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MCL coexpression mm9:643: Difference between revisions

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{{MCL_coexpression_mm9
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sterol transport;0.0179696488248507;67963!GO:0032367;intracellular cholesterol transport;0.0179696488248507;67963!GO:0030014;CCR4-NOT complex;0.0179696488248507;18983!GO:0032365;intracellular lipid transport;0.0179696488248507;67963!GO:0030521;androgen receptor signaling pathway;0.0239549372912768;15502!GO:0003730;mRNA 3'-UTR binding;0.0239549372912768;237400!GO:0050779;RNA destabilization;0.0307932992010504;237400!GO:0000242;pericentriolar material;0.0448896748248667;100986!GO:0015485;cholesterol binding;0.0487277273992434;67963!GO:0050750;low-density lipoprotein receptor binding;0.0487277273992434;15502!GO:0044265;cellular macromolecule catabolic process;0.0487277273992434;56550,237400!GO:0043285;biopolymer catabolic process;0.0487277273992434;56550,237400!GO:0005515;protein binding;0.0487277273992434;18983,100986,15502,74189,56550,237400!GO:0030518;steroid hormone receptor signaling pathway;0.0487277273992434;15502!GO:0032934;sterol binding;0.0487277273992434;67963!GO:0044450;microtubule organizing center part;0.0487277273992434;100986!GO:0030301;cholesterol transport;0.0487277273992434;67963!GO:0015918;sterol transport;0.0487277273992434;67963!GO:0043487;regulation of RNA stability;0.0487277273992434;237400!GO:0009057;macromolecule catabolic process;0.0487277273992434;56550,237400!GO:0004864;protein phosphatase inhibitor activity;0.0487277273992434;74189!GO:0042632;cholesterol homeostasis;0.0487277273992434;67963!GO:0055088;lipid homeostasis;0.0487277273992434;67963!GO:0055092;sterol homeostasis;0.0487277273992434;67963!GO:0051252;regulation of RNA metabolic process;0.0487277273992434;237400!GO:0030522;intracellular receptor-mediated signaling 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|ontology_enrichment_celltype=CL:0000540!4.83e-14!33;CL:0000047!4.83e-14!33;CL:0000031!4.83e-14!33;CL:0000404!4.83e-14!33;CL:0000221!5.78e-13!44;CL:0000133!5.78e-13!44;CL:0000117!7.99e-13!23;CL:0000337!7.99e-13!23;CL:0002319!1.40e-12!43;CL:0000393!2.78e-11!39;CL:0000211!2.78e-11!39;CL:0000055!1.64e-10!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.70e-22!73;UBERON:0001016!4.30e-22!75;UBERON:0002346!8.40e-22!64;UBERON:0003075!8.40e-22!64;UBERON:0007284!8.40e-22!64;UBERON:0004121!9.00e-21!95;UBERON:0000924!9.00e-21!95;UBERON:0006601!9.00e-21!95;UBERON:0010371!6.24e-19!73;UBERON:0001049!1.52e-18!52;UBERON:0005068!1.52e-18!52;UBERON:0006241!1.52e-18!52;UBERON:0007135!1.52e-18!52;UBERON:0000073!2.79e-18!54;UBERON:0010314!1.39e-17!92;UBERON:0003056!6.06e-16!49;UBERON:0000955!2.06e-15!47;UBERON:0006238!2.06e-15!47;UBERON:0002616!6.07e-15!46;UBERON:0002020!3.99e-13!34;UBERON:0003080!4.39e-13!40;UBERON:0002780!1.45e-12!39;UBERON:0001890!1.45e-12!39;UBERON:0006240!1.45e-12!39;UBERON:0003528!3.21e-10!29;UBERON:0002791!3.21e-10!29;UBERON:0001893!3.21e-10!29;UBERON:0000468!8.90e-07!333
