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MCL coexpression mm9:244: Difference between revisions

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|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.0508136,0.714824,0.162779,0.0666574,0.596158,0.539901,0.115611,0.158461,0.511402,0.0323879,0.311617,0.353689,0.0227086,0.122119,0.0810557,0,0.242789,1.1969,0.87688,0.531374,0.30361,0.450742,0.121635,0.179733,0.385766,0.425821,0.386136,0.585756,0.25179,0.0668555,0.261652,0.317094,0.0632527,0.704421,0.0813985,0.336858,0.01186,0.348826,1.34653,0.00589464,0.581928,0.267928,0.101264,0.0824796,0.061901,0.223571,0.189134,0.298674,0.396409,1.13031,0.230631,0.152832,0.224074,0.430267,0.44481,0.125986,1.17536,0.102941,0.768045,0.124877,0.301892,0.158445,0.815195,0.222903,0.132112,0.251098,0.562061,0.88291,0.298379,0.744997,0.0364155,0.168686,0.00101326,0.473077,0.0119716,0.170406,1.92679,0.181883,0.289046,0.568547,0.170798,0.25509,0.476703,0.668266,0.37768,2.25117e-06,0.0913171,0.388434,0.561427,1.03797,0.624114,0.381683,0.326924,0.921664,0.0435786,0.878177,0.154303,0.329091,1.05607,0.301946,0.311947,0.849786,0.415858,0.231041,0.230314,0.0775753,0.272737,0.087018,0.319852,0.0319054,0.182167,0.417326,0.313137,0.096109,0.630454,2.04084,0.00256004,0.240758,0.243704,0.515697,0.477668,0.208777,0.138324,0.18131,1.62743,1.444,0.38126,0.32171,0.560724,1.29861,1.03789,0.849872,0.534808,0.416208,0.649958,8.51851,0.439142,0.26965,0.605717,1.39723,1.00731,0.566216,0.145218,0.86826,0.641177,1.43375,0.191141,1.35822,0.774625,0.0708744,0.0270604,5.22166e-05,0.431571,0.40564,1.9297,0.500669,0.466374,0.224997,0.18698,0.0536966,0.61423,0.376993,3.06662,0.179819,0.223599,0.804679,0.309198,2.33909,0.0326711
|tfbs_overrepresentation_for_novel_motifs=0.0508136,0.714824,0.162779,0.0666574,0.596158,0.539901,0.115611,0.158461,0.511402,0.0323879,0.311617,0.353689,0.0227086,0.122119,0.0810557,0,0.242789,1.1969,0.87688,0.531374,0.30361,0.450742,0.121635,0.179733,0.385766,0.425821,0.386136,0.585756,0.25179,0.0668555,0.261652,0.317094,0.0632527,0.704421,0.0813985,0.336858,0.01186,0.348826,1.34653,0.00589464,0.581928,0.267928,0.101264,0.0824796,0.061901,0.223571,0.189134,0.298674,0.396409,1.13031,0.230631,0.152832,0.224074,0.430267,0.44481,0.125986,1.17536,0.102941,0.768045,0.124877,0.301892,0.158445,0.815195,0.222903,0.132112,0.251098,0.562061,0.88291,0.298379,0.744997,0.0364155,0.168686,0.00101326,0.473077,0.0119716,0.170406,1.92679,0.181883,0.289046,0.568547,0.170798,0.25509,0.476703,0.668266,0.37768,2.25117e-06,0.0913171,0.388434,0.561427,1.03797,0.624114,0.381683,0.326924,0.921664,0.0435786,0.878177,0.154303,0.329091,1.05607,0.301946,0.311947,0.849786,0.415858,0.231041,0.230314,0.0775753,0.272737,0.087018,0.319852,0.0319054,0.182167,0.417326,0.313137,0.096109,0.630454,2.04084,0.00256004,0.240758,0.243704,0.515697,0.477668,0.208777,0.138324,0.18131,1.62743,1.444,0.38126,0.32171,0.560724,1.29861,1.03789,0.849872,0.534808,0.416208,0.649958,8.51851,0.439142,0.26965,0.605717,1.39723,1.00731,0.566216,0.145218,0.86826,0.641177,1.43375,0.191141,1.35822,0.774625,0.0708744,0.0270604,5.22166e-05,0.431571,0.40564,1.9297,0.500669,0.466374,0.224997,0.18698,0.0536966,0.61423,0.376993,3.06662,0.179819,0.223599,0.804679,0.309198,2.33909,0.0326711
