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MCL coexpression mm9:596: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!5.16e-39!73;UBERON:0001016!2.84e-37!75;UBERON:0002346!5.46e-36!64;UBERON:0003075!5.46e-36!64;UBERON:0007284!5.46e-36!64;UBERON:0000073!3.43e-35!54;UBERON:0001049!4.48e-33!52;UBERON:0005068!4.48e-33!52;UBERON:0006241!4.48e-33!52;UBERON:0007135!4.48e-33!52;UBERON:0004121!8.47e-32!95;UBERON:0000924!8.47e-32!95;UBERON:0006601!8.47e-32!95;UBERON:0010371!1.22e-28!73;UBERON:0000955!6.44e-28!47;UBERON:0006238!6.44e-28!47;UBERON:0002616!3.31e-27!46;UBERON:0002020!3.52e-27!34;UBERON:0003056!1.14e-25!49;UBERON:0003080!2.87e-24!40;UBERON:0002780!2.12e-23!39;UBERON:0001890!2.12e-23!39;UBERON:0006240!2.12e-23!39;UBERON:0010314!1.30e-22!92;UBERON:0003528!3.20e-22!29;UBERON:0002791!3.20e-22!29;UBERON:0001893!3.20e-22!29;UBERON:0000956!1.07e-15!21;UBERON:0001869!1.07e-15!21;UBERON:0000203!1.07e-15!21;UBERON:0002619!5.81e-13!17;UBERON:0003076!5.03e-09!12;UBERON:0003057!5.03e-09!12;UBERON:0002021!8.06e-09!10;UBERON:0000411!8.06e-09!10;UBERON:0001950!8.06e-09!10;UBERON:0002420!1.13e-07!8;UBERON:0007245!1.13e-07!8;UBERON:0010009!1.13e-07!8;UBERON:0010011!1.13e-07!8;UBERON:0000454!1.13e-07!8;UBERON:0002240!8.68e-07!6;UBERON:0005174!8.68e-07!6;UBERON:0001137!8.68e-07!6
|ontology_enrichment_uberon=UBERON:0001017!5.16e-39!73;UBERON:0001016!2.84e-37!75;UBERON:0002346!5.46e-36!64;UBERON:0003075!5.46e-36!64;UBERON:0007284!5.46e-36!64;UBERON:0000073!3.43e-35!54;UBERON:0001049!4.48e-33!52;UBERON:0005068!4.48e-33!52;UBERON:0006241!4.48e-33!52;UBERON:0007135!4.48e-33!52;UBERON:0004121!8.47e-32!95;UBERON:0000924!8.47e-32!95;UBERON:0006601!8.47e-32!95;UBERON:0010371!1.22e-28!73;UBERON:0000955!6.44e-28!47;UBERON:0006238!6.44e-28!47;UBERON:0002616!3.31e-27!46;UBERON:0002020!3.52e-27!34;UBERON:0003056!1.14e-25!49;UBERON:0003080!2.87e-24!40;UBERON:0002780!2.12e-23!39;UBERON:0001890!2.12e-23!39;UBERON:0006240!2.12e-23!39;UBERON:0010314!1.30e-22!92;UBERON:0003528!3.20e-22!29;UBERON:0002791!3.20e-22!29;UBERON:0001893!3.20e-22!29;UBERON:0000956!1.07e-15!21;UBERON:0001869!1.07e-15!21;UBERON:0000203!1.07e-15!21;UBERON:0002619!5.81e-13!17;UBERON:0003076!5.03e-09!12;UBERON:0003057!5.03e-09!12;UBERON:0002021!8.06e-09!10;UBERON:0000411!8.06e-09!10;UBERON:0001950!8.06e-09!10;UBERON:0002420!1.13e-07!8;UBERON:0007245!1.13e-07!8;UBERON:0010009!1.13e-07!8;UBERON:0010011!1.13e-07!8;UBERON:0000454!1.13e-07!8;UBERON:0002240!8.68e-07!6;UBERON:0005174!8.68e-07!6;UBERON:0001137!8.68e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.737036,1.24506,0.686572,0.303186,0.1565,0.315748,1.02601,0.0908011,0.320069,2.01579,0.357058,0.385627,0.630954,0.407615,0.169024,0,1.43434,1.44151,0.279039,0.33293,0.215242,0.235703,1.04849,0.155356,0.251585,0.432737,0.265362,0.334131,0.191143,0.438367,0.860721,0.683831,1.43157,0.234079,0.505829,0.612118,0.438297,0.382372,0.126724,1.16642,0.153518,0.326286,0.407596,0.508662,0.461548,0.293566,0.512146,0.34807,0.337012,0.19345,1.39948,0.457464,0.736781,0.82076,0.837732,0.414119,0.581069,0.37415,0.0716833,0.412262,0.664611,0.46618,0.104381,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,1.21364,0.0945081,0.763255,0.870406,0.51601,0.222652,0.233965,0.50152,1.56206,1.171,0.316038,0.60374,0.464847,0.0868537,0.758319,1.5015,0.0395547,0.053731,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.391609,0.11194,0.622881,0.698838,0.512384,0.67