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MCL coexpression mm9:768: Difference between revisions

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{{MCL_coexpression_mm9
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matrix structural constituent conferring tensile strength;4.10771295641643e-05;12834,12833!GO:0005581;collagen;4.10771295641643e-05;12834,12833!GO:0005201;extracellular matrix structural constituent;7.63206163582919e-05;12834,12833!GO:0006817;phosphate transport;7.63206163582919e-05;12834,12833!GO:0044420;extracellular matrix part;0.000115595875197037;12834,12833!GO:0015698;inorganic anion transport;0.000223910627820347;12834,12833!GO:0006820;anion transport;0.000270132671971779;12834,12833!GO:0005578;proteinaceous extracellular matrix;0.000669332841020108;12834,12833!GO:0022610;biological adhesion;0.00238286012299978;12834,12833!GO:0007155;cell adhesion;0.00238286012299978;12834,12833!GO:0006811;ion transport;0.00300105931213989;12834,12833!GO:0005615;extracellular space;0.0223158697731546;12834,12833!GO:0044421;extracellular region part;0.0231415643320049;12834,12833!GO:0006810;transport;0.0247617079244335;12834,12833!GO:0051234;establishment of 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|gostat_on_MCL_coexpression=GO:0030020;extracellular matrix structural constituent conferring tensile strength;4.10771295641643e-05;12834,12833!GO:0005581;collagen;4.10771295641643e-05;12834,12833!GO:0005201;extracellular matrix structural constituent;7.63206163582919e-05;12834,12833!GO:0006817;phosphate transport;7.63206163582919e-05;12834,12833!GO:0044420;extracellular matrix part;0.000115595875197037;12834,12833!GO:0015698;inorganic anion transport;0.000223910627820347;12834,12833!GO:0006820;anion transport;0.000270132671971779;12834,12833!GO:0005578;proteinaceous extracellular matrix;0.000669332841020108;12834,12833!GO:0022610;biological adhesion;0.00238286012299978;12834,12833!GO:0007155;cell adhesion;0.00238286012299978;12834,12833!GO:0006811;ion transport;0.00300105931213989;12834,12833!GO:0005615;extracellular space;0.0223158697731546;12834,12833!GO:0044421;extracellular region part;0.0231415643320049;12834,12833!GO:0006810;transport;0.0247617079244335;12834,12833!GO:0051234;establishment of localization;0.0247617079244335;12834,12833!GO:0051179;localization;0.0295847756403502;12834,12833!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,0.394491,0.227651,0.40827,0.495658,0.880357,0.468136,0.314043,0.453212,1.21524,0.146657,1.26558,0.680035,0,0.696644,0.22065,1.34367,0.0703872,0.296085,0.403891,1.26371,0.226287,0.337218,0.534339,0.128175,0.428336,0.268347,0.319094,0.414842,0.796599,0.218674,0.364174,0.681042,0.482999,0.210533,0.480503,0.191662,0.167387,0.224094,0.419787,1.46325,0.684206,0.158271,0.383899,0.618203,0.443479,0.904531,0.271021,0.679429,1.37808,0.633942,0.937018,0.954342,0.514504,0.279148,0.471658,1.25881,1.27615,0.776777,0.569793,0.492158,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.371787,0.349958,0.735293,0.607043,0.759798,0.299972,0.90463,0.713779,0.568383,0.14134,0.873141,0.204425,0.092683,0.657454,0.623015,1.60001,1.15927,0.878077,0.809272,1.22553,0.188213,1.57525,0.444003,0.812053,0.618454,0.0816605,1.78429,0.796322,0.919715,0.680015,0.678976,1.07585,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,2.6235,0.222515,0.496288,0.398075,1.6657,1.12703,0.993019,1.56109,1.3263,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.663857,0.90286,0.387557,1.05894,0.527782,1.18781,0.398576,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,1.613,0.420221,0.621266,1.92834,0.364791,0.229209,0.32395,0.161645,0.938577,0.527659,0.526881,1.01974,0.561556,0.705025,1.65955,0.362302,1.1483,2.02526,0.763895,0.345891,0.669337,0.519673,1.77857,0.482466,0.12239
}}

Latest revision as of 15:51, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:76058710..76058755,+p@chr10:76058710..76058755
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Mm9::chr10:76058901..76058926,-p@chr10:76058901..76058926
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Mm9::chr10:76059130..76059147,-p@chr10:76059130..76059147
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Mm9::chr10:76059195..76059229,-p@chr10:76059195..76059229
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Mm9::chr10:76086063..76086077,-p1@Col6a2
Mm9::chr10:76172043..76172101,-p@chr10:76172043..76172101
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Mm9::chr10:76184201..76184218,-p@chr10:76184201..76184218
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Mm9::chr10:76186163..76186184,-p@chr10:76186163..76186184
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Mm9::chr10:76188723..76188795,-p1@Col6a1


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:0030020extracellular matrix structural constituent conferring tensile strength4.10771295641643e-05
GO:0005581collagen4.10771295641643e-05
GO:0005201extracellular matrix structural constituent7.63206163582919e-05
GO:0006817phosphate transport7.63206163582919e-05
GO:0044420extracellular matrix part0.000115595875197037
GO:0015698inorganic anion transport0.000223910627820347
GO:0006820anion transport0.000270132671971779
GO:0005578proteinaceous extracellular matrix0.000669332841020108
GO:0022610biological adhesion0.00238286012299978
GO:0007155cell adhesion0.00238286012299978
GO:0006811ion transport0.00300105931213989
GO:0005615extracellular space0.0223158697731546
GO:0044421extracellular region part0.0231415643320049
GO:0006810transport0.0247617079244335
GO:0051234establishment of localization0.0247617079244335
GO:0051179localization0.0295847756403502



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)
MA0003.10.170768
MA0004.11.02263
MA0006.10.670874
MA0007.10.991467
MA0009.10.82278
MA0014.10.119217
MA0017.12.8722
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.221677
MA0056.10
MA0057.10.549903
MA0058.11.49242
MA0059.12.33201
MA0060.10.169058
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.11.10147
MA0072.10.825495
MA0073.10.126434
MA0074.11.22546
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.12.02218
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.748482
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.11.68389
MA0115.12.12594
MA0116.11.24629
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.11.54167
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.11.43798
MA0142.10.714976
MA0143.10.571221
MA0144.10.568165
MA0145.10.442138
MA0146.10.30073
MA0147.11.12076
MA0148.10.410398
MA0149.10.879199
MA0062.20.113962
MA0035.20.482026
MA0039.20.834829
MA0138.20.630612
MA0002.20.877049
MA0137.20.287486
MA0104.20.926067
MA0047.20.533516
MA0112.20.442124
MA0065.22.7817
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.11.27884
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.11.80557
MA0160.11.06259
MA0161.10
MA0162.10.0143037
MA0163.10.542069
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.431875
MA0102.21.5442
MA0258.10.180934
MA0259.10.571417
MA0442.10
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