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MCL coexpression mm9:371: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002048!2.74e-28!14;UBERON:0000117!2.74e-28!14;UBERON:0000171!2.74e-28!14;UBERON:0000170!2.74e-28!14;UBERON:0005597!2.74e-28!14;UBERON:0000118!2.74e-28!14;UBERON:0005153!1.26e-22!17;UBERON:0005178!1.26e-22!17;UBERON:0005181!1.26e-22!17;UBERON:0002224!1.26e-22!17;UBERON:0000915!1.26e-22!17;UBERON:0008947!1.26e-22!17;UBERON:0003258!1.26e-22!17;UBERON:0005157!1.15e-18!20;UBERON:0000310!1.57e-12!6;UBERON:0001443!1.57e-12!6;UBERON:0000065!2.77e-07!41;UBERON:0001004!4.95e-07!42
|tfbs_overrepresentation_for_novel_motifs=0.128666,0.240865,0.11338,0.469866,0.458154,0.954523,0.227275,0.0241132,0.271611,0.243837,0.195931,0.218542,0.103499,0.23628,0.0644609,0,0.38962,0.19894,1.03293,1.80738,0.310483,0.552182,0.235613,0.206855,0.117721,0.256873,0.0827016,0.178177,0.26816,0.139286,0.168752,0.476579,0.196184,0.582133,0.230648,0.282877,0.413492,0.21594,0.365025,0.304085,0.203766,0.512679,0.318983,0.502107,0.0757397,0.452134,0.323935,0.188927,0.0667794,0.272179,0.978855,0.277452,0.266413,0.603398,0.619345,0.677917,0.0837141,0.602302,0.933589,0.240064,0.459084,0.284775,0.124057,0.365621,0.2499,0.399544,0.745869,1.08074,0.455021,0.938231,0.687161,0.264613,0.392313,0.650163,0.359238,0.164312,0.0142585,0.314806,0.444191,0.65245,0.0260578,0.404291,0.283653,1.48225,0.545133,0.118961,0.0773437,0.746706,0.327889,1.23935,1.90079,0.549603,0.487824,0.216228,0.155012,0.135896,0.248387,0.490297,0.324141,0.108849,0.185028,0.476334,0.58753,0.979946,0.978012,0.511961,0.42513,0.186164,1.10411,0.31304,0.785181,0.58915,0.0960466,0.199544,0.818358,1.18433,0.185755,0.475893,0.390716,0.180519,0.655146,0.348339,0.716525,0.314081,0.869916,0.447391,0.658496,0.481866,0.744444,1.75108,2.39747,0.150169,0.716744,0.251791,0.838892,0.0456113,1.33798,0.991009,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.966134,0.513419,0.326451,1.56378,0.420463,0.210988,0.497376,0.010964,0.60483,0.942446,0.251095,0.680035,0.278231,0.0699281,0.127194,0.133575,0.801233,0.544365,0.447776,0.123129,0.366469,0.245542,1.57028,1.82127,0.242298
|tfbs_overrepresentation_jaspar=MA0003.1;0.0387975,MA0004.1;0.470639,MA0006.1;0.0625076,MA0007.1;0.87679,MA0009.1;0.499857,MA0014.1;0.0202604,MA0017.1;0.259254,MA0019.1;0.344318,MA0024.1;0.461433,MA0025.1;0.712532,MA0027.1;2.09948,MA0028.1;0.067163,MA0029.1;1.96925,MA0030.1;0.448261,MA0031.1;0.417663,MA0038.1;0.256813,MA0040.1;2.19715,MA0041.1;0.353863,MA0042.1;0.334544,MA0043.1;0.586618,MA0046.1;0.531807,MA0048.1;0.038539,MA0050.1;0.533529,MA0051.1;0.728838,MA0052.1;2.22076,MA0055.1;0.0713525,MA0056.1;0,MA0057.1;0.204512,MA0058.1;0.324689,MA0059.1;0.342591,MA0060.1;0.0321237,MA0061.1;1.46405,MA0063.1;0,MA0066.1;1.28459,MA0067.1;0.817149,MA0068.1;0.214228,MA0069.1;0.518414,MA0070.1;0.509795,MA0071.1;1.01954,MA0072.1;0.502282,MA0073.1;0.000287381,MA0074.1;0.222108,MA0076.1;0.