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MCL coexpression mm9:439: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000467!1.06e-10!308;UBERON:0000480!1.06e-10!308;UBERON:0005423!2.49e-10!304;UBERON:0002050!1.34e-09!294;UBERON:0000923!2.58e-09!291;UBERON:0010316!2.58e-09!291;UBERON:0005291!2.58e-09!291;UBERON:0006598!2.58e-09!291;UBERON:0010317!2.58e-09!291;UBERON:0002532!2.58e-09!291;UBERON:0007023!5.59e-09!51;UBERON:0000468!1.59e-08!333
|ontology_enrichment_uberon=UBERON:0000467!1.06e-10!308;UBERON:0000480!1.06e-10!308;UBERON:0005423!2.49e-10!304;UBERON:0002050!1.34e-09!294;UBERON:0000923!2.58e-09!291;UBERON:0010316!2.58e-09!291;UBERON:0005291!2.58e-09!291;UBERON:0006598!2.58e-09!291;UBERON:0010317!2.58e-09!291;UBERON:0002532!2.58e-09!291;UBERON:0007023!5.59e-09!51;UBERON:0000468!1.59e-08!333
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.442013,0.157426,0.205657,0.296927,0.618816,0.286882,0.670577,0.398834,0.0604331,0.252112,0.277243,0.376789,0.296787,0.662379,0,0.46143,0.596872,0.341555,0.316699,0.133242,0.371376,0.296055,1.02912,0.16256,0.319311,0.923228,0.232181,0.366819,0.0925636,0.22152,0.552579,1.48128,0.279585,0.0978183,0.537473,0.0778621,0.274364,0.874944,0.765659,0.607192,0.225414,0.33101,0.325245,0.174452,0.197508,0.391673,0.244272,0.428134,1.22575,0.445973,0.341665,0.416592,0.683824,0.700221,0.302599,0.77262,0.26711,0.302464,0.300938,0.534331,0.349585,0.749563,0.43605,0.311703,0.471894,0.829699,1.16897,0.530087,1.02503,0.444898,0.17272,0.00693324,0.731855,0.120421,0.108578,0.279429,0.381898,1.28944,0.135947,0.174228,0.476893,0.348372,0.64715,0.623727,0.138967,0.0332815,0.231141,0.395899,1.32869,0.896685,0.62835,0.564287,1.05833,0.0649512,0.792559,0.370414,0.56686,0.391893,0.369986,1.43314,0.552324,0.667487,0.446498,0.445567,0.225081,0.498793,0.241171,0.139088,0.134388,0.170493,0.669156,0.424252,0.711663,0.903482,0.085085,0.105429,0.208431,0.462587,0.0759495,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.796971,0.558086,0.828246,1.07003,0.651613,0.580662,0.799981,0.313768,0.92434,0.204108,0.181334,0.64263,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,0.439856,0.225756,0.394362,1.65442,0.183006,0.0892035,0.236,0.00478823,0.685297,1.72899,0.313008,0.762455,0.342508,0.340691,0.516355,0.181136,0.886073,0.622933,0.522515,0.50469,0.436947,0.306938,0.563665,0.275979,0.0629756
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.442013,0.157426,0.205657,0.296927,0.618816,0.286882,0.670577,0.398834,0.0604331,0.252112,0.277243,0.376789,0.296787,0.662379,0,0.46143,0.596872,0.341555,0.316699,0.133242,0.371376,0.296055,1.02912,0.16256,0.319311,0.923228,0.232181,0.366819,0.0925636,0.22152,0.552579,1.48128,0.279585,0.0978183,0.537473,0.0778621,0.274364,0.874944,0.765659,0.607192,0.225414,0.33101,0.325245,0.174452,0.197508,0.391673,0.244272,0.428134,1.22575,0.445973,0.341665,0.416592,0.683824,0.700221,0.302599,0.77262,0.26711,0.302464,0.300938,0.534331,0.349585,0.749563,0.43605,0.311703,0.471894,0.829699,1.16897,0.530087,1.02503,0.444898,0.17272,0.00693324,0.731855,0.120421,0.108578,0.279429,0.381898,1.28944,0.135947,0.174228,0.476893,0.348372,0.64715,0.623727,0.138967,0.0332815,0.231141,0.395899,1.32869,0.896685,0.62835,0.564287,1.05833,0.0649512,0.792559,0.370414,0.56686,0.391893,0.369986,1.43314,0.552324,0.667487,0.446498,0.445567,0.225081