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MCL coexpression mm9:612: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0032433;filopodium tip;0.014134662795157;57776!GO:0031527;filopodium membrane;0.014134662795157;57776!GO:0031957;very-long-chain-fatty-acid-CoA ligase activity;0.014134662795157;94180!GO:0004111;creatine kinase activity;0.0423285488713615;12709!GO:0000038;very-long-chain fatty acid metabolic process;0.0423285488713615;94180!GO:0046847;filopodium formation;0.0423285488713615;57776!GO:0030035;microspike biogenesis;0.0423285488713615;57776!GO:0031253;cell projection membrane;0.0423285488713615;57776!GO:0006970;response to osmotic stress;0.0423285488713615;78829!GO:0004467;long-chain-fatty-acid-CoA ligase activity;0.0423285488713615;94180!GO:0030175;filopodium;0.0423285488713615;57776!GO:0015645;fatty-acid ligase activity;0.0423285488713615;94180!GO:0001676;long-chain fatty acid metabolic process;0.0423285488713615;94180!GO:0016775;phosphotransferase activity, nitrogenous group as acceptor;0.0423285488713615;12709!}}
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tip;0.014134662795157;57776!GO:0031527;filopodium membrane;0.014134662795157;57776!GO:0031957;very-long-chain-fatty-acid-CoA ligase activity;0.014134662795157;94180!GO:0004111;creatine kinase activity;0.0423285488713615;12709!GO:0000038;very-long-chain fatty acid metabolic process;0.0423285488713615;94180!GO:0046847;filopodium formation;0.0423285488713615;57776!GO:0030035;microspike biogenesis;0.0423285488713615;57776!GO:0031253;cell projection membrane;0.0423285488713615;57776!GO:0006970;response to osmotic stress;0.0423285488713615;78829!GO:0004467;long-chain-fatty-acid-CoA ligase activity;0.0423285488713615;94180!GO:0030175;filopodium;0.0423285488713615;57776!GO:0015645;fatty-acid ligase activity;0.0423285488713615;94180!GO:0001676;long-chain fatty acid metabolic process;0.0423285488713615;94180!GO:0016775;phosphotransferase activity, nitrogenous group as acceptor;0.0423285488713615;12709!|ontology_enrichment_celltype=CL:0000221!1.89e-20!44;CL:0000133!1.89e-20!44;CL:0002319!5.99e-20!43;CL:0000055!2.93e-15!49;CL:0000540!3.94e-15!33;CL:0000047!3.94e-15!33;CL:0000031!3.94e-15!33;CL:0000404!3.94e-15!33;CL:0000117!7.48e-13!23;CL:0000337!7.48e-13!23;CL:0000393!9.81e-11!39;CL:0000211!9.81e-11!39;CL:0002321!5.92e-07!70|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001016!3.22e-37!75;UBERON:0001017!3.60e-37!73;UBERON:0004121!9.25e-31!95;UBERON:0000924!9.25e-31!95;UBERON:0006601!9.25e-31!95;UBERON:0000073!3.30e-28!54;UBERON:0002346!7.28e-27!64;UBERON:0003075!7.28e-27!64;UBERON:0007284!7.28e-27!64;UBERON:0001049!1.08e-26!52;UBERON:0005068!1.08e-26!52;UBERON:0006241!1.08e-26!52;UBERON:0007135!1.08e-26!52;UBERON:0010371!8.49e-24!73;UBERON:0000955!3.96e-23!47;UBERON:0006238!3.96e-23!47;UBERON:0002616!1.51e-22!46;UBERON:0002020!7.08e-20!34;UBERON:0003080!7.39e-19!40;UBERON:0010314!1.56e-18!92;UBERON:0003056!2.23e-18!49;UBERON:0002780!3.17e-18!39;UBERON:0001890!3.17e-18!39;UBERON:0006240!3.17e-18!39;UBERON:0003528!1.44e-16!29;UBERON:0002791!1.44e-16!29;UBERON:0001893!1.44e-16!29;UBERON:0000956!3.27e-12!21;UBERON:0001869!3.27e-12!21;UBERON:0000203!3.27e-12!21;UBERON:0002619!1.88e-10!17;UBERON:0003076!2.17e-08!12;UBERON:0003057!2.17e-08!12;UBERON:0000468!1.08e-07!333;UBERON:0002021!1.31e-07!10;UBERON:0000411!1.31e-07!10;UBERON:0001950!1.31e-07!10|tfbs_overrepresentation_for_novel_motifs=0.267173,0.409645,0.245304,0.303186,0.474017,0.315748,1.02601,0.630239,0.320069,1.58153,0.357058,0.385627,0.304329,0.407615,0.504927,0,0.587245,0.150639,0.0817508,0.143041,0.215242,0.0948826,0.406794,0.155356,0.701128,1.10486,1.42253,0.334131,0