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MCL coexpression mm9:309: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!1.85e-42!31;UBERON:0005409!4.29e-26!47;UBERON:0000344!2.95e-23!15;UBERON:0001242!1.03e-18!13;UBERON:0000060!1.03e-18!13;UBERON:0001262!1.03e-18!13;UBERON:0004786!1.03e-18!13;UBERON:0004923!1.65e-13!24;UBERON:0003350!1.19e-10!9;UBERON:0004808!1.19e-10!9;UBERON:0001277!1.19e-10!9;UBERON:0002108!5.33e-10!4;UBERON:0001007!3.45e-09!116;UBERON:0001555!3.45e-09!116;UBERON:0007026!3.45e-09!116;UBERON:0004119!6.21e-09!118;UBERON:0000925!6.21e-09!118;UBERON:0006595!6.21e-09!118;UBERON:0000485!1.45e-08!11;UBERON:0000331!1.17e-07!3;UBERON:0002116!1.17e-07!3;UBERON:0001204!1.17e-07!3;UBERON:0001168!1.17e-07!3;UBERON:0004921!1.64e-07!114
|ontology_enrichment_uberon=UBERON:0000160!1.85e-42!31;UBERON:0005409!4.29e-26!47;UBERON:0000344!2.95e-23!15;UBERON:0001242!1.03e-18!13;UBERON:0000060!1.03e-18!13;UBERON:0001262!1.03e-18!13;UBERON:0004786!1.03e-18!13;UBERON:0004923!1.65e-13!24;UBERON:0003350!1.19e-10!9;UBERON:0004808!1.19e-10!9;UBERON:0001277!1.19e-10!9;UBERON:0002108!5.33e-10!4;UBERON:0001007!3.45e-09!116;UBERON:0001555!3.45e-09!116;UBERON:0007026!3.45e-09!116;UBERON:0004119!6.21e-09!118;UBERON:0000925!6.21e-09!118;UBERON:0006595!6.21e-09!118;UBERON:0000485!1.45e-08!11;UBERON:0000331!1.17e-07!3;UBERON:0002116!1.17e-07!3;UBERON:0001204!1.17e-07!3;UBERON:0001168!1.17e-07!3;UBERON:0004921!1.64e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.29922,0.734167,0.264934,0.357342,0.13626,0.759467,0.515388,0.528496,0.850536,0.461701,0.44746,0.165604,0.312494,0.181267,0.35264,0,0.321317,0.882528,0.134195,0.723488,0.825721,0.107343,0.533361,0.577208,0.274696,0.199623,0.444085,0.408692,0.184101,0.720335,0.122529,1.04073,0.126384,0.377102,0.353617,2.36141,0.117656,0.95082,0.458864,1.29658,0.132316,0.125454,0.274829,0.155231,0.232229,0.696406,0.260475,0.139809,0.201406,0.187406,0.307679,0.218134,0.281475,0.524674,0.540069,0.185973,0.437247,0.157588,1.62294,0.542937,0.386651,0.224758,0.187517,0.298968,1.07232,0.330595,0.662968,0.992392,0.382806,0.851665,0.0683061,0.0128424,0.057172,0.569888,0.103611,0.090663,0.376861,0.252107,0.973528,0.22435,0.165658,0.33504,0.223742,0.145927,0.468641,0.0449409,0.11084,0.721171,0.264106,1.14963,0.72731,0.472928,0.41392,0.142148,0.021752,0.0808213,0.151563,0.416272,0.260664,0.239551,0.117729,0.403003,0.509378,0.308141,0.307322,0.394918,0.933867,0.137427,0.0645424,0.481537,0.605231,0.510939,0.0629804,0.149001,0.733862,0.032139,0.146366,0.112806,0.322341,0.27556,0.574718,0.282956,0.581967,0.251444,0.784453,0.375593,0.178582,0.408257,0.661578,0.609497,0.494561,0.347036,0.634573,0.568121,0.753996,0.883015,0.641946,0.397628,0.708276,1.51166,1.11861,0.667289,1.77606,0.411967,0.81698,8.52686,0.262785,1.47245,0.0944245,0.138001,0.0248378,0.0140779,0.526055,0.0191336,0.194455,0.598868,0.218838,0.377109,0.0878751,0.310177,0.717087,0.467905,0.375957,0.28683,0.299755,0.1895,0.280354,0.1646,0.0956157
