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MCL coexpression mm9:1359: Difference between revisions

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{{MCL_coexpression_mm9
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limb morphogenesis;0.00065475994242359;22418,14119!GO:0035113;embryonic appendage morphogenesis;0.00065475994242359;22418,14119!GO:0035107;appendage morphogenesis;0.00065475994242359;22418,14119!GO:0035108;limb morphogenesis;0.00065475994242359;22418,14119!GO:0048736;appendage development;0.00065475994242359;22418,14119!GO:0060173;limb development;0.00065475994242359;22418,14119!GO:0048598;embryonic morphogenesis;0.00364497440348794;22418,14119!GO:0008449;N-acetylglucosamine-6-sulfatase activity;0.00388934532256473;240725!GO:0004065;arylsulfatase activity;0.00388934532256473;240725!GO:0005578;proteinaceous extracellular matrix;0.004908708499464;22418,14119!GO:0001527;microfibril;0.00530307154345109;14119!GO:0043205;fibril;0.00583305907228608;14119!GO:0005615;extracellular space;0.00685678692274165;22418,14119,240725!GO:0044421;extracellular region part;0.00758169276701373;22418,14119,240725!GO:0009790;embryonic development;0.00801825903984703;22418,14119!GO:0008484;sulfuric ester hydrolase activity;0.00801825903984703;240725!GO:0007223;Wnt receptor signaling pathway, calcium modulating pathway;0.0137143189205113;22418!GO:0032502;developmental process;0.0142864295074839;22418,14119,240725!GO:0005509;calcium ion binding;0.0198651830124596;14119,240725!GO:0007254;JNK cascade;0.0250313368902236;22418!GO:0031098;stress-activated protein kinase signaling pathway;0.0254983854132012;22418!GO:0006790;sulfur metabolic process;0.0290711091763703;240725!GO:0005201;extracellular matrix structural constituent;0.0290711091763703;14119!GO:0030324;lung development;0.0290711091763703;22418!GO:0009653;anatomical structure morphogenesis;0.0290711091763703;22418,14119!GO:0030323;respiratory tube development;0.0290711091763703;22418!GO:0044420;extracellular matrix part;0.0395641908496913;14119!GO:0000165;MAPKKK cascade;0.0483697919197377;22418!GO:0016055;Wnt receptor signaling 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|gostat_on_MCL_coexpression=GO:0030326;embryonic limb morphogenesis;0.00065475994242359;22418,14119!GO:0035113;embryonic appendage morphogenesis;0.00065475994242359;22418,14119!GO:0035107;appendage morphogenesis;0.00065475994242359;22418,14119!GO:0035108;limb morphogenesis;0.00065475994242359;22418,14119!GO:0048736;appendage development;0.00065475994242359;22418,14119!GO:0060173;limb development;0.00065475994242359;22418,14119!GO:0048598;embryonic morphogenesis;0.00364497440348794;22418,14119!GO:0008449;N-acetylglucosamine-6-sulfatase activity;0.00388934532256473;240725!GO:0004065;arylsulfatase activity;0.00388934532256473;240725!GO:0005578;proteinaceous extracellular matrix;0.004908708499464;22418,14119!GO:0001527;microfibril;0.00530307154345109;14119!GO:0043205;fibril;0.00583305907228608;14119!GO:0005615;extracellular space;0.00685678692274165;22418,14119,240725!GO:0044421;extracellular region part;0.00758169276701373;22418,14119,240725!GO:0009790;embryonic development;0.00801825903984703;22418,14119!GO:0008484;sulfuric ester hydrolase activity;0.00801825903984703;240725!GO:0007223;Wnt receptor signaling pathway, calcium modulating pathway;0.0137143189205113;22418!GO:0032502;developmental process;0.0142864295074839;22418,14119,240725!GO:0005509;calcium ion binding;0.0198651830124596;14119,240725!GO:0007254;JNK cascade;0.0250313368902236;22418!GO:0031098;stress-activated protein kinase signaling pathway;0.0254983854132012;22418!GO:0006790;sulfur metabolic process;0.0290711091763703;240725!GO:0005201;extracellular matrix structural constituent;0.0290711091763703;14119!GO:0030324;lung development;0.0290711091763703;22418!GO:0009653;anatomical structure morphogenesis;0.0290711091763703;22418,14119!GO:0030323;respiratory tube development;0.0290711091763703;22418!GO:0044420;extracellular matrix part;0.0395641908496913;14119!GO:0000165;MAPKKK cascade;0.0483697919197377;22418!GO:0016055;Wnt receptor signaling pathway;0.0483697919197377;22418!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!5.25e-10!333
|tfbs_overrepresentation_for_novel_motifs=2.1342,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,0.283981,0.599767,0.632897,0.247704,0.6581,0.955327,0,0.856992,0.338549,0.232269,0.442204,1.09054,0.108444,0.657163,2.47195,0.472505,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,0.204204,0.364821,1.36145,0.326478,0.629145,3.14083,0.27383,0.907317,0.56353,0.0995018,0.366415,0.0417367,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.995874,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.366795,1.156,0.599223,0.19692,1.11463,0.763395,0.922432,1.10012,0.254777,0.874787,0.722675,0.676326,1.03903,0.0539203,4.27671,0.534643,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,1.826,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,1.09461,1.21641,1.0885,1.10269,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,2.82232,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.540361,0.0987301,1.10596,0.287383,1.62569,1.18867,2.85697,1.74506,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.0323861
|tfbs_overrepresentation_jaspar=MA0003.1;0.135108,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;2.22952,MA0009.1;0.987341,MA0014.1;0.304529,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.161427,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.895081,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;1.46111,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;2.84212,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;4.59943,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;2.43957,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;2.53503,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;0.0392287,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.181031,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;1.24549,MA0065.2;0.380324,MA0150.1;1.29346,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.933846,MA0155.1;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.397553,MA0163.1;0.0423021,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;1.5775,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:29323284..29323305,+p11@Wnt5a
Mm9::chr18:58369710..58369721,-p1@Fbn2
p1@LOC100047082
Mm9::chr1:12682486..12682500,+p7@Sulf1
Mm9::chr1:12682514..12682566,+p2@Sulf1
Mm9::chr1:12682570..12682620,+p1@Sulf1
Mm9::chr1:12682623..12682635,+p6@Sulf1


