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MCL coexpression mm9:899: Difference between revisions

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|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.0293268,0.367606,1.10802,0.720982,0.448401,1.33049,0.991481,0.535519,0.687027,0.494602,2.24724,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.160384,1.03863,1.58838,0.0622758,0.549359,0.258745,0.978733,0.577606,0.909128,0.469052,0.818708,1.23861,0.455168,0.843667,0.250677,0.425071,1.38756,0.185086,0.242032,0.522578,0.221921,0.195877,0.256422,2.02865,0.450632,0.27776,0.0824666,0.423266,0.662995,0.484612,0.170971,0.825035,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.844204,0.513517,0.877107,0.555328,0.823643,0.613749,1.067,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.140213,0.131016,0.136938,0.651651,0.806481,0.892913,0.179489,0.759925,0.612313,0.167672,0.920903,0.108172,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,1.10739,0.982739,0.859272,0.663249,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,1.01313,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0131724
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.0293268,0.367606,1.10802,0.720982,0.448401,1.33049,0.991481,0.535519,0.687027,0.494602,2.24724,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.160384,1.03863,1.58838,0.0622758,0.549359,0.258745,0.978733,0.577606,0.909128,0.469052,0.818708,1.23861,0.455168,0.843667,0.250677,0.425071,1.38756,0.185086,0.242032,0.522578,0.221921,0.195877,0.256422,2.02865,0.450632,0.27776,0.0824666,0.423266,0.662995,0.484612,0.170971,0.825035,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.844204,0.513517,0.877107,0.555328,0.823643,0.613749,1.067,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.140213,0.131016,0.136938,0.651651,0.806481,0.892913,0.179489,0.759925,0.612313,0.167672,0.920903,0.108172,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,1.10739,0.982739,0.859272,0.663249,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,1.01313,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0131724
|tfbs_overrepresentation_jaspar=MA0003.1;0.241599,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.0611475,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;1.93095,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;1.88628,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;1.13456,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;1.2091,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;9.70453,MA0074.1;2.26329,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;1.50158,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.064239,MA0089.1;0,MA0090.1;1.03628,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.633896,MA0115.1;0.969632,MA0116.1;2.10578,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;1.29098,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;1.49307,MA0144.1;0.225588,MA0145.1;0.0701568,MA0146.1;0.0169049,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.962263,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;2.43328,MA0138.2;0.675599,MA0002.2;0.513194,MA0137.2;0.863775,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;1.35639,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.330759,MA0155.1;0.0804339,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.71453,MA0163.1;0.669601,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.0769949,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:29, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:32176593..32176609,+p1@Hba-x
Mm9::chr11:32177564..32177584,+p@chr11:32177564..32177584
+
Mm9::chr11:32177586..32177613,+p@chr11:32177586..32177613
+
Mm9::chr11:32177763..32177774,-p@chr11:32177763..32177774
-
Mm9::chr11:32177907..32177928,+p@chr11:32177907..32177928
+
Mm9::chr11:32178001..32178041,-p@chr11:32178001..32178041
-
Mm9::chr7:110991668..110991683,-p1@Hbb-bh1
Mm9::chr9:107393090..107393091,-p@chr9:107393090..107393091
-


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:0005833hemoglobin complex2.34126131238934e-06
GO:0019825oxygen binding2.80951357486722e-06
GO:0005344oxygen transporter activity2.84073039236574e-06
GO:0015671oxygen transport2.84073039236574e-06
GO:0015669gas transport2.84073039236574e-06
GO:0044445cytosolic part0.000113707257738376
GO:0020037heme binding0.000119111669267808
GO:0046906tetrapyrrole binding0.000119111669267808
GO:0005506iron ion binding0.000746966414710529
GO:0005829cytosol0.000883685669748234
GO:0022892substrate-specific transporter activity0.00581718299353757
GO:0043234protein complex0.0157762381643388
GO:0032991macromolecular complex0.0231208919643697
GO:0006810transport0.026242027419916
GO:0046914transition metal ion binding0.026242027419916
GO:0051234establishment of localization0.026242027419916
GO:0051179localization0.0314763853360248
GO:0044444cytoplasmic part0.0405311614336615
GO:0043169cation binding0.0409248041331591
GO:0046872metal ion binding0.0454595127799532
GO:0043167ion binding0.0454595127799532



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)
MA0003.10.241599
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.0611475
MA0017.10.296816
MA0019.10.688051
MA0024.11.93095
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.11.88628
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.11.13456
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.2091
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.19.70453
MA0074.12.26329
MA0076.10.315013
MA0077.10.851175
MA0078.11.50158
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.11.03628
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.633896
MA0115.10.969632
MA0116.12.10578
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.11.29098
MA0141.10.325895
MA0142.10.761136
MA0143.11.49307
MA0144.10.225588
MA0145.10.0701568
MA0146.10.0169049
MA0147.10.236889
MA0148.10.450593
MA0149.10.962263
MA0062.20.137653
MA0035.20.524137
MA0039.22.43328
MA0138.20.675599
MA0002.20.513194
MA0137.20.863775
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.21.35639
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.688775
MA0160.10.453546
MA0161.10
MA0162.10.71453
MA0163.10.669601
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.0769949
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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