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MCL coexpression mm9:294: Difference between revisions

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{{MCL_coexpression_mm9
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coagulation;0.000340458915674949;14724,14723,14064!GO:0007599;hemostasis;0.000340458915674949;14724,14723,14064!GO:0050817;coagulation;0.000340458915674949;14724,14723,14064!GO:0050878;regulation of body fluid levels;0.000559822179556468;14724,14723,14064!GO:0042060;wound healing;0.00064459655927215;14724,14723,14064!GO:0022610;biological adhesion;0.000753716298755037;14724,110829,14723,170736,225825!GO:0007155;cell adhesion;0.000753716298755037;14724,110829,14723,170736,225825!GO:0009611;response to wounding;0.0184153247875671;14724,14723,14064!GO:0008568;microtubule-severing ATPase activity;0.023574368266565;231912!GO:0044425;membrane part;0.0265953009987638;14724,225825,243816,54368,17540,110829,71326,14723,170736,14064!GO:0044459;plasma membrane part;0.0329559532940279;14724,243816,110829,14723,170736!GO:0016020;membrane;0.0331299589695205;14724,225825,12229,243816,54368,17540,110829,71326,14723,170736,14064!GO:0009605;response to external stimulus;0.0376011125980134;14724,14723,14064!GO:0051225;spindle assembly;0.045405110629882;545486!GO:0005518;collagen binding;0.0494248735724735;243816!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0009569!1.23e-08!66;UBERON:0002048!3.71e-08!14;UBERON:0000117!3.71e-08!14;UBERON:0000171!3.71e-08!14;UBERON:0000170!3.71e-08!14;UBERON:0005597!3.71e-08!14;UBERON:0000118!3.71e-08!14|tfbs_overrepresentation_for_novel_motifs=0.266398,0.132787,0.0658715,0.321531,0.514709,0.341268,0.156184,1.73745,0.140055,0.153187,0.407767,0.14888,0.0458222,0.163767,0.891169,0,0.298759,0.0255171,0.10903,0.267797,0.051421,0.389275,0.49061,2.08675,0.521552,0.181283,0.0993251,0.370572,0.363703,0.13193,0.350793,0.987057,0.259177,0.508566,0.0322491,0.855826,0.0983807,0.146713,0.399193,0.547658,0.503057,0.11102,0.12636,0.569818,0.107155,0.306585,0.673722,1.2796,0.704379,0.369578,0.285502,0.199013,0.820548,0.498054,0.513233,0.168251,0.171288,0.435923,0.554451,0.166967,0.362491,0.592731,0.531917,0.277045,0.175326,0.307787,0.634702,0.961967,0.358731,0.821947,0.0582314,0.476705,0.0149026,0.542659,0.00481868,0.294934,0.173584,0.2317,0.920839,0.434586,0.280111,0.312115,0.204396,0.0081512,0.442898,0.00443853,0.00184039,0.132169,0.243285,1.11866,0.698467,0.447112,0.389188,0.531976,0.0781271,0.574151,0.691289,0.391493,0.239959,0.505942,1.49089,0.378494,0.482983,0.285951,0.285156,0.110785,0.331187,0.775412,0.0548223,0.429471,0.257525,0.484521,0.764025,0.133166,0.704965,0.497898,0.0576282,0.326633,0.299754,0.095335,0.547427,0.724052,0.182466,0.65337,0.755173,0.35168,0.161211,0.38364,0.633325,0.858725,0.468394,0.0936722,0.606596,1.00646,0.72494,0.0346041,0.0810586,0.111771,1.62757,1.47999,1.08773,0.638981,1.6721,0.387274,0.280284,0.358643,0.678914,1.44084,0.082151,0.116723,0.13621,0.0639904,0.499416,0.069779,0.522826,0.571287,0.199688,0.941747,0.557767,0.0809296,0.688329,0.442174,0.928175,0.0730739,0.277809,0.171615,0.738351,0.147927,0.166102|tfbs_overrepresentation_jaspar=MA0003.1;0.0727645,MA0004.1;0.322185,MA0006.1;0.0308664,MA0007.1;0.0901516,MA0009.1;0.400415,MA0014.1;0.00690241,MA0017.1;0.152143,MA0019.1;0.257924,MA0024.1;0.364667,MA0025.1;0.602538,MA0027.1;1.97512,MA0028.1;0.136208,MA0029.1;0.917544,MA0030.1;0.352483,MA0031.1;0.32434,MA0038.1;0.181232,MA0040.1;0.410788,MA0041.1;0.0630027,MA0042.1;0.0577521,MA0043.1;0.482118,MA0046.1;0.430358,MA0048.1;0.0121117,MA0050.1;0.117881,MA0051.1;0.548815,MA0052.1;0.417501,MA0055.1;0.94951,MA0056.1;0,MA0057.1;0.290249,MA0058.1;0.446594,MA0059.1;0.0599213,MA0060.1;0.329818,MA0061.1;0.991138,MA0063.1;0,MA0066.1;0.174169,MA0067.1;0.70379,MA0068.1;0.680731,MA0069.1;0.417784,MA0070.1;0.409709,MA0071.1;0.374768,MA0072.1;0.402681,MA0073.1;0.00677223,MA0074.1;0.903107,MA0076.1;0.0450749,MA0077.1;0.384853,MA0078.1;0.60168,MA0081.1;0.244432,MA0083.1;4.21023,MA0084.1;1.01381,MA0087.1;0.444612,MA0088.1;0.0384374,MA0089.1;0,MA0090.1;0.277096,MA0091.1;1.14651,MA0092.1;0.2775,MA0093.1;0.335373,MA0095.1;0,MA0098.1;0,MA0100.1;0.445082,MA0101.1;0.227319,MA0103.1;0.163216,MA0105.1;0.165073,MA0106.1;0.214456,MA0107.1;1.00453,MA0108.2;0.274781,MA0109.1;0,MA0111.1;0.615225,MA0113.1;0.56883,MA0114.1;0.0818254,MA0115.1;0.484531,MA0116.1;0.299509,MA0117.1;0.45687,MA0119.1;0.0637713,MA0122.1;0.473843,MA0124.1;0.654966,MA0125.1;0.587987,MA0130.1;0,MA0131.1;0.254613,MA0132.1;0,MA0133.1;0,MA0135.1;0.513709,MA0136.1;0.492774,MA0139.1;0.122529,MA0140.1;5.14552,MA0141.1;0.0490679,MA0142.1;1.52057,MA0143.1;1.76106,MA0144.1;1.8012,MA0145.1;0.302418,MA0146.1;0.0280795,MA0147.1;0.021447,MA0148.1;0.344344,MA0149.1;0.0658075,MA0062.2;0.00456066,MA0035.2;4.3236,MA0039.2;0.00552665,MA0138.2;0.248854,MA0002.2;1.72864,MA0137.2;1.1037,MA0104.2;0.0534126,MA0047.2;0.180736,MA0112.2;0.0042849,MA0065.2;0.0170927,MA0150.1;2.7631,MA0151.1;0,MA0152.1;0.180805,MA0153.1;0.528268,MA0154.1;4.1878,MA0155.1;0.542146,MA0156.1;0.171056,MA0157.1;0.288518,MA0158.1;0,MA0159.1;0.0238005,MA0160.1;0.348502,MA0161.1;0,MA0162.1;0.000117763,MA0163.1;0.174212,MA0164.1;0.164307,MA0080.2;0.361601,MA0018.2;0.508301,MA0099.2;1.2687,MA0079.2;0.00186607,MA0102.2;1.06444,MA0258.1;0.0719402,MA0259.1;0.0191137,MA0442.1;0}}
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|gostat_on_MCL_coexpression=GO:0007596;blood coagulation;0.000340458915674949;14724,14723,14064!GO:0007599;hemostasis;0.000340458915674949;14724,14723,14064!GO:0050817;coagulation;0.000340458915674949;14724,14723,14064!GO:0050878;regulation of body fluid levels;0.000559822179556468;14724,14723,14064!GO:0042060;wound healing;0.00064459655927215;14724,14723,14064!GO:0022610;biological adhesion;0.000753716298755037;14724,110829,14723,170736,225825!GO:0007155;cell adhesion;0.000753716298755037;14724,110829,14723,170736,225825!GO:0009611;response to wounding;0.0184153247875671;14724,14723,14064!GO:0008568;microtubule-severing ATPase activity;0.023574368266565;231912!GO:0044425;membrane part;0.0265953009987638;14724,225825,243816,54368,17540,110829,71326,14723,170736,14064!GO:0044459;plasma membrane part;0.0329559532940279;14724,243816,110829,14723,170736!GO:0016020;membrane;0.0331299589695205;14724,225825,12229,243816,54368,17540,110829,71326,14723,170736,14064!GO:0009605;response to external stimulus;0.0376011125980134;14724,14723,14064!GO:0051225;spindle assembly;0.045405110629882;545486!GO:0005518;collagen binding;0.0494248735724735;243816!
}}