526,0.862562,1.63583,0.803823,0.571268,0.57027,0.3259,0.627019,0.344504,1.18615,0.619563,0.261228,0.805555,0.219561,0.361667,1.04639,0.463309,1.39764,0.306448,0.58848,0.139554,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.95011,0.787341,0.296885,0.940498,0.426575,1.06766,0.092963,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.757925,0.477267,0.445509,0.983868,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.265096,0.752802,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.141416,0.384198,0.365903
|tfbs_overrepresentation_for_novel_motifs=0.737036,1.24506,0.686572,0.303186,0.1565,0.315748,1.02601,0.0908011,0.320069,2.01579,0.357058,0.385627,0.630954,0.407615,0.169024,0,1.43434,1.44151,0.279039,0.33293,0.215242,0.235703,1.04849,0.155356,0.251585,0.432737,0.265362,0.334131,0.191143,0.438367,0.860721,0.683831,1.43157,0.234079,0.505829,0.612118,0.438297,0.382372,0.126724,1.16642,0.153518,0.326286,0.407596,0.508662,0.461548,0.293566,0.512146,0.34807,0.337012,0.19345,1.39948,0.457464,0.736781,0.82076,0.837732,0.414119,0.581069,0.37415,0.0716833,0.412262,0.664611,0.46618,0.104381,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,1.21364,0.0945081,0.763255,0.870406,0.51601,0.222652,0.233965,0.50152,1.56206,1.171,0.316038,0.60374,0.464847,0.0868537,0.758319,1.5015,0.0395547,0.053731,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.391609,0.11194,0.622881,0.698838,0.512384,0.67526,0.862562,1.63583,0.803823,0.571268,0.57027,0.3259,0.627019,0.344504,1.18615,0.619563,0.261228,0.805555,0.219561,0.361667,1.04639,0.463309,1.39764,0.306448,0.58848,0.139554,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.95011,0.787341,0.296885,0.940498,0.426575,1.06766,0.092963,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.757925,0.477267,0.445509,0.983868,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.265096,0.752802,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.141416,0.384198,0.365903
|tfbs_overrepresentation_jaspar=MA0003.1;0.829197,MA0004.1;1.48666,MA0006.1;0.16569,MA0007.1;0.790701,MA0009.1;0.709264,MA0014.1;2.06593,MA0017.1;0.186015,MA0019.1;0.535691,MA0024.1;0.667197,MA0025.1;0.936082,MA0027.1;2.34178,MA0028.1;0.516099,MA0029.1;0.64639,MA0030.1;0.65267,MA0031.1;0.618697,MA0038.1;0.432665,MA0040.1;0.721328,MA0041.1;0.239557,MA0042.1;0.228771,MA0043.1;0.802848,MA0046.1;1.76106,MA0048.1;1.99126,MA0050.1;0.337476,MA0051.1;1.12244,MA0052.1;0.729105,MA0055.1;2.91199,MA0056.1;0,MA0057.1;0.350222,MA0058.1;2.60652,MA0059.1;3.52028,MA0060.1;0.108526,MA0061.1;0.129002,MA0063.1;0,MA0066.1;1.08293,MA0067.1;1.04514,MA0068.1;1.919,MA0069.1;0.729433,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;2.17834,MA0074.1;0.390075,MA0076.1;0.582294,MA0077.1;0.691048,MA0078.1;0.471303,MA0081.1;0.702944,MA0083.1;0.802078,MA0084.1;1.3693,MA0087.1;0.760279,MA0088.1;0.742898,MA0089.1;0,MA0090.1;0.27428,MA0091.1;0.315003,MA0092.1;0.753925,MA0093.1;2.2957,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;0.240622,MA0103.1;0.566591,MA0105.1;0.226879,MA0106.1;1.20346,MA0107.1;0.189625,MA0108.2;0.557195,MA0109.1;0,MA0111.1;0.78079,MA0113.1;0.452439,MA0114.1;0.127366,MA0115.1;0.805567,MA0116.1;0.496352,MA0117.1;0.774259,MA0119.1;0.241106,MA0122.1;0.793507,MA0124.1;0.992825,MA0125.1;0.920215,MA0130.1;0,MA0131.1;0.531427,MA0132.1;0,MA0133.1;0,MA0135.1;0.838263,MA0136.1;0.408073,MA0139.1;0.61859,MA0140.1;0.379562,MA0141.1;0.210047,