0840393,MA0077.1;0.48317,MA0078.1;0.289095,MA0081.1;0.757603,MA0083.1;0.585897,MA0084.1;1.1333,MA0087.1;0.546952,MA0088.1;0.0150058,MA0089.1;0,MA0090.1;0.825782,MA0091.1;0.163657,MA0092.1;0.133927,MA0093.1;0.531479,MA0095.1;0,MA0098.1;0,MA0100.1;0.213782,MA0101.1;0.355777,MA0103.1;0.57683,MA0105.1;0.848889,MA0106.1;0.295186,MA0107.1;1.4231,MA0108.2;0.952664,MA0109.1;0,MA0111.1;0.14244,MA0113.1;0.273246,MA0114.1;0.656298,MA0115.1;0.589161,MA0116.1;0.839093,MA0117.1;0.559943,MA0119.1;0.356648,MA0122.1;0.577888,MA0124.1;0.766819,MA0125.1;0.697415,MA0130.1;0,MA0131.1;0.340612,MA0132.1;0,MA0133.1;0,MA0135.1;0.619844,MA0136.1;0.236653,MA0139.1;0.245643,MA0140.1;0.2137,MA0141.1;0.0898383,MA0142.1;0.40532,MA0143.1;0.285913,MA0144.1;0.164087,MA0145.1;0.134183,MA0146.1;0.124121,MA0147.1;0.0471319,MA0148.1;3.71461,MA0149.1;0.113293,MA0062.2;0.0144279,MA0035.2;0.217072,MA0039.2;0.101331,MA0138.2;0.334152,MA0002.2;0.251244,MA0137.2;0.618368,MA0104.2;0.0278464,MA0047.2;1.31332,MA0112.2;0.625195,MA0065.2;0.254194,MA0150.1;0.145553,MA0151.1;0,MA0152.1;0.712054,MA0153.1;0.635107,MA0154.1;0.90272,MA0155.1;0.164369,MA0156.1;0.0836044,MA0157.1;0.986187,MA0158.1;0,MA0159.1;0.423802,MA0160.1;0.167661,MA0161.1;0,MA0162.1;0.16309,MA0163.1;0.865154,MA0164.1;1.2408,MA0080.2;0.266721,MA0018.2;0.683803,MA0099.2;0.329046,MA0079.2;0.00171301,MA0102.2;1.18455,MA0258.1;0.956776,MA0259.1;0.0431217,MA0442.1;0
}}

Latest revision as of 15:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:85306222..85306234,+p8@Bcas3
Mm9::chr11:85306239..85306253,+p10@Bcas3
Mm9::chr12:57354134..57354149,+p3@Gm19990
Mm9::chr12:57354215..57354235,+p2@Gm19990
Mm9::chr12:57354237..57354248,+p4@Gm19990
Mm9::chr12:57446759..57446775,-p@chr12:57446759..57446775
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Mm9::chr12:57622327..57622338,-p@chr12:57622327..57622338
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Mm9::chr12:57622375..57622384,-p@chr12:57622375..57622384
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Mm9::chr12:57624241..57624253,-p@chr12:57624241..57624253
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Mm9::chr13:113825435..113825439,+p1@Cdc20b
Mm9::chr14:115241755..115241762,-p@chr14:115241755..115241762
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Mm9::chr17:67043365..67043374,-p17@Ptprm
Mm9::chr17:67043399..67043410,-p9@Ptprm
Mm9::chr1:128367418..128367444,-p@chr1:128367418..128367444
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Mm9::chr2:147864024..147864035,-p1@ENSMUST00000132070
Mm9::chr3:40604700..40604708,+p5@Plk4
Mm9::chr5:28785382..28785394,-p@chr5:28785382..28785394
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Mm9::chr5:28785436..28785450,-p@chr5:28785436..28785450
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Mm9::chr6:124729655..124729666,-p4@Lrrc23
Mm9::chr6:14853484..14853504,+p14@Foxp2
Mm9::chr9:15432284..15432295,-p4@Ccdc67