Latest revision as of 15:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:57814850..57814868,+p9@Lims1
Mm9::chr11:102028513..102028537,-p@chr11:102028513..102028537
-
Mm9::chr11:70452620..70452677,+p1@Gp1ba
Mm9::chr11:70453863..70453874,+p@chr11:70453863..70453874
+
Mm9::chr13:60841293..60841307,+p@chr13:60841293..60841307
+
Mm9::chr13:96466806..96466824,+p3@F2rl2
Mm9::chr13:96466850..96466876,+p2@F2rl2
Mm9::chr13:96466887..96466934,+p1@F2rl2
Mm9::chr15:84087557..84087581,+p3@Parvb
Mm9::chr15:84087591..84087602,+p4@Parvb
Mm9::chr16:18621697..18621708,-p2@Gp1bb
Mm9::chr16:18621715..18621730,-p4@Gp1bb
Mm9::chr16:18621732..18621762,-p1@Gp1bb
Mm9::chr16:34040370..34040382,-p@chr16:34040370..34040382
-
Mm9::chr17:35203116..35203134,-p1@AU023871
Mm9::chr17:35203139..35203150,-p2@AU023871
Mm9::chr17:35222554..35222560,-p1@Ly6g6f
Mm9::chr17:48499216..48499251,+p1@Treml1
Mm9::chr18:89346357..89346381,+p2@Cd226
Mm9::chr2:174276179..174276209,+p1@Tubb1
Mm9::chr4:155628818..155628829,-p@chr4:155628818..155628829
-
Mm9::chr4:43571009..43571021,-p@chr4:43571009..43571021
-
Mm9::chr5:149740396..149740401,-p7@Katnal1
Mm9::chr6:87728058..87728076,+p2@Gp9
Mm9::chr6:87728078..87728106,+p1@Gp9
Mm9::chr7:118070193..118070219,-p5@Mrvi1
Mm9::chr7:4349307..4349330,-p1@Gp6
Mm9::chrX:131118106..131118120,-p4@Btk


