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MCL coexpression mm9:242: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003102!1.60e-10!22;UBERON:0000026!2.70e-09!12;UBERON:0004708!2.70e-09!12;UBERON:0002101!2.70e-09!12;UBERON:0004357!2.70e-09!12;UBERON:0004347!2.70e-09!12;UBERON:0005732!2.70e-09!12;UBERON:0005733!2.70e-09!12;UBERON:0010707!2.36e-08!13;UBERON:0001444!5.10e-07!11;UBERON:0000970!7.60e-07!9;UBERON:0000019!7.60e-07!9;UBERON:0000047!7.60e-07!9;UBERON:0010312!7.60e-07!9;UBERON:0004088!7.60e-07!9;UBERON:0002104!7.60e-07!9;UBERON:0001456!7.60e-07!9;UBERON:0003072!7.60e-07!9;UBERON:0004128!7.60e-07!9;UBERON:0003071!7.60e-07!9
|ontology_enrichment_uberon=UBERON:0003102!1.60e-10!22;UBERON:0000026!2.70e-09!12;UBERON:0004708!2.70e-09!12;UBERON:0002101!2.70e-09!12;UBERON:0004357!2.70e-09!12;UBERON:0004347!2.70e-09!12;UBERON:0005732!2.70e-09!12;UBERON:0005733!2.70e-09!12;UBERON:0010707!2.36e-08!13;UBERON:0001444!5.10e-07!11;UBERON:0000970!7.60e-07!9;UBERON:0000019!7.60e-07!9;UBERON:0000047!7.60e-07!9;UBERON:0010312!7.60e-07!9;UBERON:0004088!7.60e-07!9;UBERON:0002104!7.60e-07!9;UBERON:0001456!7.60e-07!9;UBERON:0003072!7.60e-07!9;UBERON:0004128!7.60e-07!9;UBERON:0003071!7.60e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.422253,0.0255683,0.371261,0.0666574,0.596158,0.539901,0.115611,0.973465,0.751461,0.11433,0.0936327,0.717373,0.702703,0.122119,0.398921,0,0.242789,1.58718,0.625284,0.369002,0.556637,0.450742,0.121635,0.353993,0.170342,0.425821,0.583947,0.278895,0.102635,0.387828,0.941675,0.317094,0.333399,0.491045,0.658002,0.0239827,0.0576457,0.107538,0.127365,0.0322356,0.348026,0.267928,0.265508,0.209525,1.22659,0.223571,0.189134,0.298674,0.185079,1.13031,0.230631,0.46489,0.224074,0.430267,0.44481,0.396933,0.505438,0.102941,0.35402,0.787009,0.816048,0.158445,1.84361,0.222903,0.132112,0.251098,0.562061,0.88291,0.298379,0.744997,0.335924,0.168686,0.07885,0.473077,0.195056,0.661119,0.317894,0.181883,2.19475,0.568547,0.170798,0.25509,0.157582,0.448811,0.37768,0.00801193,0.731025,0.0670085,0.192291,1.03797,0.624114,0.381683,0.326924,0.921664,0.684502,0.218716,0.688646,0.329091,0.554221,0.45446,0.155159,0.31688,0.415858,0.653326,0.651622,0.565143,0.272737,0.611912,0.0339046,0.0319054,0.408259,0.417326,0.571749,0.096109,0.630454,0.575631,0.198502,0.0681828,0.243704,0.515697,0.477668,0.208777,0.428436,0.534903,0.679524,0.291798,0.119921,0.32171,0.560724,0.627985,0.401936,0.0637522,0.534808,0.133513,0.649958,1.51534,0.439142,0.569198,0.605717,1.39723,1.00731,0.566216,0.145218,0.325124,0.22586,0.268482,0.191141,1.35822,0.201136,0.602416,0.398609,0.00914543,0.431571,0.0379768,0.414892,0.500669,0.909695,0.089777,0.18698,0.766477,0.61423,0.376993,0.29213,0.40381,1.19004,0.128895,0.309198,0.713664,0.0915529