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:0031223auditory behavior0.0254752643401085
GO:0042297vocal learning0.0254752643401085
GO:0043022ribosome binding0.0407436763680501
GO:0007638mechanosensory behavior0.0407436763680501
GO:0048745smooth muscle development0.0407436763680501



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
lung2.74e-2814
respiratory tube2.74e-2814
respiration organ2.74e-2814
pair of lungs2.74e-2814
lung primordium2.74e-2814
lung bud2.74e-2814
epithelial bud1.26e-2217
thoracic cavity element1.26e-2217
thoracic segment organ1.26e-2217
thoracic cavity1.26e-2217
thoracic segment of trunk1.26e-2217
respiratory primordium1.26e-2217
endoderm of foregut1.26e-2217
epithelial fold1.15e-1820
breast1.57e-126
chest1.57e-126
respiratory tract2.77e-0741
respiratory system4.95e-0742


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)
MA0003.10.0387975
MA0004.10.470639
MA0006.10.0625076
MA0007.10.87679
MA0009.10.499857
MA0014.10.0202604
MA0017.10.259254
MA0019.10.344318
MA0024.10.461433
MA0025.10.712532
MA0027.12.09948
MA0028.10.067163
MA0029.11.96925
MA0030.10.448261
MA0031.10.417663
MA0038.10.256813
MA0040.12.19715
MA0041.10.353863
MA0042.10.334544
MA0043.10.586618
MA0046.10.531807
MA0048.10.038539
MA0050.10.533529
MA0051.10.728838
MA0052.12.22076
MA0055.10.0713525
MA0056.10
MA0057.10.204512
MA0058.10.324689
MA0059.10.342591
MA0060.10.0321237
MA0061.11.46405
MA0063.10
MA0066.11.28459
MA0067.10.817149
MA0068.10.214228
MA0069.10.518414
MA0070.10.509795
MA0071.11.01954
MA0072.10.502282
MA0073.10.000287381
MA0074.10.222108
MA0076.10.0840393
MA0077.10.48317
MA0078.10.289095
MA0081.10.757603
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.10.0150058
MA0089.10
MA0090.10.825782
MA0091.10.163657
MA0092.10.133927
MA0093.10.531479
MA0095.10
MA0098.10
MA0100.10.213782
MA0101.10.355777
MA0103.10.57683
MA0105.10.848889
MA0106.10.295186
MA0107.11.4231
MA0108.20.952664
MA0109.10
MA0111.10.14244
MA0113.10.273246
MA0114.10.656298
MA0115.10.589161
MA0116.10.839093
MA0117.10.559943
MA0119.10.356648
MA0122.10.577888
MA0124.10.766819
MA0125.10.697415
MA0130.10
MA0131.10.340612
MA0132.10
MA0133.10
MA0135.10.619844
MA0136.10.236653
MA0139.10.245643
MA0140.10.2137
MA0141.10.0898383
MA0142.10.40532
MA0143.10.285913
MA0144.10.164087
MA0145.10.134183
MA0146.10.124121
MA0147.10.0471319
MA0148.13.71461
MA0149.10.113293
MA0062.20.0144279
MA0035.20.217072
MA0039.20.101331
MA0138.20.334152
MA0002.20.251244
MA0137.20.618368
MA0104.20.0278464
MA0047.21.31332
MA0112.20.625195
MA0065.20.254194
MA0150.10.145553
MA0151.10
MA0152.10.712054
MA0153.10.635107
MA0154.10.90272
MA0155.10.164369
MA0156.10.0836044
MA0157.10.986187
MA0158.10
MA0159.10.423802
MA0160.10.167661
MA0161.10
MA0162.10.16309
MA0163.10.865154
MA0164.11.2408
MA0080.20.266721
MA0018.20.683803
MA0099.20.329046
MA0079.20.00171301
MA0102.21.18455
MA0258.10.956776
MA0259.10.0431217
MA0442.10
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