|tfbs_overrepresentation_for_novel_motifs=0.29922,0.734167,0.264934,0.357342,0.13626,0.759467,0.515388,0.528496,0.850536,0.461701,0.44746,0.165604,0.312494,0.181267,0.35264,0,0.321317,0.882528,0.134195,0.723488,0.825721,0.107343,0.533361,0.577208,0.274696,0.199623,0.444085,0.408692,0.184101,0.720335,0.122529,1.04073,0.126384,0.377102,0.353617,2.36141,0.117656,0.95082,0.458864,1.29658,0.132316,0.125454,0.274829,0.155231,0.232229,0.696406,0.260475,0.139809,0.201406,0.187406,0.307679,0.218134,0.281475,0.524674,0.540069,0.185973,0.437247,0.157588,1.62294,0.542937,0.386651,0.224758,0.187517,0.298968,1.07232,0.330595,0.662968,0.992392,0.382806,0.851665,0.0683061,0.0128424,0.057172,0.569888,0.103611,0.090663,0.376861,0.252107,0.973528,0.22435,0.165658,0.33504,0.223742,0.145927,0.468641,0.0449409,0.11084,0.721171,0.264106,1.14963,0.72731,0.472928,0.41392,0.142148,0.021752,0.0808213,0.151563,0.416272,0.260664,0.239551,0.117729,0.403003,0.509378,0.308141,0.307322,0.394918,0.933867,0.137427,0.0645424,0.481537,0.605231,0.510939,0.0629804,0.149001,0.733862,0.032139,0.146366,0.112806,0.322341,0.27556,0.574718,0.282956,0.581967,0.251444,0.784453,0.375593,0.178582,0.408257,0.661578,0.609497,0.494561,0.347036,0.634573,0.568121,0.753996,0.883015,0.641946,0.397628,0.708276,1.51166,1.11861,0.667289,1.77606,0.411967,0.81698,8.52686,0.262785,1.47245,0.0944245,0.138001,0.0248378,0.0140779,0.526055,0.0191336,0.194455,0.598868,0.218838,0.377109,0.0878751,0.310177,0.717087,0.467905,0.375957,0.28683,0.299755,0.1895,0.280354,0.1646,0.0956157
|tfbs_overrepresentation_jaspar=MA0003.1;0.0475636,MA0004.1;0.111027,MA0006.1;0.0376667,MA0007.1;0.336966,MA0009.1;0.425374,MA0014.1;0.0120813,MA0017.1;0.0466354,MA0019.1;0.279241,MA0024.1;0.388875,MA0025.1;0.630472,MA0027.1;2.00714,MA0028.1;0.0410625,MA0029.1;0.371051,MA0030.1;0.376415,MA0031.1;0.347586,MA0038.1;0.199569,MA0040.1;0.435948,MA0041.1;1.3889,MA0042.1;1.32848,MA0043.1;0.5085,MA0046.1;0.45588,MA0048.1;0.402145,MA0050.1;0.132769,MA0051.1;0.205659,MA0052.1;0.442788,MA0055.1;0.388062,MA0056.1;0,MA0057.1;1.68091,MA0058.1;0.0648829,MA0059.1;0.0701674,MA0060.1;0.197606,MA0061.1;0.1011,MA0063.1;0,MA0066.1;0.192176,MA0067.1;0.732677,MA0068.1;0.562635,MA0069.1;0.443076,MA0070.1;0.434849,MA0071.1;0.413073,MA0072.1;0.427684,MA0073.1;0.459931,MA0074.1;0.16874,MA0076.1;0.0537082,MA0077.1;0.409496,MA0078.1;0.228674,MA0081.1;0.0806296,MA0083.1;2.18678,MA0084.1;1.04444,MA0087.1;0.470385,MA0088.1;0.205212,MA0089.1;0,MA0090.1;0.64191,MA0091.1;0.118208,MA0092.1;0.642661,MA0093.1;0.0438751