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;0.129525,MA0145.1;0.109043,MA0146.1;0.142424,MA0147.1;1.36583,MA0148.1;0.317692,MA0149.1;0.686277,MA0062.2;0.235333,MA0035.2;0.383789,MA0039.2;1.65042,MA0138.2;2.24007,MA0002.2;0.0901987,MA0137.2;0.207733,MA0104.2;1.1126,MA0047.2;0.431964,MA0112.2;0.109037,MA0065.2;0.109524,MA0150.1;0.790482,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;0.16541,MA0155.1;0.87909,MA0156.1;0.200311,MA0157.1;0.574484,MA0158.1;0,MA0159.1;0.145521,MA0160.1;0.85749,MA0161.1;0,MA0162.1;2.56357,MA0163.1;2.01048,MA0164.1;0.408402,MA0080.2;0.190316,MA0018.2;0.417217,MA0099.2;0.518072,MA0079.2;3.893,MA0102.2;1.42135,MA0258.1;0.118033,MA0259.1;0.812279,MA0442.1;0
}}
}}

Revision as of 12:00, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:104171642..104171655,+p@chr11:104171642..104171655
+
Mm9::chr11:104171701..104171731,+p@chr11:104171701..104171731
+
Mm9::chr12:73313193..73313244,-p@chr12:73313193..73313244
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Mm9::chr12:73313326..73313392,-p@chr12:73313326..73313392
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Mm9::chr12:73324386..73324412,-p@chr12:73324386..73324412
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Mm9::chr15:44579907..44579923,-p7@Sybu
Mm9::chr16:20619899..20619944,-p@chr16:20619899..20619944
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Mm9::chr16:42249172..42249185,-p@chr16:42249172..42249185
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Mm9::chr1:84692327..84692341,-p5@Dner
Mm9::chr1:84692342..84692353,-p6@Dner
Mm9::chr3:95023823..95023839,-p@chr3:95023823..95023839
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Mm9::chr8:96334719..96334728,+p13@Gnao1


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:0043005neuron projection0.01507268662812
GO:0007220Notch receptor processing0.0206975803128446
GO:0005112Notch binding0.0206975803128446
GO:0005519cytoskeletal regulatory protein binding0.0206975803128446
GO:0042995cell projection0.0206975803128446
GO:0051605protein maturation via proteolysis0.0206975803128446
GO:0007026negative regulation of microtubule depolymerization0.0206975803128446
GO:0051604protein maturation0.0206975803128446
GO:0031114regulation of microtubule depolymerization0.0206975803128446
GO:0007019microtubule depolymerization0.0206975803128446
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0206975803128446
GO:0031110regulation of microtubule polymerization or depolymerization0.0222860376811327
GO:0031109microtubule polymerization or depolymerization0.0222860376811327
GO:0007212dopamine receptor signaling pathway0.0266009680357124
GO:0051261protein depolymerization0.0413067546960271
GO:0005834heterotrimeric G-protein complex0.0413067546960271
GO:0051129negative regulation of cellular component organization and biogenesis0.0413067546960271
GO:0008016regulation of heart contraction0.0413067546960271
GO:0010001glial cell differentiation0.0413067546960271
GO:0042063gliogenesis0.0413067546960271
GO:0060047heart contraction0.0413067546960271
GO:0003015heart process0.0413067546960271
GO:0030425dendrite0.0413067546960271
GO:0019897extrinsic to plasma membrane0.0413067546960271
GO:0007219Notch signaling pathway0.0413067546960271
GO:0051128regulation of cellular component organization and biogenesis0.0426065032114335
GO:0043025cell soma0.0426065032114335
GO:0030424axon0.0426065032114335