|tfbs_overrepresentation_jaspar=MA0003.1;3.48864e-05,MA0004.1;0.236932,MA0006.1;0.0171128,MA0007.1;0.219791,MA0009.1;0.337492,MA0014.1;0.000355467,MA0017.1;0.241082,MA0019.1;1.12004,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;0.266391,MA0038.1;0.425709,MA0040.1;0.347276,MA0041.1;0.155958,MA0042.1;0.947573,MA0043.1;0.415031,MA0046.1;0.365786,MA0048.1;2.85038,MA0050.1;0.0833996,MA0051.1;0.438574,MA0052.1;1.66407,MA0055.1;3.65553,MA0056.1;0,MA0057.1;0.400394,MA0058.1;0.321312,MA0059.1;1.3849,MA0060.1;0.0330811,MA0061.1;1.3697,MA0063.1;0,MA0066.1;0.131108,MA0067.1;0.629308,MA0068.1;0.0408448,MA0069.1;0.353886,MA0070.1;0.346258,MA0071.1;0.997391,MA0072.1;0.900621,MA0073.1;0.790757,MA0074.1;0.360358,MA0076.1;0.026875,MA0077.1;0.32285,MA0078.1;0.487084,MA0081.1;0.171296,MA0083.1;0.414379,MA0084.1;0.934141,MA0087.1;0.988345,MA0088.1;0.0349852,MA0089.1;0,MA0090.1;0.767293,MA0091.1;1.37545,MA0092.1;0.439746,MA0093.1;0.228542,MA0095.1;0,MA0098.1;0,MA0100.1;0.106017,MA0101.1;0.360528,MA0103.1;0.779364,MA0105.1;0.470028,MA0106.1;0.166496,MA0107.1;0.468235,MA0108.2;1.83985,MA0109.1;0,MA0111.1;0.214084,MA0113.1;0.149628,MA0114.1;0.128478,MA0115.1;0.417336,MA0116.1;0.199556,MA0117.1;0.390961,MA0119.1;0.361635,MA0122.1;0.407133,MA0124.1;0.581749,MA0125.1;0.516802,MA0130.1;0,MA0131.1;0.202517,MA0132.1;0,MA0133.1;0,MA0135.1;1.13195,MA0136.1;0.12239,MA0139.1;0.281795,MA0140.1;1.15809,MA0141.1;0.292243,MA0142.1;0.255956,MA0143.1;0.159321,MA0144.1;0.00943699,MA0145.1;0.0880184,MA0146.1;0.0149325,MA0147.1;0.147758,MA0148.1;0.0735508,MA0149.1;0.0420811,MA0062.2;0.0113082,MA0035.2;0.350941,MA0039.2;0.142882,MA0138.2;0.197313,MA0002.2;0.469896,MA0137.2;0.120024,MA0104.2;0.0828464,MA0047.2;0.136816,MA0112.2;0.00121577,MA0065.2;0.379406,MA0150.1;0.826816,MA0151.1;0,MA0152.1;0.839367,MA0153.1;0.459241,MA0154.1;0.448933,MA0155.1;0.0255211,MA0156.1;0.112124,MA0157.1;0.233393,MA0158.1;0,MA0159.1;0.822926,MA0160.1;0.936328,MA0161.1;0,MA0162.1;0.000472344,MA0163.1;0.0186969,MA0164.1;0.776858,MA0080.2;0.0236909,MA0018.2;0.401707,MA0099.2;0.563653,MA0079.2;0.00962531,MA0102.2;0.984244,MA0258.1;0.0394148,MA0259.1;0.0485446,MA0442.1;0
}}
}}

Revision as of 11:25, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127934445..127934460,-p@chr10:127934445..127934460
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Mm9::chr11:11736215..11736234,-p6@Ddc
Mm9::chr11:66891795..66891809,+p1@Myh3
Mm9::chr11:67090670..67090685,+p3@Myh8
Mm9::chr11:78860985..78860998,-p@chr11:78860985..78860998
-
