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MCL coexpression mm9:1266: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000066!6.29e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!8.48e-13!31;UBERON:0005409!2.92e-11!47;UBERON:0004119!1.02e-10!118;UBERON:0000925!1.02e-10!118;UBERON:0006595!1.02e-10!118;UBERON:0001007!5.78e-10!116;UBERON:0001555!5.78e-10!116;UBERON:0007026!5.78e-10!116;UBERON:0004923!3.51e-09!24;UBERON:0004921!4.32e-09!114;UBERON:0000344!6.55e-08!15;UBERON:0005256!6.51e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.0600685,0.464605,0.535892,0.346849,0.550971,1.55624,0.247459,0.257202,0.283981,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.89822,1.90111,0.86893,0.426133,0.713088,0.657163,0.345236,1.19059,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,0.589948,0.364821,0.335531,0.326478,1.52228,0.303703,0.27383,0.907317,0.56353,0.0995018,0.366415,0.368882,0.524258,0.77511,1.43855,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.742129,0.827522,1.62226,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.11437,1.156,0.208101,0.19692,0.589776,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.198949,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.871473,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,1.42973,0.435642,0.428007,0.484547,1.0885,1.10269,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,1.30967,1.2285,0.679647,1.35909,0.706252,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,1.83209,2.10357,0.503174,0.348692,1.03315,0.667976,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,1.52669,0.30995
|tfbs_overrepresentation_jaspar=MA0003.1;2.22936,MA0004.1;8.44922,MA0006.1;0.945134,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;1.27243,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;1.50576,MA0050.1;1.41229,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;3.51526,MA0056.1;0,MA0057.1;0.149949,MA0058.1;12.9581,MA0059.1;5.16505,MA0060.1;0.275911,MA0061.1;2.28505,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.467569,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;9.97809,MA0074.1;1.54084,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;0.725434,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;13.4849,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;1.16089,MA0103.1;0.398766,MA0105.1;1.72386,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.822296,MA0115.1;1.08851,MA0116.1;0.944657,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;1.1226,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;0.379391,MA0146.1;1.41218,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;3.08685,MA0138.2;1.85228,MA0002.2;0.689262,MA0137.2;0.416331,MA0104.2;3.75187,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;1.81707,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;1.33283,MA0156.1;1.04798,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.881902,MA0160.1;0.556423,MA0161.1;0,MA0162.1;1.08528,MA0163.1;1.95647,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;8.20668,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;1.5079,MA0442.1;0
}}

Latest revision as of 16:39, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:101443550..101443626,+p1@Tmem106a
Mm9::chr11:118263140..118263278,-p1@Lgals3bp
Mm9::chr2:174264398..174264439,-p1@Ctsz
Mm9::chr2:174264441..174264460,-p4@Ctsz
Mm9::chr8:13159208..13159215,+p3@Lamp1
Mm9::chr8:13159228..13159314,+p1@Lamp1


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:0005764lysosome0.013106516696916
GO:0000323lytic vacuole0.013106516696916
GO:0005773vacuole0.013106516696916
GO:0004720protein-lysine 6-oxidase activity0.0190825445023009
GO:0005771multivesicular body0.0190825445023009
GO:0048770pigment granule0.0190825445023009
GO:0042470melanosome0.0190825445023009
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.0267023902742217
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0296595690334634
GO:0005044scavenger receptor activity0.0311220741306491
GO:0005770late endosome0.0311220741306491
GO:0042383sarcolemma0.0311220741306491



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
epithelial cell6.29e-0725

Uber Anatomy
Ontology termp-valuen
intestine8.48e-1331
gastrointestinal system2.92e-1147
endoderm-derived structure1.02e-10118
endoderm1.02e-10118
presumptive endoderm1.02e-10118
digestive system5.78e-10116
digestive tract5.78e-10116
primitive gut5.78e-10116
organ component layer3.51e-0924
subdivision of digestive tract4.32e-09114
mucosa6.55e-0815
trunk mesenchyme6.51e-0745


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)
MA0003.12.22936
MA0004.18.44922
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.11.27243
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
MA0048.11.50576
MA0050.11.41229
MA0051.10.695779
MA0052.11.00829
MA0055.13.51526
MA0056.10
MA0057.10.149949
MA0058.112.9581
MA0059.15.16505
MA0060.10.275911
MA0061.12.28505
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.19.97809
MA0074.11.54084
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.113.4849
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.11.72386
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.822296
MA0115.11.08851
MA0116.10.944657
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.11.41218
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.23.08685
MA0138.21.85228
MA0002.20.689262
MA0137.20.416331
MA0104.23.75187
MA0047.20.685741
MA0112.20.37938
MA0065.21.81707
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.11.33283
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.881902
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.11.95647
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.28.20668
MA0102.21.7182
MA0258.10.290587
MA0259.11.5079
MA0442.10
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