.558665,0.438367,0.860721,0.683831,0.891038,0.866746,0.169391,0.130126,0.142225,0.382372,0.398832,0.707364,0.153518,0.870859,0.990451,0.170547,3.85103,0.293566,0.512146,0.34807,0.852381,0.19345,0.570705,0.457464,0.187938,0.82076,0.837732,0.414119,0.200484,0.977003,0.250759,0.412262,0.664611,1.17701,0.694361,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.650349,0.0945081,0.251765,0.870406,0.240236,0.222652,0.504564,1.2527,0.648171,0.624196,1.08483,0.60374,0.464847,0.0868537,0.758319,3.80134,0.0395547,0.43877,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.12392,0.11194,0.0892768,0.698838,0.512384,0.0434558,0.142282,0.683562,0.803823,0.571268,0.57027,0.3259,0.627019,0.344504,0.222586,0.619563,1.33189,0.805555,0.626352,3.5024,1.04639,0.463309,0.278854,1.49689,0.58848,1.37401,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.95011,0.787341,0.296885,0.940498,1.91515,1.06766,0.092963,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.276297,0.477267,1.18603,0.0825345,0.822286,0.747142,0.425729,0.901933,0.458393,0.178202,0.265096,0.274055,1.02862,0.757491,0.652135,0.719007,0.561023,0.418964,1.99824,0.384198,0.113306|tfbs_overrepresentation_jaspar=MA0003.1;3.86695,MA0004.1;0.303605,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;0.173587,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;0.743934,MA0048.1;0.382561,MA0050.1;0.337476,MA0051.1;0.440863,MA0052.1;0.729105,MA0055.1;1.22156,MA0056.1;0,MA0057.1;1.40292,MA0058.1;0.223242,MA0059.1;0.233271,MA0060.1;0.713464,MA0061.1;1.89666,MA0063.1;0,MA0066.1;0.422624,MA0067.1;1.04514,MA0068.1;0.361347,MA0069.1;0.729433,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;5.39395,MA0074.1;0.390075,MA0076.1;0.582294,MA0077.1;0.691048,MA0078.1;0.471303,MA0081.1;0.252371,MA0083.1;0.802078,MA0084.1;1.3693,MA0087.1;0.760279,MA0088.1;0.24301,MA0089.1;0,MA0090.1;0.27428,MA0091.1;1.52754,MA0092.1;0.274547,MA0093.1;0.179936,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;1.25479,MA0103.1;1.07649,MA0105.1;3.62968,MA0106.1;0.478503,MA0107.1;1.05738,MA0108.2;0.557195,MA0109.1;0,MA0111.1;0.286331,MA0113.1;0.452439,MA0114.1;0.127366,MA0115.1;0.805567,MA0116.1;0.496352,MA0117.1;0.774259,MA0119.1;0.676816,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;4.16003,MA0140.1;0.988903,MA0141.1;1.13771,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;0.807435,MA0145.1;0.793629,MA0146.1;0.0195411,MA0147.1;0.845188,MA0148.1;0.317692,MA0149.1;0.245177,MA0062.2;0.0662974,MA0035.2;0.383789,MA0039.2;1.37659,MA0138.2;1.30053,MA0002.2;0.302282,MA0137.2;0.207733,MA0104.2;0.670538,MA0047.2;0.431964,MA0112.2;0.109037,MA0065.2;1.15835,MA0150.1;0.290598,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;0.376318,MA0155.1;0.127763,MA0156.1;0.200311,MA0157.1;0.574484,MA0158.1;0,MA0159.1;0.145521,MA0160.1;0.320315,MA0161.1;0,MA0162.1;1.03289,MA0163.1;3.87586,MA0164.1;0.408402,MA0080.2;0.190316,MA0018.2;0.417217,MA0099.2;0.518072,MA0079.2;6.82653,MA0102.2;1.42135,MA0258.1;0.756558,MA0259.1;0.130633,MA0442.1;0}}

Latest revision as of 15:36, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:112909747..112909802,-p@chr12:112909747..112909802
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Mm9::chr12:81620208..81620217,+p@chr12:81620208..81620217
+
Mm9::chr15:30387606..30387623,+p@chr15:30387606..30387623
+
Mm9::chr5:138199481..138199491,+p16@Tsc22d4
Mm9::chr5:143040448..143040453,-p@chr5:143040448..143040453
-
Mm9::chr5:143084702..143084734,-p1@Mmd2
Mm9::chr5:143084739..143084762,-p2@Mmd2
Mm9::chr7:4071127..4071157,+p2@Ttyh1
Mm9::chr7:4071158..4071198,+p1@Ttyh1
Mm9::chr7:4071200..4071211,+p3@Ttyh1
Mm9::chr8:97519491..97519521,+p@chr8:97519491..97519521
+