GO:0000226microtubule cytoskeleton organization and biogenesis0.0426065032114335
GO:0048741skeletal muscle fiber development0.0426065032114335
GO:0048747muscle fiber development0.0426065032114335
GO:0051248negative regulation of protein metabolic process0.043139354940474
GO:0019898extrinsic to membrane0.043139354940474



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
central nervous system5.16e-3973
nervous system2.84e-3775
neurectoderm5.46e-3664
neural plate5.46e-3664
presumptive neural plate5.46e-3664
regional part of nervous system3.43e-3554
neural tube4.48e-3352
neural rod4.48e-3352
future spinal cord4.48e-3352
neural keel4.48e-3352
ectoderm-derived structure8.47e-3295
ectoderm8.47e-3295
presumptive ectoderm8.47e-3295
ecto-epithelium1.22e-2873
brain6.44e-2847
future brain6.44e-2847
regional part of brain3.31e-2746
gray matter3.52e-2734
pre-chordal neural plate1.14e-2549
anterior neural tube2.87e-2440
regional part of forebrain2.12e-2339
forebrain2.12e-2339
future forebrain2.12e-2339
structure with developmental contribution from neural crest1.30e-2292
brain grey matter3.20e-2229
regional part of telencephalon3.20e-2229
telencephalon3.20e-2229
cerebral cortex1.07e-1521
cerebral hemisphere1.07e-1521
pallium1.07e-1521
regional part of cerebral cortex5.81e-1317
posterior neural tube5.03e-0912
chordal neural plate5.03e-0912
occipital lobe8.06e-0910
visual cortex8.06e-0910
neocortex8.06e-0910
basal ganglion1.13e-078
nuclear complex of neuraxis1.13e-078
aggregate regional part of brain1.13e-078
collection of basal ganglia1.13e-078
cerebral subcortex1.13e-078
spinal cord8.68e-076
dorsal region element8.68e-076
dorsum8.68e-076


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)
MA0003.10.829197
MA0004.11.48666
MA0006.10.16569
MA0007.10.790701
MA0009.10.709264
MA0014.12.06593
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.516099
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.11.76106
MA0048.11.99126
MA0050.10.337476
MA0051.11.12244
MA0052.10.729105
MA0055.12.91199
MA0056.10
MA0057.10.350222
MA0058.12.60652
MA0059.13.52028
MA0060.10.108526
MA0061.10.129002
MA0063.10
MA0066.11.08293
MA0067.11.04514
MA0068.11.919
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.12.17834
MA0074.10.390075
MA0076.10.582294
MA0077.10.691048
MA0078.10.471303
MA0081.10.702944
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.742898
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.753925
MA0093.12.2957
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.566591
MA0105.10.226879
MA0106.11.20346
MA0107.10.189625
MA0108.20.557195
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.10.127366
MA0115.10.805567
MA0116.10.496352
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.61859
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.109043
MA0146.10.142424
MA0147.11.36583
MA0148.10.317692
MA0149.10.686277
MA0062.20.235333
MA0035.20.383789
MA0039.21.65042
MA0138.22.24007
MA0002.20.0901987
MA0137.20.207733
MA0104.21.1126
MA0047.20.431964
MA0112.20.109037
MA0065.20.109524
MA0150.10.790482
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.16541
MA0155.10.87909
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.85749
MA0161.10
MA0162.12.56357
MA0163.12.01048
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.23.893
MA0102.21.42135
MA0258.10.118033
MA0259.10.812279
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:596&oldid=2573991"