,0.498793,0.241171,0.139088,0.134388,0.170493,0.669156,0.424252,0.711663,0.903482,0.085085,0.105429,0.208431,0.462587,0.0759495,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.796971,0.558086,0.828246,1.07003,0.651613,0.580662,0.799981,0.313768,0.92434,0.204108,0.181334,0.64263,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,0.439856,0.225756,0.394362,1.65442,0.183006,0.0892035,0.236,0.00478823,0.685297,1.72899,0.313008,0.762455,0.342508,0.340691,0.516355,0.181136,0.886073,0.622933,0.522515,0.50469,0.436947,0.306938,0.563665,0.275979,0.0629756
|tfbs_overrepresentation_jaspar=MA0003.1;0.0188216,MA0004.1;0.594255,MA0006.1;0.315449,MA0007.1;0.195085,MA0009.1;0.576798,MA0014.1;0.060408,MA0017.1;0.110433,MA0019.1;0.413421,MA0024.1;0.536784,MA0025.1;0.795679,MA0027.1;2.19092,MA0028.1;0.100975,MA0029.1;0.51708,MA0030.1;0.523021,MA0031.1;0.490954,MA0038.1;0.319246,MA0040.1;0.588314,MA0041.1;0.906864,MA0042.1;0.144042,MA0043.1;0.666547,MA0046.1;0.609938,MA0048.1;0.0741002,MA0050.1;0.235075,MA0051.1;0.326637,MA0052.1;1.45222,MA0055.1;0.273388,MA0056.1;0,MA0057.1;0.56493,MA0058.1;0.431697,MA0059.1;0.451977,MA0060.1;0.0544856,MA0061.1;0.887454,MA0063.1;0,MA0066.1;0.310219,MA0067.1;0.902253,MA0068.1;0.176958,MA0069.1;0.59606,MA0070.1;0.587119,MA0071.1;0.661266,MA0072.1;0.579318,MA0073.1;0.00992177,MA0074.1;0.281183,MA0076.1;0.122031,MA0077.1;0.559443,MA0078.1;0.354249,MA0081.1;0.163204,MA0083.1;0.665805,MA0084.1;1.22195,MA0087.1;0.625609,MA0088.1;0.383684,MA0089.1;0,MA0090.1;0.181323,MA0091.1;0.215731,MA0092.1;0.535473,MA0093.1;0.344191,MA0095.1;0,MA0098.1;0,MA0100.1;1.37158,MA0101.1;0.153616,MA0103.1;0.751604,MA0105.1;0.804637,MA0106.1;2.54697,MA0107.1;0.113208,MA0108.2;1.10626,MA0109.1;0,MA0111.1;0.191411,MA0113.1;0.337108,MA0114.1;0.512575,MA0115.1;0.669167,MA0116.1;0.0949327,MA0117.1;0.639033,MA0119.1;0.154009,MA0122.1;1.58164,MA0124.1;0.851049,MA0125.1;0.780232,MA0130.1;0,MA0131.1;0.409473,MA0132.1;0,MA0133.1;0,MA0135.1;0.700734,MA0136.1;0.297196,MA0139.1;0.656302,MA0140.1;0.271883,MA0141.1;0.129134,MA0142.1;0.477975,MA0143.1;0.350815,MA0144.1;0.890316,MA0145.1;0.420675,MA0146.1;0.0854498,MA0147.1;0.0750034,MA0148.1;0.622748,MA0149.1;0.157322,MA0062.2;0.0281188,MA0035.2;0.275617,MA0039.2;0.0508806,MA0138.2;0.402586,MA0002.2;0.667016,MA0137.2;0.127311,MA0104.2;0.0483916,MA0047.2;0.318614,MA0112.2;0.114544,MA0065.2;0.241475,MA0150.1;1.69816,MA0151.1;0,MA0152.1;0.318703,MA0153.1;0.716409,MA0154.1;0.366592,MA0155.1;0.484511,MA0156.1;0.121496,MA0157.1;0.4495,MA0158.1;0,MA0159.1;0.274824,MA0160.1;0.628052,MA0161.1;0,MA0162.1;0.0194213,MA0163.1;0.177682,MA0164.1;0.297489,MA0080.2;0.113741,MA0018.2;0.305372,MA0099.2;0.397135,MA0079.2;0.0657156,MA0102.2;1.27355,MA0258.1;0.478272,MA0259.1;0.0696308,MA0442.1;0
}}
}}

Revision as of 11:45, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:77902441..77902456,-p@chr10:77902441..77902456
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Mm9::chr11:105916198..105916232,+p@chr11:105916198..105916232
+
Mm9::chr13:94973538..94973566,-p@chr13:94973538..94973566
-
Mm9::chr15:36700750..36700765,-p@chr15:36700750..36700765
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Mm9::chr19:7502163..7502190,-p@chr19:7502163..7502190
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Mm9::chr1:34876772..34876809,-p@chr1:34876772..34876809
