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MCL coexpression mm9:1196: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000468!3.78e-09!333;UBERON:0007100!1.98e-07!18;UBERON:0000948!1.98e-07!18;UBERON:0005498!1.98e-07!18;UBERON:0004140!1.98e-07!18;UBERON:0009881!1.98e-07!18;UBERON:0004141!1.98e-07!18;UBERON:0003084!1.98e-07!18;UBERON:0007005!1.98e-07!18;UBERON:0004139!1.98e-07!18;UBERON:0004291!1.98e-07!18
|ontology_enrichment_uberon=UBERON:0000468!3.78e-09!333;UBERON:0007100!1.98e-07!18;UBERON:0000948!1.98e-07!18;UBERON:0005498!1.98e-07!18;UBERON:0004140!1.98e-07!18;UBERON:0009881!1.98e-07!18;UBERON:0004141!1.98e-07!18;UBERON:0003084!1.98e-07!18;UBERON:0007005!1.98e-07!18;UBERON:0004139!1.98e-07!18;UBERON:0004291!1.98e-07!18
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,1.05921,0.480627,2.24578,0.495263,1.43443,0.206208,0.215218,0.478312,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.112498,0.374752,0.988929,0.598814,0.29769,1.89054,0.62766,0.542568,0.516511,0.344372,0.446946,0.50223,0.897561,0.289148,0.498917,1.53201,0.468714,0.279977,0.57142,0.717242,0.652422,0.295233,1.26538,1.93015,0.851774,0.0275764,1.18381,0.714592,1.31862,0.219744,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,1.59144,1.47148,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.611537,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,1.14907,0.812889,0.663039,0.200155,0.975495,0.0369809,1.96285,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.127063,1.40122,0.897279,2.33242,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,0.735764,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.813943,0.452587,0.0736236,1.04192,0.243291,1.5029,1.12411,0.655955,0.327731,0.435579,1.98168,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,1.03935
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,1.05921,0.480627,2.24578,0.495263,1.43443,0.206208,0.215218,0.478312,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.112498,0.374752,0.988929,0.598814,0.29769,1.89054,0.62766,0.542568,0.516511,0.344372,0.446946,0.50223,0.897561,0.289148,0.498917,1.53201,0.468714,0.279977,0.57142,0.717242,0.652422,0.295233,1.26538,1.93015,0.851774,0.0275764,1.18381,0.714592,1.31862,0.219744,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,1.59144,1.47148,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.611537,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,1.14907,0.812889,0.663039,0.200155,0.975495,0.0369809,1.96285,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.127063,1.40122,0.897279,2.33242,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,0.735764,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.813943,0.452587,0.0736236,1.04192,0.243291,1.5029,1.12411,0.655955,0.327731,0.435579,1.98168,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,1.03935
|tfbs_overrepresentation_jaspar=MA0003.1;0.188259,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.222567,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.648475,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;1.33382,MA0063.1;0,MA0066.1;2.54082,MA0067.1;1.27078,MA0068.1;0.385183,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.00223012,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;1.60783,MA0081.1;0.420276,MA0083.1;5.41262,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.0841779,MA0089.1;0,MA0090.1;1.1347,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.0468,MA0103.1;0.348572,MA0105.1;0.9471,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.719313,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;1.04809,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;2.58258,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;2.05933,MA0145.1;0.0910975,MA0146.1;1.57153,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.367001,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;1.70505,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;1.5617,MA0065.2;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;1.5176,MA0153.1;1.07519,MA0154.1;0.792589,MA0155.1;0.687925,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.127623,MA0163.1;0.519779,MA0164.1;1.46244,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.000323799,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;1.34223,MA0442.1;0
}}
}}

Revision as of 12:57, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr3:137728133..137728161,+p@chr3:137728133..137728161
+
Mm9::chr6:112409709..112409743,+p1@Cav3
Mm9::chr6:112409745..112409752,+p5@Cav3
Mm9::chr7:149846882..149846893,-p12@Igf2
Mm9::chr7:149846894..149846945,-p3@Igf2
Mm9::chr7:149846948..149846963,-p9@Igf2
Mm9::chr7:149847093..149847111,-p7@Igf2