Mm9::chr9:54509473..54509523,-p1@Acsbg1


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:0032433filopodium tip0.014134662795157
GO:0031527filopodium membrane0.014134662795157
GO:0031957very-long-chain-fatty-acid-CoA ligase activity0.014134662795157
GO:0004111creatine kinase activity0.0423285488713615
GO:0000038very-long-chain fatty acid metabolic process0.0423285488713615
GO:0046847filopodium formation0.0423285488713615
GO:0030035microspike biogenesis0.0423285488713615
GO:0031253cell projection membrane0.0423285488713615
GO:0006970response to osmotic stress0.0423285488713615
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0423285488713615
GO:0030175filopodium0.0423285488713615
GO:0015645fatty-acid ligase activity0.0423285488713615
GO:0001676long-chain fatty acid metabolic process0.0423285488713615
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0423285488713615



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
nervous system3.22e-3775
central nervous system3.60e-3773
ectoderm-derived structure9.25e-3195
ectoderm9.25e-3195
presumptive ectoderm9.25e-3195
regional part of nervous system3.30e-2854
neurectoderm7.28e-2764
neural plate7.28e-2764
presumptive neural plate7.28e-2764
neural tube1.08e-2652
neural rod1.08e-2652
future spinal cord1.08e-2652
neural keel1.08e-2652
ecto-epithelium8.49e-2473
brain3.96e-2347
future brain3.96e-2347
regional part of brain1.51e-2246
gray matter7.08e-2034
anterior neural tube7.39e-1940
structure with developmental contribution from neural crest1.56e-1892
pre-chordal neural plate2.23e-1849
regional part of forebrain3.17e-1839
forebrain3.17e-1839
future forebrain3.17e-1839
brain grey matter1.44e-1629
regional part of telencephalon1.44e-1629
telencephalon1.44e-1629
cerebral cortex3.27e-1221
cerebral hemisphere3.27e-1221
pallium3.27e-1221
regional part of cerebral cortex1.88e-1017
posterior neural tube2.17e-0812
chordal neural plate2.17e-0812
multi-cellular organism1.08e-07333
occipital lobe1.31e-0710
visual cortex1.31e-0710
neocortex1.31e-0710


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)
MA0003.13.86695
MA0004.10.303605
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
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.382561
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.11.22156
MA0056.10
MA0057.11.40292
MA0058.10.223242
MA0059.10.233271
MA0060.10.713464
MA0061.11.89666
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.361347
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.15.39395
MA0074.10.390075
MA0076.10.582294
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.24301
MA0089.10
MA0090.10.27428
MA0091.11.52754
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.11.25479
MA0103.11.07649
MA0105.13.62968
MA0106.10.478503
MA0107.11.05738
MA0108.20.557195
MA0109.10
MA0111.10.286331
MA0113.10.452439
MA0114.10.127366
MA0115.10.805567
MA0116.10.496352
MA0117.10.774259
MA0119.10.676816
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.14.16003
MA0140.10.988903
MA0141.11.13771
MA0142.10.604892
MA0143.10.467531
MA0144.10.807435
MA0145.10.793629
MA0146.10.0195411
MA0147.10.845188
MA0148.10.317692
MA0149.10.245177
MA0062.20.0662974
MA0035.20.383789
MA0039.21.37659
MA0138.21.30053
MA0002.20.302282
MA0137.20.207733
MA0104.20.670538
MA0047.20.431964
MA0112.20.109037
MA0065.21.15835
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.376318
MA0155.10.127763
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.320315
MA0161.10
MA0162.11.03289
MA0163.13.87586
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.26.82653
MA0102.21.42135
MA0258.10.756558
MA0259.10.130633
MA0442.10
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