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:0007596blood coagulation0.000340458915674949
GO:0007599hemostasis0.000340458915674949
GO:0050817coagulation0.000340458915674949
GO:0050878regulation of body fluid levels0.000559822179556468
GO:0042060wound healing0.00064459655927215
GO:0022610biological adhesion0.000753716298755037
GO:0007155cell adhesion0.000753716298755037
GO:0009611response to wounding0.0184153247875671
GO:0008568microtubule-severing ATPase activity0.023574368266565
GO:0044425membrane part0.0265953009987638
GO:0044459plasma membrane part0.0329559532940279
GO:0016020membrane0.0331299589695205
GO:0009605response to external stimulus0.0376011125980134
GO:0051225spindle assembly0.045405110629882
GO:0005518collagen binding0.0494248735724735



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
subdivision of trunk1.23e-0866
lung3.71e-0814
respiratory tube3.71e-0814
respiration organ3.71e-0814
pair of lungs3.71e-0814
lung primordium3.71e-0814
lung bud3.71e-0814


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)
MA0003.10.0727645
MA0004.10.322185
MA0006.10.0308664
MA0007.10.0901516
MA0009.10.400415
MA0014.10.00690241
MA0017.10.152143
MA0019.10.257924
MA0024.10.364667
MA0025.10.602538
MA0027.11.97512
MA0028.10.136208
MA0029.10.917544
MA0030.10.352483
MA0031.10.32434
MA0038.10.181232
MA0040.10.410788
MA0041.10.0630027
MA0042.10.0577521
MA0043.10.482118
MA0046.10.430358
MA0048.10.0121117
MA0050.10.117881
MA0051.10.548815
MA0052.10.417501
MA0055.10.94951
MA0056.10
MA0057.10.290249
MA0058.10.446594
MA0059.10.0599213
MA0060.10.329818
MA0061.10.991138
MA0063.10
MA0066.10.174169
MA0067.10.70379
MA0068.10.680731
MA0069.10.417784
MA0070.10.409709
MA0071.10.374768
MA0072.10.402681
MA0073.10.00677223
MA0074.10.903107
MA0076.10.0450749
MA0077.10.384853
MA0078.10.60168
MA0081.10.244432
MA0083.14.21023
MA0084.11.01381
MA0087.10.444612
MA0088.10.0384374
MA0089.10
MA0090.10.277096
MA0091.11.14651
MA0092.10.2775
MA0093.10.335373
MA0095.10
MA0098.10
MA0100.10.445082
MA0101.10.227319
MA0103.10.163216
MA0105.10.165073
MA0106.10.214456
MA0107.11.00453
MA0108.20.274781
MA0109.10
MA0111.10.615225
MA0113.10.56883
MA0114.10.0818254
MA0115.10.484531
MA0116.10.299509
MA0117.10.45687
MA0119.10.0637713
MA0122.10.473843
MA0124.10.654966
MA0125.10.587987
MA0130.10
MA0131.10.254613
MA0132.10
MA0133.10
MA0135.10.513709
MA0136.10.492774
MA0139.10.122529
MA0140.15.14552
MA0141.10.0490679
MA0142.11.52057
MA0143.11.76106
MA0144.11.8012
MA0145.10.302418
MA0146.10.0280795
MA0147.10.021447
MA0148.10.344344
MA0149.10.0658075
MA0062.20.00456066
MA0035.24.3236
MA0039.20.00552665
MA0138.20.248854
MA0002.21.72864
MA0137.21.1037
MA0104.20.0534126
MA0047.20.180736
MA0112.20.0042849
MA0065.20.0170927
MA0150.12.7631
MA0151.10
MA0152.10.180805
MA0153.10.528268
MA0154.14.1878
MA0155.10.542146
MA0156.10.171056
MA0157.10.288518
MA0158.10
MA0159.10.0238005
MA0160.10.348502
MA0161.10
MA0162.10.000117763
MA0163.10.174212
MA0164.10.164307
MA0080.20.361601
MA0018.20.508301
MA0099.21.2687
MA0079.20.00186607
MA0102.21.06444
MA0258.10.0719402
MA0259.10.0191137
MA0442.10
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