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MCL coexpression mm9:982: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!2.68e-07!64;UBERON:0003075!2.68e-07!64;UBERON:0007284!2.68e-07!64
|tfbs_overrepresentation_for_novel_motifs=0.393008,4.53349,0.367606,0.434198,0.260188,0.448401,0.538088,0.991481,1.02512,0.386846,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.703873,0.938682,0.29826,0.332107,1.26895,0.549359,0.258745,0.978733,0.577606,0.909128,0.469052,1.48474,0.757024,0.455168,0.843667,0.699026,0.425071,0.276324,0.185086,0.242032,0.522578,0.221921,0.195877,0.712303,0.460258,0.0558565,0.27776,1.7835,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.433216,0.131016,0.42492,0.651651,0.806481,0.336166,1.61056,0.759925,0.612313,0.167672,0.920903,0.025519,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.903338,0.887702,0.386136,0.96962,0.337254,0.499714,1.21576,0.708441,0.946242,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,1.91673,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,1.76809,0.569994,1.06851,0.605358,0.782826,3.67764,1.03572,1.1977,0.920047,0.810622,0.998505,0.714896,0.562634,0.240994,0.524587,0.166768
|tfbs_overrepresentation_jaspar=MA0003.1;0.400153,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.0611475,MA0017.1;0.804572,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;2.49613,MA0027.1;2.51754,MA0028.1;1.40661,MA0029.1;0.804619,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;0.685543,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.282934,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;1.71306,MA0061.1;2.61807,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;0.00886773,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.853781,MA0089.1;0,MA0090.1;0.401197,MA0091.1;4.01428,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;1.93163,MA0106.1;5.02552,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;1.85023,MA0115.1;0.969632,MA0116.1;0.27152,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;0.519484,MA0141.1;0.869985,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.640537,MA0145.1;0.0701568,MA0146.1;5.05861,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.84271,MA0035.2;0.524137,MA0039.2;3.28465,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;2.36417,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.527225,MA0065.2;1.35639,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.579465,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.230918,MA0163.1;0.212034,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;1.19114,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.643936,MA0442.1;0
}}

Latest revision as of 16:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:193801249..193801270,+p2@Rd3
Mm9::chr1:193801274..193801281,+p5@Rd3
Mm9::chr1:193801282..193801326,+p1@Rd3
Mm9::chr2:129626404..129626434,+p4@Stk35
Mm9::chr4:117545153..117545165,-p4@Ccdc24
Mm9::chr4:117545168..117545198,-p1@Ccdc24
Mm9::chr4:117545201..117545219,-p3@Ccdc24
Mm9::chr5:108026552..108026564,-p3@Glmn


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:0005171hepatocyte growth factor receptor binding0.0119980277214704
GO:0045086positive regulation of interleukin-2 biosynthetic process0.038362143778
GO:0045076regulation of interleukin-2 biosynthetic process0.038362143778
GO:0042094interleukin-2 biosynthetic process0.038362143778
GO:0032623interleukin-2 production0.038362143778



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
neurectoderm2.68e-0764
neural plate2.68e-0764
presumptive neural plate2.68e-0764


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)
MA0003.10.400153
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.0611475
MA0017.10.804572
MA0019.10.688051
MA0024.10.826339
MA0025.12.49613
MA0027.12.51754
MA0028.11.40661
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.11.71306
MA0061.12.61807
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.00886773
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.14.01428
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.11.93163
MA0106.15.02552
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.11.85023
MA0115.10.969632
MA0116.10.27152
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
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.10.640537
MA0145.10.0701568
MA0146.15.05861
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.84271
MA0035.20.524137
MA0039.23.28465
MA0138.20.675599
MA0002.20.172399
MA0137.22.36417
MA0104.20.54394
MA0047.20.576767
MA0112.20.527225
MA0065.21.35639
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.579465
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.212034
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.21.19114
MA0102.21.59466
MA0258.10.60477
MA0259.10.643936
MA0442.10
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