|tfbs_overrepresentation_for_novel_motifs=0.422253,0.0255683,0.371261,0.0666574,0.596158,0.539901,0.115611,0.973465,0.751461,0.11433,0.0936327,0.717373,0.702703,0.122119,0.398921,0,0.242789,1.58718,0.625284,0.369002,0.556637,0.450742,0.121635,0.353993,0.170342,0.425821,0.583947,0.278895,0.102635,0.387828,0.941675,0.317094,0.333399,0.491045,0.658002,0.0239827,0.0576457,0.107538,0.127365,0.0322356,0.348026,0.267928,0.265508,0.209525,1.22659,0.223571,0.189134,0.298674,0.185079,1.13031,0.230631,0.46489,0.224074,0.430267,0.44481,0.396933,0.505438,0.102941,0.35402,0.787009,0.816048,0.158445,1.84361,0.222903,0.132112,0.251098,0.562061,0.88291,0.298379,0.744997,0.335924,0.168686,0.07885,0.473077,0.195056,0.661119,0.317894,0.181883,2.19475,0.568547,0.170798,0.25509,0.157582,0.448811,0.37768,0.00801193,0.731025,0.0670085,0.192291,1.03797,0.624114,0.381683,0.326924,0.921664,0.684502,0.218716,0.688646,0.329091,0.554221,0.45446,0.155159,0.31688,0.415858,0.653326,0.651622,0.565143,0.272737,0.611912,0.0339046,0.0319054,0.408259,0.417326,0.571749,0.096109,0.630454,0.575631,0.198502,0.0681828,0.243704,0.515697,0.477668,0.208777,0.428436,0.534903,0.679524,0.291798,0.119921,0.32171,0.560724,0.627985,0.401936,0.0637522,0.534808,0.133513,0.649958,1.51534,0.439142,0.569198,0.605717,1.39723,1.00731,0.566216,0.145218,0.325124,0.22586,0.268482,0.191141,1.35822,0.201136,0.602416,0.398609,0.00914543,0.431571,0.0379768,0.414892,0.500669,0.909695,0.089777,0.18698,0.766477,0.61423,0.376993,0.29213,0.40381,1.19004,0.128895,0.309198,0.713664,0.0915529
|tfbs_overrepresentation_jaspar=MA0003.1;0.307054,MA0004.1;0.236932,MA0006.1;0.0779732,MA0007.1;0.219791,MA0009.1;0.337492,MA0014.1;0.00116405,MA0017.1;0.0974641,MA0019.1;0.205515,MA0024.1;0.303927,MA0025.1;0.530879,MA0027.1;1.89129,MA0028.1;0.0853493,MA0029.1;0.287662,MA0030.1;0.292547,MA0031.1;0.735243,MA0038.1;0.425709,MA0040.1;0.917619,MA0041.1;0.358096,MA0042.1;0.947573,MA0043.1;0.415031,MA0046.1;0.958577,MA0048.1;1.41666,MA0050.1;0.0833996,MA0051.1;0.142335,MA0052.1;1.66407,MA0055.1;1.05766,MA0056.1;0,MA0057.1;0.400394,MA0058.1;0.321312,MA0059.1;0.343818,MA0060.1;0.0330811,MA0061.1;0.270316,MA0063.1;0,MA0066.1;0.81435,MA0067.1;0.629308,MA0068.1;0.27724,MA0069.1;0.353886,MA0070.1;0.915359,MA0071.1;0.592313,MA0072.1;0.339628,MA0073.1;0.99103,MA0074.1;0.728934,MA0076.1;0.026875,MA0077.1;0.32285,MA0078.1;0.487084,MA0081.1;0.0448552,MA0083.1;1.06501,MA0084.1;0.934141,MA0087.1;0.988345,MA0088.1;0.217787,MA0089.1;0,MA0090.1;0.198563,MA0091.1;0.0722516,MA0092.1;1.17403,MA0093.1;0.435418,MA0095.1;0,MA0098.1;0,MA0100.1;0.106017,MA0101.1;0.157214,MA0103.1;0.484679,MA0105.1;0.176234,MA0106.1;0.963897,MA0107.1;0.101094,MA0108.2;2.58977,MA0109.1;0,MA0111.1;0.467988,MA0113.1;0.45689,MA0114.1;0.458548,MA0115.1;0.417336,MA0116.1;1.31795,MA0117.1;0.390