Mm9::chr11:85553408..85553419,+p@chr11:85553408..85553419
+
Mm9::chr11:85553433..85553449,+p@chr11:85553433..85553449
+
Mm9::chr11:85553450..85553467,+p@chr11:85553450..85553467
+
Mm9::chr14:61748215..61748225,+p@chr14:61748215..61748225
+
Mm9::chr16:87553762..87553775,+p3@ORF63
Mm9::chr17:57144287..57144315,-p@chr17:57144287..57144315
-
Mm9::chr18:14490364..14490376,+p@chr18:14490364..14490376
+
Mm9::chr18:9282716..9282737,-p1@Gjd4
Mm9::chr1:195024087..195024100,-p4@Traf3ip3
Mm9::chr1:20659960..20659965,+p@chr1:20659960..20659965
+
Mm9::chr1:89087199..89087215,+p1@Chrnd
Mm9::chr2:26927636..26927690,-p1@Tmem8c
Mm9::chr2:26927695..26927706,-p3@Tmem8c
Mm9::chr2:26927723..26927736,-p2@Tmem8c
Mm9::chr2:32231819..32231835,+p@chr2:32231819..32231835
+
Mm9::chr4:57509423..57509468,-p@chr4:57509423..57509468
-
Mm9::chr7:149850690..149850736,-p@chr7:149850690..149850736
-
Mm9::chr7:149851034..149851062,+p1@ENSMUST00000124393
Mm9::chr7:149851708..149851725,+p@chr7:149851708..149851725
+
Mm9::chr7:52895254..52895267,+p3@Mamstr
Mm9::chr7:56627564..56627586,+p@chr7:56627564..56627586
+
Mm9::chr7:56627587..56627609,+p@chr7:56627587..56627609
+
Mm9::chr7:56627610..56627621,+p@chr7:56627610..56627621
+
Mm9::chr7:97763588..97763602,+p@chr7:97763588..97763602
+
Mm9::chr8:15060314..15060346,+p4@Myom2
Mm9::chrX:109058005..109058019,+p@chrX:109058005..109058019
+
Mm9::chrX:22843877..22843932,-p4@Klhl13
Mm9::chrX:46817103..46817150,+p3@Arhgap36
Mm9::chrX:47132360..47132371,-p@chrX:47132360..47132371
-


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:0032982myosin filament9.76695101994067e-07
GO:0005863striated muscle thick filament9.76695101994067e-07
GO:0005859muscle myosin complex9.76695101994067e-07
GO:0016460myosin II complex1.12649264147249e-06
GO:0006941striated muscle contraction5.86459433916485e-06
GO:0016459myosin complex3.89099431944124e-05
GO:0030017sarcomere5.20620022734386e-05
GO:0044449contractile fiber part5.2126216070485e-05
GO:0030016myofibril5.81250692676225e-05
GO:0043292contractile fiber5.81250692676225e-05
GO:0003012muscle system process6.07654751973719e-05
GO:0006936muscle contraction6.07654751973719e-05
GO:0015629actin cytoskeleton0.000671897870755431
GO:0043234protein complex0.00211056088786752
GO:0004058aromatic-L-amino-acid decarboxylase activity0.00426596541207838
GO:0032991macromolecular complex0.00552955323598374
GO:0044430cytoskeletal part0.00993483187520388
GO:0042166acetylcholine binding0.0248561824957541
GO:0008307structural constituent of muscle0.0269067972055477
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.0304186392640424
GO:0042423catecholamine biosynthetic process0.0304186392640424
GO:0003779actin binding0.0308597819321685
GO:0005856cytoskeleton0.0309000988926995
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.0372342674965943
GO:0043176amine binding0.0382907622951478
GO:0022829wide pore channel activity0.0410022296813245