|tfbs_overrepresentation_for_novel_motifs=0.29262,1.82801,0.269904,0.878892,0.52369,0.342839,0.425757,0.106126,0.732132,1.35304,0.385334,0.414631,1.70121,0.437133,0.189961,0,0.619876,0.170475,0.318616,0.387499,0.238546,0.521547,0.436294,0.520732,0.276437,0.4628,0.304017,0.361771,0.213277,0.231659,0.349031,0.717576,0.973026,0.270473,0.19035,1.69598,0.94339,0.411296,0.445168,1.85421,0.173534,0.353696,0.255102,0.191571,0.812209,0.319944,0.543674,0.376103,0.081888,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.288386,0.441884,0.698157,0.496904,0.769309,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,1.30396,0.110167,1.25712,0.905636,0.277092,0.258161,0.270351,0.532872,0.681539,0.242107,0.110993,0.636582,0.495545,0.101814,0.792744,1.70871,0.0106044,0.860726,0.548334,3.32472,1.07554,0.797601,0.730003,0.181374,0.861126,0.129056,0.694736,0.732731,0.543917,0.197581,0.161581,0.717305,0.838603,0.603683,0.602672,0.930972,0.660145,0.372438,0.246223,0.240055,0.781068,0.840348,0.243062,0.390066,1.0825,0.172131,0.566805,0.886406,0.621127,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,0.0275241,0.300001,0.934673,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,1.01111,0.0664621,1.52804,0.857198,0.415832,0.455644,0.93735,0.488969,0.199652,0.290467,0.299755,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,0.939822,0.413167,1.96561
|tfbs_overrepresentation_jaspar=MA0003.1;1.57537,MA0004.1;0.879856,MA0006.1;0.547312,MA0007.1;0.850001,MA0009.1;0.743257,MA0014.1;3.26278,MA0017.1;1.12929,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.199479,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.0494654,MA0056.1;0,MA0057.1;1.55717,MA0058.1;0.690295,MA0059.1;0.257372,MA0060.1;0.789184,MA0061.1;1.42191,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;1.12865,MA0069.1;0.76361,MA0070.1;1.78222,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;7.10156,MA0074.1;0.419185,MA0076.1;0.635923,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.760108,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.28966,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;0.58345,MA0095.1;0,MA0098.1;0,MA0100.1;1.05226,MA0101.1;0.73212,MA0103.1;0.216742,MA0105.1;0.556739,MA0106.1;0.509454,MA0107.1;1.14406,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.876865,MA0115.1;0.84036,MA0116.1;2.34252,MA0117.1;0.808813,MA0119.1;0.265536,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.103495,MA0140.1;1.85338,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;1.4253,MA0145.1;0.133285,MA0146.1;3.1027,MA0147.1;0.475899,MA0148.1;0.344843,MA0149.1;0.742998,MA0062.2;0.968877,MA0035.2;2.79233,MA0039.2;4.27224,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;1.21712,MA0104.2;0.369356,MA0047.2;0.46201,MA0112.2;1.7522,MA0065.2;0.574339,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.0529077,MA0155.1;1.41584,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.957875,MA0160.1;0.347545,MA0161.1;0,MA0162.1;2.86908,MA0163.1;1.8528,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;1.13559,MA0099.2;0.549696,MA0079.2;22.519,MA0102.2;1.45844,MA0258.1;0.833943,MA0259.1;0.891672,MA0442.1;0
}}