961,MA0119.1;0.361635,MA0122.1;1.04923,MA0124.1;0.581749,MA0125.1;0.516802,MA0130.1;0,MA0131.1;0.202517,MA0132.1;0,MA0133.1;0,MA0135.1;1.97829,MA0136.1;0.12239,MA0139.1;0.00361073,MA0140.1;0.344645,MA0141.1;0.292243,MA0142.1;0.255956,MA0143.1;0.481013,MA0144.1;0.271931,MA0145.1;1.16721,MA0146.1;0.0531943,MA0147.1;0.299116,MA0148.1;0.544719,MA0149.1;0.0420811,MA0062.2;0.0113082,MA0035.2;0.350941,MA0039.2;0.0517257,MA0138.2;1.71103,MA0002.2;1.63049,MA0137.2;0.287214,MA0104.2;0.18206,MA0047.2;1.35709,MA0112.2;1.43399,MA0065.2;0.534182,MA0150.1;0.478298,MA0151.1;0,MA0152.1;0.424765,MA0153.1;0.459241,MA0154.1;0.634733,MA0155.1;0.461564,MA0156.1;0.0266647,MA0157.1;0.658826,MA0158.1;0,MA0159.1;0.32227,MA0160.1;0.0748272,MA0161.1;0,MA0162.1;0.00167933,MA0163.1;0.159383,MA0164.1;0.776858,MA0080.2;0.0236909,MA0018.2;0.127843,MA0099.2;0.563653,MA0079.2;0.0014863,MA0102.2;0.984244,MA0258.1;1.25765,MA0259.1;0.134189,MA0442.1;0
}}
}}

Revision as of 11:25, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:106931839..106931851,-p3@Myf6
Mm9::chr10:51742326..51742340,+p1@Vgll2
Mm9::chr10:88000033..88000035,-p@chr10:88000033..88000035
-
Mm9::chr10:88046497..88046508,-p@chr10:88046497..88046508
-
Mm9::chr10:88067762..88067778,-p1@Mybpc1
Mm9::chr11:107577727..107577734,-p6@Cacng1
Mm9::chr11:107577831..107577842,-p3@Cacng1
Mm9::chr11:107577885..107577896,-p5@Cacng1
Mm9::chr11:12328972..12328994,-p@chr11:12328972..12328994
-
Mm9::chr11:12329018..12329031,-p@chr11:12329018..12329031
-
Mm9::chr11:78873345..78873355,-p7@Ksr1
Mm9::chr13:93564764..93564780,-p1@Thbs4
Mm9::chr14:31693300..31693332,+p@chr14:31693300..31693332
+
Mm9::chr14:33498875..33498884,+p@chr14:33498875..33498884
+
Mm9::chr15:76993500..76993516,-p@chr15:76993500..76993516
-
Mm9::chr18:32545213..32545226,+p@chr18:32545213..32545226
+
Mm9::chr1:165655254..165655267,-p1@Mettl11b
Mm9::chr2:73418345..73418410,-p1@Chrna1
Mm9::chr2:76670190..76670193,-p@chr2:76670190..76670193
-
Mm9::chr3:84397469..84397485,+p1@Tigd4
Mm9::chr4:43536546..43536571,-p5@Tpm2
Mm9::chr5:36128800..36128827,+p@chr5:36128800..36128827
+
Mm9::chr5:64967413..64967417,+p@chr5:64967413..64967417
+
Mm9::chr6:58730505..58730520,-p@chr6:58730505..58730520
-
Mm9::chr6:58730529..58730561,-p@chr6:58730529..58730561
-
Mm9::chr7:52895334..52895382,+p2@Mamstr
Mm9::chr7:54101585..54101607,+p5@Ldha
Mm9::chr8:126406981..126407012,-p@chr8:126406981..126407012
-
Mm9::chr8:126420134..126420176,+p@chr8:126420134..126420176
+
Mm9::chr8:81337109..81337174,-p2@Lsm6
Mm9::chr9:65113480..65113500,+p2@Cilp
Mm9::chrX:106640734..106640792,+p@chrX:106640734..106640792
+
Mm9::chrX:35673654..35673656,+p@chrX:35673654..35673656
+
Mm9::chrX:69061573..69061628,+p2@Vma21


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:0007519skeletal muscle development0.00734772280482354