GO:0005243gap junction channel activity0.0410022296813245
GO:0005922connexon complex0.0410022296813245
GO:0008092cytoskeletal protein binding0.0437506936400608
GO:0042401biogenic amine biosynthetic process0.0473077587822354
GO:0022803passive transmembrane transporter activity0.0473077587822354
GO:0015267channel activity0.0473077587822354
GO:0030054cell junction0.0473077587822354
GO:0016831carboxy-lyase activity0.0473077587822354
GO:0005921gap junction0.0473077587822354
GO:0042398amino acid derivative biosynthetic process0.0485726485829697
GO:0018958phenol metabolic process0.0485726485829697
GO:0006584catecholamine metabolic process0.0485726485829697



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><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)
MA0003.13.48864e-05
MA0004.10.236932
MA0006.10.0171128
MA0007.10.219791
MA0009.10.337492
MA0014.10.000355467
MA0017.10.241082
MA0019.11.12004
MA0024.10.303927
MA0025.10.530879
MA0027.11.89129
MA0028.10.0853493
MA0029.10.287662
MA0030.10.292547
MA0031.10.266391
MA0038.10.425709
MA0040.10.347276
MA0041.10.155958
MA0042.10.947573
MA0043.10.415031
MA0046.10.365786
MA0048.12.85038
MA0050.10.0833996
MA0051.10.438574
MA0052.11.66407
MA0055.13.65553
MA0056.10
MA0057.10.400394
MA0058.10.321312
MA0059.11.3849
MA0060.10.0330811
MA0061.11.3697
MA0063.10
MA0066.10.131108
MA0067.10.629308
MA0068.10.0408448
MA0069.10.353886
MA0070.10.346258
MA0071.10.997391
MA0072.10.900621
MA0073.10.790757
MA0074.10.360358
MA0076.10.026875
MA0077.10.32285
MA0078.10.487084
MA0081.10.171296
MA0083.10.414379
MA0084.10.934141
MA0087.10.988345
MA0088.10.0349852
MA0089.10
MA0090.10.767293
MA0091.11.37545
MA0092.10.439746
MA0093.10.228542
MA0095.10
MA0098.10
MA0100.10.106017
MA0101.10.360528
MA0103.10.779364
MA0105.10.470028
MA0106.10.166496
MA0107.10.468235
MA0108.21.83985
MA0109.10
MA0111.10.214084
MA0113.10.149628
MA0114.10.128478
MA0115.10.417336
MA0116.10.199556
MA0117.10.390961
MA0119.10.361635
MA0122.10.407133
MA0124.10.581749
MA0125.10.516802
MA0130.10
MA0131.10.202517
MA0132.10
MA0133.10
MA0135.11.13195
MA0136.10.12239
MA0139.10.281795
MA0140.11.15809
MA0141.10.292243
MA0142.10.255956
MA0143.10.159321
MA0144.10.00943699
MA0145.10.0880184
MA0146.10.0149325
MA0147.10.147758
MA0148.10.0735508
MA0149.10.0420811
MA0062.20.0113082
MA0035.20.350941
MA0039.20.142882
MA0138.20.197313
MA0002.20.469896
MA0137.20.120024
MA0104.20.0828464
MA0047.20.136816
MA0112.20.00121577
MA0065.20.379406
MA0150.10.826816
MA0151.10
MA0152.10.839367
MA0153.10.459241
MA0154.10.448933
MA0155.10.0255211
MA0156.10.112124
MA0157.10.233393
MA0158.10
MA0159.10.822926
MA0160.10.936328
MA0161.10
MA0162.10.000472344
MA0163.10.0186969
MA0164.10.776858
MA0080.20.0236909
MA0018.20.401707
MA0099.20.563653
MA0079.20.00962531
MA0102.20.984244
MA0258.10.0394148
MA0259.10.0485446
MA0442.10
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