Latest revision as of 15:39, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79850331..79850375,-p1@Mex3d
Mm9::chr12:86114023..86114033,-p6@Npc2
Mm9::chr12:86114037..86114041,-p7@Npc2
Mm9::chr15:85166651..85166662,+p7@Atxn10
Mm9::chr18:35931142..35931212,+p3@Ube2d2
Mm9::chr19:42160809..42160824,-p2@Morn4
Mm9::chr2:178062216..178062239,+p7@Phactr3
Mm9::chr4:40670050..40670064,+p3@Dnaja1
Mm9::chr5:3927857..3927888,+p3@Akap9
Mm9::chr8:111775598..111775613,-p1@ENSMUST00000079189
Mm9::chr8:41596652..41596700,-p2@Cnot7


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:0032366intracellular sterol transport0.0179696488248507
GO:0032367intracellular cholesterol transport0.0179696488248507
GO:0030014CCR4-NOT complex0.0179696488248507
GO:0032365intracellular lipid transport0.0179696488248507
GO:0030521androgen receptor signaling pathway0.0239549372912768
GO:0003730mRNA 3'-UTR binding0.0239549372912768
GO:0050779RNA destabilization0.0307932992010504
GO:0000242pericentriolar material0.0448896748248667
GO:0015485cholesterol binding0.0487277273992434
GO:0050750low-density lipoprotein receptor binding0.0487277273992434
GO:0044265cellular macromolecule catabolic process0.0487277273992434
GO:0043285biopolymer catabolic process0.0487277273992434
GO:0005515protein binding0.0487277273992434
GO:0030518steroid hormone receptor signaling pathway0.0487277273992434
GO:0032934sterol binding0.0487277273992434
GO:0044450microtubule organizing center part0.0487277273992434
GO:0030301cholesterol transport0.0487277273992434
GO:0015918sterol transport0.0487277273992434
GO:0043487regulation of RNA stability0.0487277273992434
GO:0009057macromolecule catabolic process0.0487277273992434
GO:0004864protein phosphatase inhibitor activity0.0487277273992434
GO:0042632cholesterol homeostasis0.0487277273992434
GO:0055088lipid homeostasis0.0487277273992434
GO:0055092sterol homeostasis0.0487277273992434
GO:0051252regulation of RNA metabolic process0.0487277273992434
GO:0030522intracellular receptor-mediated signaling pathway0.0496001682551745



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 system1.70e-2273
nervous system4.30e-2275
neurectoderm8.40e-2264
neural plate8.40e-2264
presumptive neural plate8.40e-2264
ectoderm-derived structure9.00e-2195
ectoderm9.00e-2195
presumptive ectoderm9.00e-2195
ecto-epithelium6.24e-1973
neural tube1.52e-1852
neural rod1.52e-1852
future spinal cord1.52e-1852
neural keel1.52e-1852
regional part of nervous system2.79e-1854
structure with developmental contribution from neural crest1.39e-1792
pre-chordal neural plate6.06e-1649
brain2.06e-1547
future brain2.06e-1547
regional part of brain6.07e-1546
gray matter3.99e-1334
anterior neural tube4.39e-1340
regional part of forebrain1.45e-1239
forebrain1.45e-1239
future forebrain1.45e-1239
brain grey matter3.21e-1029
regional part of telencephalon3.21e-1029
telencephalon3.21e-1029
multi-cellular organism8.90e-07333


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)
MA0003.11.57537
MA0004.10.879856
MA0006.10.547312
MA0007.10.850001
MA0009.10.743257
MA0014.13.26278
MA0017.11.12929
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.199479
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.0494654
MA0056.10
MA0057.11.55717
MA0058.10.690295
MA0059.10.257372
MA0060.10.789184
MA0061.11.42191
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.11.12865
MA0069.10.76361
MA0070.11.78222
MA0071.10.364454
MA0072.10.745922
MA0073.17.10156
MA0074.10.419185
MA0076.10.635923
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.28966
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.10.58345
MA0095.10
MA0098.10
MA0100.11.05226
MA0101.10.73212
MA0103.10.216742
MA0105.10.556739
MA0106.10.509454
MA0107.11.14406
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.876865
MA0115.10.84036
MA0116.12.34252
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.103495
MA0140.11.85338
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.11.4253
MA0145.10.133285
MA0146.13.1027
MA0147.10.475899
MA0148.10.344843
MA0149.10.742998
MA0062.20.968877
MA0035.22.79233
MA0039.24.27224
MA0138.20.555696
MA0002.20.105469
MA0137.21.21712
MA0104.20.369356
MA0047.20.46201
MA0112.21.7522
MA0065.20.574339
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.0529077
MA0155.11.41584
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.957875
MA0160.10.347545
MA0161.10
MA0162.12.86908
MA0163.11.8528
MA0164.10.437937
MA0080.20.212408
MA0018.21.13559
MA0099.20.549696
MA0079.222.519
MA0102.21.45844
MA0258.10.833943
MA0259.10.891672
MA0442.10
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