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Mm9::chr2:158262760..158262777,+p@chr2:158262760..158262777
+
Mm9::chr2:180702329..180702342,+p3@Arfgap1
Mm9::chr6:124885388..124885412,+p@chr6:124885388..124885412
+
Mm9::chr6:124885755..124885780,+p@chr6:124885755..124885780
+
Mm9::chr6:124885797..124885818,+p@chr6:124885797..124885818
+
Mm9::chr7:148620128..148620139,-p10@Slc25a22
Mm9::chr7:17501146..17501162,-p@chr7:17501146..17501162
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Mm9::chr7:4093691..4093711,+p3@Leng8
Mm9::chr8:35199718..35199721,-p@chr8:35199718..35199721
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Mm9::chr8:42078178..42078192,-p@chr8:42078178..42078192
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Mm9::chrX:20275840..20275858,+p@chrX:20275840..20275858
+


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:0008478pyridoxal kinase activity0.0148773000776254
GO:0042819vitamin B6 biosynthetic process0.0148773000776254
GO:0042816vitamin B6 metabolic process0.0148773000776254
GO:0008615pyridoxine biosynthetic process0.0148773000776254
GO:0008614pyridoxine metabolic process0.0148773000776254



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><br>uberon_data<br><br>


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)
MA0003.10.0188216
MA0004.10.594255
MA0006.10.315449
MA0007.10.195085
MA0009.10.576798
MA0014.10.060408
MA0017.10.110433
MA0019.10.413421
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.10.100975
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.10.319246
MA0040.10.588314
MA0041.10.906864
MA0042.10.144042
MA0043.10.666547
MA0046.10.609938
MA0048.10.0741002
MA0050.10.235075
MA0051.10.326637
MA0052.11.45222
MA0055.10.273388
MA0056.10
MA0057.10.56493
MA0058.10.431697
MA0059.10.451977
MA0060.10.0544856
MA0061.10.887454
MA0063.10
MA0066.10.310219
MA0067.10.902253
MA0068.10.176958
MA0069.10.59606
MA0070.10.587119
MA0071.10.661266
MA0072.10.579318
MA0073.10.00992177
MA0074.10.281183
MA0076.10.122031
MA0077.10.559443
MA0078.10.354249
MA0081.10.163204
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.10.383684
MA0089.10
MA0090.10.181323
MA0091.10.215731
MA0092.10.535473
MA0093.10.344191
MA0095.10
MA0098.10
MA0100.11.37158
MA0101.10.153616
MA0103.10.751604
MA0105.10.804637
MA0106.12.54697
MA0107.10.113208
MA0108.21.10626
MA0109.10
MA0111.10.191411
MA0113.10.337108
MA0114.10.512575
MA0115.10.669167
MA0116.10.0949327
MA0117.10.639033
MA0119.10.154009
MA0122.11.58164
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.10.700734
MA0136.10.297196
MA0139.10.656302
MA0140.10.271883
MA0141.10.129134
MA0142.10.477975
MA0143.10.350815
MA0144.10.890316
MA0145.10.420675
MA0146.10.0854498
MA0147.10.0750034
MA0148.10.622748
MA0149.10.157322
MA0062.20.0281188
MA0035.20.275617
MA0039.20.0508806
MA0138.20.402586
MA0002.20.667016
MA0137.20.127311
MA0104.20.0483916
MA0047.20.318614
MA0112.20.114544
MA0065.20.241475
MA0150.11.69816
MA0151.10
MA0152.10.318703
MA0153.10.716409
MA0154.10.366592
MA0155.10.484511
MA0156.10.121496
MA0157.10.4495
MA0158.10
MA0159.10.274824
MA0160.10.628052
MA0161.10
MA0162.10.0194213
MA0163.10.177682
MA0164.10.297489
MA0080.20.113741
MA0018.20.305372
MA0099.20.397135
MA0079.20.0657156
MA0102.21.27355
MA0258.10.478272
MA0259.10.0696308
MA0442.10
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