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:0051354negative regulation of oxidoreductase activity0.00366270264369207
GO:0051001negative regulation of nitric-oxide synthase activity0.00366270264369207
GO:0005159insulin-like growth factor receptor binding0.00366270264369207
GO:0018445prothoracicotrophic hormone activity0.00366270264369207
GO:0050999regulation of nitric-oxide synthase activity0.00366270264369207
GO:0031579lipid raft organization and biogenesis0.00366270264369207
GO:0051925regulation of calcium ion transport via voltage-gated calcium channel0.00366270264369207
GO:0051341regulation of oxidoreductase activity0.00480716552389701
GO:0043409negative regulation of MAPKKK cascade0.00712133649185093
GO:0051924regulation of calcium ion transport0.00823950059692129
GO:0016599caveolar membrane0.00823950059692129
GO:0046716muscle maintenance0.00823950059692129
GO:0005901caveola0.00823950059692129
GO:0030315T-tubule0.00823950059692129
GO:0007009plasma membrane organization and biogenesis0.0085444331595649
GO:0043269regulation of ion transport0.00961196052071523
GO:0042632cholesterol homeostasis0.0110661950770426
GO:0055088lipid homeostasis0.0110661950770426
GO:0055092sterol homeostasis0.0110661950770426
GO:0043408regulation of MAPKKK cascade0.0110661950770426
GO:0006641triacylglycerol metabolic process0.0110661950770426
GO:0005184neuropeptide hormone activity0.0110661950770426
GO:0006639acylglycerol metabolic process0.0123685928740176
GO:0046486glycerolipid metabolic process0.0123685928740176
GO:0006638neutral lipid metabolic process0.0123685928740176
GO:0006662glycerol ether metabolic process0.0123685928740176
GO:0042593glucose homeostasis0.0123685928740176
GO:0042383sarcolemma0.0123685928740176
GO:0033500carbohydrate homeostasis0.0123685928740176
GO:0045121lipid raft0.0144084586727577
GO:0006469negative regulation of protein kinase activity0.0144084586727577
GO:0033673negative regulation of kinase activity0.0144084586727577
GO:0051348negative regulation of transferase activity0.0147472431754467
GO:0042391regulation of membrane potential0.0158184497285886
GO:0043086negative regulation of catalytic activity0.0170620003455702
GO:0048513organ development0.0170620003455702
GO:0048731system development0.0252956453033153
GO:0051049regulation of transport0.0282740943699344
GO:0009968negative regulation of signal transduction0.0295120490852277
GO:0048856anatomical structure development0.0318117007811852
GO:0006816calcium ion transport0.0321158751667335
GO:0005179hormone activity0.0353633963699973
GO:0000165MAPKKK cascade0.0353633963699973
GO:0007275multicellular organismal development0.035923362439894
GO:0045859regulation of protein kinase activity0.035923362439894
GO:0043549regulation of kinase activity0.035923362439894
GO:0015674di-, tri-valent inorganic cation transport0.035923362439894
GO:0051338regulation of transferase activity0.035923362439894
GO:0055082cellular chemical homeostasis0.0372851529850379
GO:0006873cellular ion homeostasis0.0372851529850379
GO:0008083growth factor activity0.0373021045432671
GO:0007517muscle development0.0389795489121627
GO:0050801ion homeostasis0.0389795489121627
GO:0010324membrane invagination0.0389795489121627
GO:0006897endocytosis0.0389795489121627
GO:0048878chemical homeostasis0.0471827861399006
GO:0019725cellular homeostasis0.0471827861399006
GO:0032502developmental process0.0473012205455537
GO:0007243protein kinase cascade0.0473012205455537
GO:0016044membrane organization and biogenesis0.0494671991631394



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>

Uber Anatomy
Ontology termp-valuen
multi-cellular organism3.78e-09333
primary circulatory organ1.98e-0718
heart1.98e-0718
primitive heart tube1.98e-0718
primary heart field1.98e-0718
anterior lateral plate mesoderm1.98e-0718
heart tube1.98e-0718
heart primordium1.98e-0718
cardiac mesoderm1.98e-0718
cardiogenic plate1.98e-0718
heart rudiment1.98e-0718


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)
MA0003.10.188259
MA0004.10.481116
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.10.222567
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.648475
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.11.33382
MA0063.10
MA0066.12.54082
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.00223012
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.11.60783
MA0081.10.420276
MA0083.15.41262
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.11.1347
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.10.9471
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.11.04809
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.12.58258
MA0142.10.814115
MA0143.10.665982
MA0144.12.05933
MA0145.10.0910975
MA0146.11.57153
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.367001
MA0138.20.727395
MA0002.20.205289
MA0137.21.70505
MA0104.20.218974
MA0047.20.626803
MA0112.21.5617
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.11.5176
MA0153.11.07519
MA0154.10.792589
MA0155.10.687925
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.10.519779
MA0164.11.46244
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.000323799
MA0102.21.65195
MA0258.10.688848
MA0259.11.34223
MA0442.10
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