON:0006601!3.88e-18!95;UBERON:0000955!5.28e-18!47;UBERON:0006238!5.28e-18!47;UBERON:0002616!6.79e-18!46;UBERON:0002346!7.65e-17!64;UBERON:0003075!7.65e-17!64;UBERON:0007284!7.65e-17!64;UBERON:0003080!1.63e-16!40;UBERON:0002020!2.74e-16!34;UBERON:0002780!3.37e-16!39;UBERON:0001890!3.37e-16!39;UBERON:0006240!3.37e-16!39;UBERON:0003528!1.51e-13!29;UBERON:0002791!1.51e-13!29;UBERON:0001893!1.51e-13!29;UBERON:0010314!6.01e-13!92;UBERON:0003056!7.42e-12!49;UBERON:0010371!9.24e-12!73;UBERON:0000956!7.38e-10!21;UBERON:0001869!7.38e-10!21;UBERON:0000203!7.38e-10!21;UBERON:0002619!2.23e-08!17
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,0.283981,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,0.713088,0.657163,0.345236,1.19059,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,1.60284,0.204204,0.956447,0.144368,0.871288,0.629145,0.303703,0.752287,0.342638,0.56353,0.327433,0.366415,1.45501,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,1.50238,0.21472,0.663395,0.939962,1.72013,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,1.30328,0.740068,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.768392,0.827903,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,2.08158,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,2.48865,0.183562,0.667976,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,1.28815
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,0.283981,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,0.713088,0.657163,0.345236,1.19059,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,1.60284,0.204204,0.956447,0.144368,0.871288,0.629145,0.303703,0.752287,0.342638,0.56353,0.327433,0.366415,1.45501,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,1.50238,0.21472,0.663395,0.939962,1.72013,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,1.30328,0.740068,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.768392,0.827903,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,2.08158,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,2.48865,0.183562,0.667976,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,1.28815
|tfbs_overrepresentation_jaspar=MA0003.1;0.730824,MA0004.1;0.536396,MA0006.1;0.945134,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;1.72321,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;0.161427,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;1.11298,MA0059.1;1.14076,MA0060.1;1.38604,MA0061.1;0.827788,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.467569,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.401473,MA0074.1;1.54084,MA0076.1;1.04996,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;2.36749,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.988233,MA0095.1;0,MA0098.1;0,MA0100.1;1.51574,MA0101.1;1.16089,MA0103.1;0.398766,MA0105.1;1.72386,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;1.92698,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,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;0.682297,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;2.42438,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;2.47808,MA0035.2;0.630778,MA0039.2;1.39094,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.933846,MA0155.1;1.33283,MA0156.1;1.04798,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.881902,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.176524,MA0163.1;0.372305,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;2.41728,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}
}}

Revision as of 13:05, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:120459934..120459954,+p4@Anapc11
Mm9::chr16:17530781..17530882,-p2@Thap7
Mm9::chr17:34742844..34742884,+p1@Agpat1
Mm9::chr17:36394802..36394816,-p2@Rpp21
Mm9::chr4:147514791..147514807,+p4@Mad2l2
Mm9::chr5:45911521..45911566,+p1@Med28


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:0007067mitosis0.0324891498879796
GO:0000087M phase of mitotic cell cycle0.0324891498879796
GO:0007094mitotic cell cycle spindle assembly checkpoint0.0324891498879796
GO:0031577spindle checkpoint0.0324891498879796
GO:0000278mitotic cell cycle0.0324891498879796
GO:0000279M phase0.0324891498879796
GO:0051301cell division0.0324891498879796
GO:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.0324891498879796
GO:0022403cell cycle phase0.0324891498879796
GO:0004526ribonuclease P activity0.0324891498879796
GO:0004549tRNA-specific ribonuclease activity0.0324891498879796
GO:0007093mitotic cell cycle checkpoint0.0324891498879796
GO:0016411acylglycerol O-acyltransferase activity0.0324891498879796
GO:0016891endoribonuclease activity, producing 5'-phosphomonoesters0.0463685948603288
GO:0016893endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0475920528897136



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
non-terminally differentiated cell2.09e-1949
ectodermal cell3.16e-1944
neurectodermal cell3.16e-1944
neural cell5.01e-1943
animal cell2.19e-15115
eukaryotic cell2.19e-15115
somatic cell4.23e-15118
electrically responsive cell1.62e-1339
electrically active cell1.62e-1339
neuron4.12e-1333
neuronal stem cell4.12e-1333
neuroblast4.12e-1333
electrically signaling cell4.12e-1333
embryonic cell4.62e-1270
somatic stem cell5.58e-1291
multi fate stem cell5.58e-1291
CNS neuron (sensu Vertebrata)1.07e-1123
neuroblast (sensu Vertebrata)1.07e-1123
stem cell1.51e-1097
migratory neural crest cell4.74e-0710
neuron associated cell4.74e-0710
glial cell (sensu Vertebrata)4.74e-0710
neuron associated cell (sensu Vertebrata)4.74e-0710
glial cell4.74e-0710
glioblast4.74e-0710
glioblast (sensu Vertebrata)4.74e-0710

Uber Anatomy
Ontology termp-valuen
nervous system3.86e-3075
central nervous system2.72e-2973
regional part of nervous system3.87e-2254
neural tube8.56e-2152
neural rod8.56e-2152
future spinal cord8.56e-2152
neural keel8.56e-2152
ectoderm-derived structure3.88e-1895
ectoderm3.88e-1895
presumptive ectoderm3.88e-1895
brain5.28e-1847
future brain5.28e-1847
regional part of brain6.79e-1846
neurectoderm7.65e-1764
neural plate7.65e-1764
presumptive neural plate7.65e-1764
anterior neural tube1.63e-1640
gray matter2.74e-1634
regional part of forebrain3.37e-1639
forebrain3.37e-1639
future forebrain3.37e-1639
brain grey matter1.51e-1329
regional part of telencephalon1.51e-1329
telencephalon1.51e-1329
structure with developmental contribution from neural crest6.01e-1392
pre-chordal neural plate7.42e-1249
ecto-epithelium9.24e-1273
cerebral cortex7.38e-1021
cerebral hemisphere7.38e-1021
pallium7.38e-1021
regional part of cerebral cortex2.23e-0817


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)
MA0003.10.730824
MA0004.10.536396
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.883128
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.11.72321
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
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.10.457693
MA0058.11.11298
MA0059.11.14076
MA0060.11.38604
MA0061.10.827788
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.401473
MA0074.11.54084
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.12.36749
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.11.51574
MA0101.11.16089
MA0103.10.398766
MA0105.11.72386
MA0106.10.737893
MA0107.11.0169
MA0108.21.92698
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
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
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.12.42438
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.22.47808
MA0035.20.630778
MA0039.21.39094
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.37938
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.933846
MA0155.11.33283
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.881902
MA0160.10.556423
MA0161.10
MA0162.10.176524
MA0163.10.372305
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.22.41728
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1280&oldid=2574675"