GO:0014706striated muscle development0.00775833203002776
GO:0007517muscle development0.0129032388852135



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
surface structure1.60e-1022
appendage2.70e-0912
paired limb/fin2.70e-0912
limb2.70e-0912
paired limb/fin bud2.70e-0912
limb bud2.70e-0912
limb/fin field2.70e-0912
limb field2.70e-0912
appendage girdle complex2.36e-0813
subdivision of head5.10e-0711
eye7.60e-079
camera-type eye7.60e-079
simple eye7.60e-079
immature eye7.60e-079
ocular region7.60e-079
visual system7.60e-079
face7.60e-079
optic cup7.60e-079
optic vesicle7.60e-079
eye primordium7.60e-079


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)
MA0003.10.307054
MA0004.10.236932
MA0006.10.0779732
MA0007.10.219791
MA0009.10.337492
MA0014.10.00116405
MA0017.10.0974641
MA0019.10.205515
MA0024.10.303927
MA0025.10.530879
MA0027.11.89129
MA0028.10.0853493
MA0029.10.287662
MA0030.10.292547
MA0031.10.735243
MA0038.10.425709
MA0040.10.917619
MA0041.10.358096
MA0042.10.947573
MA0043.10.415031
MA0046.10.958577
MA0048.11.41666
MA0050.10.0833996
MA0051.10.142335
MA0052.11.66407
MA0055.11.05766
MA0056.10
MA0057.10.400394
MA0058.10.321312
MA0059.10.343818
MA0060.10.0330811
MA0061.10.270316
MA0063.10
MA0066.10.81435
MA0067.10.629308
MA0068.10.27724
MA0069.10.353886
MA0070.10.915359
MA0071.10.592313
MA0072.10.339628
MA0073.10.99103
MA0074.10.728934
MA0076.10.026875
MA0077.10.32285
MA0078.10.487084
MA0081.10.0448552
MA0083.11.06501
MA0084.10.934141
MA0087.10.988345
MA0088.10.217787
MA0089.10
MA0090.10.198563
MA0091.10.0722516
MA0092.11.17403
MA0093.10.435418
MA0095.10
MA0098.10
MA0100.10.106017
MA0101.10.157214
MA0103.10.484679
MA0105.10.176234
MA0106.10.963897
MA0107.10.101094
MA0108.22.58977
MA0109.10
MA0111.10.467988
MA0113.10.45689
MA0114.10.458548
MA0115.10.417336
MA0116.11.31795
MA0117.10.390961
MA0119.10.361635
MA0122.11.04923
MA0124.10.581749
MA0125.10.516802
MA0130.10
MA0131.10.202517
MA0132.10
MA0133.10
MA0135.11.97829
MA0136.10.12239
MA0139.10.00361073
MA0140.10.344645
MA0141.10.292243
MA0142.10.255956
MA0143.10.481013
MA0144.10.271931
MA0145.11.16721
MA0146.10.0531943
MA0147.10.299116
MA0148.10.544719
MA0149.10.0420811
MA0062.20.0113082
MA0035.20.350941
MA0039.20.0517257
MA0138.21.71103
MA0002.21.63049
MA0137.20.287214
MA0104.20.18206
MA0047.21.35709
MA0112.21.43399
MA0065.20.534182
MA0150.10.478298
MA0151.10
MA0152.10.424765
MA0153.10.459241
MA0154.10.634733
MA0155.10.461564
MA0156.10.0266647
MA0157.10.658826
MA0158.10
MA0159.10.32227
MA0160.10.0748272
MA0161.10
MA0162.10.00167933
MA0163.10.159383
MA0164.10.776858
MA0080.20.0236909
MA0018.20.127843
MA0099.20.563653
MA0079.20.0014863
MA0102.20.984244
MA0258.11.25765
MA0259.10.134189
MA0442.10
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