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MCL coexpression mm9:1823: Difference between revisions

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{{MCL_coexpression_mm9
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signaling pathway;0.00690297485344875;11502,16412!GO:0042685;cardioblast cell fate specification;0.00690297485344875;16412!GO:0042684;cardioblast cell fate commitment;0.00690297485344875;16412!GO:0010002;cardioblast differentiation;0.0155299915344662;16412!GO:0015074;DNA integration;0.0172536553033409;67533!GO:0008907;integrase activity;0.0172536553033409;67533!GO:0045214;sarcomere organization;0.0258663047178699;16412!GO:0031594;neuromuscular junction;0.0258663047178699;16412!GO:0030239;myofibril assembly;0.0258663047178699;16412!GO:0055002;striated muscle cell development;0.0258663047178699;16412!GO:0055001;muscle cell development;0.0258663047178699;16412!GO:0035051;cardiac cell differentiation;0.0258663047178699;16412!GO:0031032;actomyosin structure organization and biogenesis;0.0275771186494365;16412!GO:0048628;myoblast maturation;0.0275771186494365;16412!GO:0048627;myoblast development;0.0275771186494365;16412!GO:0005178;integrin binding;0.0275771186494365;16412!GO:0001708;cell 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004535!5.31e-12!23;UBERON:0001009!5.31e-12!23;UBERON:0004872!4.25e-10!33;UBERON:0007100!2.79e-09!18;UBERON:0000948!2.79e-09!18;UBERON:0005498!2.79e-09!18;UBERON:0004140!2.79e-09!18;UBERON:0009881!2.79e-09!18;UBERON:0004141!2.79e-09!18;UBERON:0003084!2.79e-09!18;UBERON:0007005!2.79e-09!18;UBERON:0004139!2.79e-09!18;UBERON:0004291!2.79e-09!18;UBERON:0003103!4.71e-09!43;UBERON:0003914!1.34e-08!47;UBERON:0005178!1.38e-07!17;UBERON:0005181!1.38e-07!17;UBERON:0002224!1.38e-07!17;UBERON:0000915!1.38e-07!17;UBERON:0008947!1.38e-07!17;UBERON:0003258!1.38e-07!17;UBERON:0002100!1.85e-07!90;UBERON:0005157!6.61e-07!20;UBERON:0009569!9.85e-07!66
|tfbs_overrepresentation_for_novel_motifs=1.37236,0.293744,1.31238,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.746305,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,1.15581,0.645258,0.626183,1.03545,0.395107,0.253145,1.08876,0.454919,0.384813,0.699032,0.360612,0.328675,0.401916,1.52768,0.134724,0.426986,0.84962,0.591277,1.97509,0.658142,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,2.19087,0.30684,1.45025,1.23259,4.66673,0.686172,0.253065,0.835925,0.997094,0.494135,0.830212,0.948899,0.794502,0.293164,1.1148,2.60379,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,1.64321,0.607321,0.932233,0.991416,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,1.05179,1.21592,4.96832,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,2.31811,0.90208,0.741834,0.383572,0.701187,1.60845
}}

Latest revision as of 17:33, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr6:146837003..146837110,+p1@Ppfibp1
Mm9::chr6:146837115..146837127,+p3@Ppfibp1
Mm9::chr8:131209646..131209682,+p1@Itgb1
Mm9::chr8:131209686..131209718,+p2@Itgb1
Mm9::chr8:26127215..26127349,-p1@Adam9


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:0007229integrin-mediated signaling pathway0.00690297485344875
GO:0042685cardioblast cell fate specification0.00690297485344875
GO:0042684cardioblast cell fate commitment0.00690297485344875
GO:0010002cardioblast differentiation0.0155299915344662
GO:0015074DNA integration0.0172536553033409
GO:0008907integrase activity0.0172536553033409
GO:0045214sarcomere organization0.0258663047178699
GO:0031594neuromuscular junction0.0258663047178699
GO:0030239myofibril assembly0.0258663047178699
GO:0055002striated muscle cell development0.0258663047178699
GO:0055001muscle cell development0.0258663047178699
GO:0035051cardiac cell differentiation0.0258663047178699
GO:0031032actomyosin structure organization and biogenesis0.0275771186494365
GO:0048628myoblast maturation0.0275771186494365
GO:0048627myoblast development0.0275771186494365
GO:0005178integrin binding0.0275771186494365
GO:0001708cell fate specification0.0275771186494365
GO:0000082G1/S transition of mitotic cell cycle0.0275771186494365
GO:0042383sarcolemma0.0299818981115443
GO:0051146striated muscle cell differentiation0.0299818981115443
GO:0008305integrin complex0.0334681497734881
GO:0045445myoblast differentiation0.0338223891700692
GO:0051325interphase0.0353002695801633
GO:0051329interphase of mitotic cell cycle0.0353002695801633
GO:0032403protein complex binding0.0404828395410406
GO:0019717synaptosome0.0413022244570754
GO:0042692muscle cell differentiation0.0440267199851479
GO:0007160cell-matrix adhesion0.0440267199851479
GO:0048741skeletal muscle fiber development0.0440267199851479
GO:0048747muscle fiber development0.0440267199851479
GO:0031589cell-substrate adhesion0.0445963435747367
GO:0043235receptor complex0.0462527062824946
GO:0048469cell maturation0.0462527062824946



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>


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)
MA0003.13.33169
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.13.97269
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.11.68574
MA0058.10.50032
MA0059.10.513699
MA0060.10.881183
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.15.74006
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.13.48984
MA0091.10.617887
MA0092.11.39225
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.11.29932
MA0103.10.460936
MA0105.10.693075
MA0106.10.809991
MA0107.11.15122
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.949408
MA0115.11.16466
MA0116.10.419688
MA0117.12.55337
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.927481
MA0146.12.29697
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.21.30506
MA0035.20.700704
MA0039.24.4018
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.20.157681
MA0065.21.48609
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.11105
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.16.08017
MA0163.11.79895
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.29.67608
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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