,MA0095.1;0,MA0098.1;0,MA0100.1;0.161426,MA0101.1;0.257705,MA0103.1;0.739353,MA0105.1;0.0317065,MA0106.1;0.234207,MA0107.1;0.0483046,MA0108.2;0.296634,MA0109.1;0,MA0111.1;0.100423,MA0113.1;0.614015,MA0114.1;0.0229266,MA0115.1;0.51095,MA0116.1;0.34339,MA0117.1;0.48285,MA0119.1;0.258451,MA0122.1;0.500096,MA0124.1;0.683426,MA0125.1;0.615761,MA0130.1;0,MA0131.1;0.27582,MA0132.1;0,MA0133.1;0,MA0135.1;0.540552,MA0136.1;0.535598,MA0139.1;0.513965,MA0140.1;0.486044,MA0141.1;0.211574,MA0142.1;0.336004,MA0143.1;0.22579,MA0144.1;0.249943,MA0145.1;0.0632599,MA0146.1;0.210382,MA0147.1;0.11258,MA0148.1;0.381264,MA0149.1;2.56178,MA0062.2;0.00633014,MA0035.2;0.164312,MA0039.2;0.00284482,MA0138.2;0.743216,MA0002.2;0.153717,MA0137.2;0.0570096,MA0104.2;0.0666678,MA0047.2;0.199051,MA0112.2;0.131476,MA0065.2;0.0244329,MA0150.1;0.10301,MA0151.1;0,MA0152.1;0.199123,MA0153.1;0.55531,MA0154.1;0.59291,MA0155.1;0.646088,MA0156.1;0.436777,MA0157.1;0.310784,MA0158.1;0,MA0159.1;0.0295363,MA0160.1;0.385618,MA0161.1;0,MA0162.1;0.0635176,MA0163.1;0.0938305,MA0164.1;1.02621,MA0080.2;0.182919,MA0018.2;0.188226,MA0099.2;0.26517,MA0079.2;0.759451,MA0102.2;1.09525,MA0258.1;0.423098,MA0259.1;0.024064,MA0442.1;0
}}
}}

Revision as of 11:32, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80858012..80858019,+p@chr10:80858012..80858019
+
Mm9::chr13:76081122..76081144,-p3@Rhobtb3
Mm9::chr16:4756879..4756881,+p7@Hmox2
Mm9::chr16:78302789..78302793,+p@chr16:78302789..78302793
+
Mm9::chr1:132748706..132748715,+p@chr1:132748706..132748715
+
Mm9::chr2:121189397..121189406,+p@chr2:121189397..121189406
+
Mm9::chr2:33226902..33226909,-p3@Ralgps1
Mm9::chr3:122602255..122602301,+p@chr3:122602255..122602301
+
Mm9::chr3:122602361..122602377,+p@chr3:122602361..122602377
+
Mm9::chr4:119329240..119329253,-p@chr4:119329240..119329253
-
Mm9::chr4:119329314..119329324,-p@chr4:119329314..119329324
-
Mm9::chr6:128626637..128626642,+p@chr6:128626637..128626642
+
Mm9::chr6:134555788..134555789,+p@chr6:134555788..134555789
+
Mm9::chr6:3150760..3150769,+p@chr6:3150760..3150769
+
Mm9::chr6:40719029..40719070,+p@chr6:40719029..40719070
+
Mm9::chr6:71154894..71154926,+p@chr6:71154894..71154926
+
Mm9::chr6:78323409..78323416,+p@chr6:78323409..78323416
+
Mm9::chr7:147282990..147283018,+p@chr7:147282990..147283018
+
Mm9::chr7:20257042..20257052,-p@chr7:20257042..20257052
-
Mm9::chr7:20257138..20257177,-p@chr7:20257138..20257177
-
Mm9::chr7:29626625..29626644,+p@chr7:29626625..29626644
+
Mm9::chr9:46038350..46038357,+p@chr9:46038350..46038357
+
Mm9::chr9:46038468..46038479,+p@chr9:46038468..46038479
+
Mm9::chr9:46041182..46041206,-p@chr9:46041182..46041206
-
Mm9::chr9:46051458..46051468,+p@chr9:46051458..46051468
+
Mm9::chr9:98410082..98410102,+p@chr9:98410082..98410102
+