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:0030326embryonic limb morphogenesis0.00065475994242359
GO:0035113embryonic appendage morphogenesis0.00065475994242359
GO:0035107appendage morphogenesis0.00065475994242359
GO:0035108limb morphogenesis0.00065475994242359
GO:0048736appendage development0.00065475994242359
GO:0060173limb development0.00065475994242359
GO:0048598embryonic morphogenesis0.00364497440348794
GO:0008449N-acetylglucosamine-6-sulfatase activity0.00388934532256473
GO:0004065arylsulfatase activity0.00388934532256473
GO:0005578proteinaceous extracellular matrix0.004908708499464
GO:0001527microfibril0.00530307154345109
GO:0043205fibril0.00583305907228608
GO:0005615extracellular space0.00685678692274165
GO:0044421extracellular region part0.00758169276701373
GO:0009790embryonic development0.00801825903984703
GO:0008484sulfuric ester hydrolase activity0.00801825903984703
GO:0007223Wnt receptor signaling pathway, calcium modulating pathway0.0137143189205113
GO:0032502developmental process0.0142864295074839
GO:0005509calcium ion binding0.0198651830124596
GO:0007254JNK cascade0.0250313368902236
GO:0031098stress-activated protein kinase signaling pathway0.0254983854132012
GO:0006790sulfur metabolic process0.0290711091763703
GO:0005201extracellular matrix structural constituent0.0290711091763703
GO:0030324lung development0.0290711091763703
GO:0009653anatomical structure morphogenesis0.0290711091763703
GO:0030323respiratory tube development0.0290711091763703
GO:0044420extracellular matrix part0.0395641908496913
GO:0000165MAPKKK cascade0.0483697919197377
GO:0016055Wnt receptor signaling pathway0.0483697919197377



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
multi-cellular organism5.25e-10333


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)
MA0003.10.135108
MA0004.10.536396
MA0006.10.359699
MA0007.12.22952
MA0009.10.987341
MA0014.10.304529
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.11.46111
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.12.84212
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.14.59943
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.12.43957
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.12.53503
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.181031
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.21.24549
MA0065.20.380324
MA0150.11.29346
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.933846
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.397553
MA0163.10.0423021
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.21.5775
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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