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:0004392heme oxygenase (decyclizing) activity0.00985977183377446
GO:0006788heme oxidation0.00985977183377446
GO:0006787porphyrin catabolic process0.00985977183377446
GO:0033015tetrapyrrole catabolic process0.00985977183377446
GO:0042168heme metabolic process0.0337632798031105
GO:0006778porphyrin metabolic process0.0337632798031105
GO:0033013tetrapyrrole metabolic process0.0337632798031105
GO:0042440pigment metabolic process0.0466313321866766
GO:0051187cofactor catabolic process0.0466313321866766



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>cell_data<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)
MA0003.10.0475636
MA0004.10.111027
MA0006.10.0376667
MA0007.10.336966
MA0009.10.425374
MA0014.10.0120813
MA0017.10.0466354
MA0019.10.279241
MA0024.10.388875
MA0025.10.630472
MA0027.12.00714
MA0028.10.0410625
MA0029.10.371051
MA0030.10.376415
MA0031.10.347586
MA0038.10.199569
MA0040.10.435948
MA0041.11.3889
MA0042.11.32848
MA0043.10.5085
MA0046.10.45588
MA0048.10.402145
MA0050.10.132769
MA0051.10.205659
MA0052.10.442788
MA0055.10.388062
MA0056.10
MA0057.11.68091
MA0058.10.0648829
MA0059.10.0701674
MA0060.10.197606
MA0061.10.1011
MA0063.10
MA0066.10.192176
MA0067.10.732677
MA0068.10.562635
MA0069.10.443076
MA0070.10.434849
MA0071.10.413073
MA0072.10.427684
MA0073.10.459931
MA0074.10.16874
MA0076.10.0537082
MA0077.10.409496
MA0078.10.228674
MA0081.10.0806296
MA0083.12.18678
MA0084.11.04444
MA0087.10.470385
MA0088.10.205212
MA0089.10
MA0090.10.64191
MA0091.10.118208
MA0092.10.642661
MA0093.10.0438751
MA0095.10
MA0098.10
MA0100.10.161426
MA0101.10.257705
MA0103.10.739353
MA0105.10.0317065
MA0106.10.234207
MA0107.10.0483046
MA0108.20.296634
MA0109.10
MA0111.10.100423
MA0113.10.614015
MA0114.10.0229266
MA0115.10.51095
MA0116.10.34339
MA0117.10.48285
MA0119.10.258451
MA0122.10.500096
MA0124.10.683426
MA0125.10.615761
MA0130.10
MA0131.10.27582
MA0132.10
MA0133.10
MA0135.10.540552
MA0136.10.535598
MA0139.10.513965
MA0140.10.486044
MA0141.10.211574
MA0142.10.336004
MA0143.10.22579
MA0144.10.249943
MA0145.10.0632599
MA0146.10.210382
MA0147.10.11258
MA0148.10.381264
MA0149.12.56178
MA0062.20.00633014
MA0035.20.164312
MA0039.20.00284482
MA0138.20.743216
MA0002.20.153717
MA0137.20.0570096
MA0104.20.0666678
MA0047.20.199051
MA0112.20.131476
MA0065.20.0244329
MA0150.10.10301
MA0151.10
MA0152.10.199123
MA0153.10.55531
MA0154.10.59291
MA0155.10.646088
MA0156.10.436777
MA0157.10.310784
MA0158.10
MA0159.10.0295363
MA0160.10.385618
MA0161.10
MA0162.10.0635176
MA0163.10.0938305
MA0164.11.02621
MA0080.20.182919
MA0018.20.188226
MA0099.20.26517
MA0079.20.759451
MA0102.21.09525
MA0258.10.423098
MA0259.10.024064
MA0442.10
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