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MCL coexpression mm9:1303: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!1.40e-28!73;UBERON:0001016!1.50e-28!75;UBERON:0004121!2.96e-26!95;UBERON:0000924!2.96e-26!95;UBERON:0006601!2.96e-26!95;UBERON:0002346!1.53e-24!64;UBERON:0003075!1.53e-24!64;UBERON:0007284!1.53e-24!64;UBERON:0010314!8.33e-22!92;UBERON:0000073!2.08e-21!54;UBERON:0010371!1.19e-20!73;UBERON:0001049!3.93e-20!52;UBERON:0005068!3.93e-20!52;UBERON:0006241!3.93e-20!52;UBERON:0007135!3.93e-20!52;UBERON:0003056!1.27e-17!49;UBERON:0000955!2.08e-17!47;UBERON:0006238!2.08e-17!47;UBERON:0002616!8.61e-17!46;UBERON:0003080!2.77e-15!40;UBERON:0002780!1.10e-14!39;UBERON:0001890!1.10e-14!39;UBERON:0006240!1.10e-14!39;UBERON:0002020!2.04e-14!34;UBERON:0003528!8.38e-12!29;UBERON:0002791!8.38e-12!29;UBERON:0001893!8.38e-12!29;UBERON:0000956!5.75e-09!21;UBERON:0001869!5.75e-09!21;UBERON:0000203!5.75e-09!21;UBERON:0002619!5.41e-08!17;UBERON:0002021!6.17e-08!10;UBERON:0000411!6.17e-08!10;UBERON:0001950!6.17e-08!10;UBERON:0000468!7.83e-07!333;UBERON:0002410!9.36e-07!9
|ontology_enrichment_uberon=UBERON:0001017!1.40e-28!73;UBERON:0001016!1.50e-28!75;UBERON:0004121!2.96e-26!95;UBERON:0000924!2.96e-26!95;UBERON:0006601!2.96e-26!95;UBERON:0002346!1.53e-24!64;UBERON:0003075!1.53e-24!64;UBERON:0007284!1.53e-24!64;UBERON:0010314!8.33e-22!92;UBERON:0000073!2.08e-21!54;UBERON:0010371!1.19e-20!73;UBERON:0001049!3.93e-20!52;UBERON:0005068!3.93e-20!52;UBERON:0006241!3.93e-20!52;UBERON:0007135!3.93e-20!52;UBERON:0003056!1.27e-17!49;UBERON:0000955!2.08e-17!47;UBERON:0006238!2.08e-17!47;UBERON:0002616!8.61e-17!46;UBERON:0003080!2.77e-15!40;UBERON:0002780!1.10e-14!39;UBERON:0001890!1.10e-14!39;UBERON:0006240!1.10e-14!39;UBERON:0002020!2.04e-14!34;UBERON:0003528!8.38e-12!29;UBERON:0002791!8.38e-12!29;UBERON:0001893!8.38e-12!29;UBERON:0000956!5.75e-09!21;UBERON:0001869!5.75e-09!21;UBERON:0000203!5.75e-09!21;UBERON:0002619!5.41e-08!17;UBERON:0002021!6.17e-08!10;UBERON:0000411!6.17e-08!10;UBERON:0001950!6.17e-08!10;UBERON:0000468!7.83e-07!333;UBERON:0002410!9.36e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,1.35778,0.645383,0.691572,0.7141,0.283981,1.46067,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.89822,0.232269,1.3999,0.426133,0.108444,1.58083,0.345236,0.472505,0.686615,1.1909,0.572827,0.394364,0.534301,1.37295,0.960397,0.892985,0.204204,0.364821,0.144368,0.326478,0.629145,0.303703,1.37841,0.342638,0.56353,0.0995018,0.959963,0.161543,0.524258,0.77511,1.43855,0.284064,0.397446,0.839084,1.69993,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,1.59383,0.939962,0.724164,1.36208,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,3.68882,0.11437,1.156,0.208101,1.70884,0.204132,0.763395,0.922432,1.92862,2.82147,0.874787,0.722675,0.240896,1.03903,0.198949,0.0610418,1.62034,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,2.36799,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,1.79935,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.706252,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,1.94251,0.564002,0.778321,2.10357,0.503174,0.348692,1.03315,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,1.60971,0.325308,0.63125,0.5667
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,1.35778,0.645383,0.691572,0.7141,0.283981,1.46067,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.89822,0.232269,1.3999,0.426133,0.108444,1.58083,0.345236,0.472505,0.686615,1.1909,0.572827,0.394364,0.534301,1.37295,0.960397,0.892985,0.204204,0.364821,0.144368,0.326478,0.629145,0.303703,1.37841,0.342638,0.56353,0.0995018,0.959963,0.161543,0.524258,0.77511,1.43855,0.284064,0.397446,0.839084,1.69993,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,1.59383,0.939962,0.724164,1.36208,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,3.68882,0.11437,1.156,0.208101,1.70884,0.204132,0.763395,0.922432,1.92862,2.82147,0.874787,0.722675,0.240896,1.03903,0.198949,0.0610418,1.62034,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,2.36799,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,1.79935,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.706252,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,1.94251,0.564002,0.778321,2.10357,0.503174,0.348692,1.03315,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,1.60971,0.325308,0.63125,0.5667
|tfbs_overrepresentation_jaspar=MA0003.1;0.04894,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;2.22952,MA0009.1;0.987341,MA0014.1;0.12867,MA0017.1;1.7816,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;0.212634,MA0056.1;0,MA0057.1;0.457693,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;2.1282,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.000157319,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;0.55008,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;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;1.68825,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.944657,MA0117.1;1.05576,MA0119.1;1.16221,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;0.682297,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;3.36067,MA0143.1;1.72325,MA0144.1;0.307873,MA0145.1;1.24552,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;0.328366,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,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;0.70356,MA0163.1;0.664494,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.911432,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}
}}

Revision as of 13:07, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:72080123..72080142,-p2@Slc13a5
Mm9::chr15:18748419..18748446,+p3@Cdh10
Mm9::chr15:18748455..18748481,+p1@Cdh10
Mm9::chr15:18748708..18748717,+p4@Cdh10
Mm9::chr15:18853092..18853096,+p@chr15:18853092..18853096
+
Mm9::chr6:125095277..125095296,+p3@Iffo1


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:0015141succinate transmembrane transporter activity0.00160699774110706
GO:0015744succinate transport0.00160699774110706
GO:0006842tricarboxylic acid transport0.00160699774110706
GO:0015137citrate transmembrane transporter activity0.00160699774110706
GO:0015142tricarboxylic acid transmembrane transporter activity0.00160699774110706
GO:0015746citrate transport0.00160699774110706
GO:0005310dicarboxylic acid transmembrane transporter activity0.00602492081764192
GO:0006835dicarboxylic acid transport0.00602492081764192
GO:0046943carboxylic acid transmembrane transporter activity0.0240666654828289
GO:0005342organic acid transmembrane transporter activity0.0240666654828289
GO:0046942carboxylic acid transport0.0240666654828289
GO:0015849organic acid transport0.0240666654828289
GO:0031402sodium ion binding0.0288609803336571
GO:0007156homophilic cell adhesion0.0288609803336571
GO:0006814sodium ion transport0.0358882749621469
GO:0015293symporter activity0.0399306889399139
GO:0015291secondary active transmembrane transporter activity0.0471791609237227
GO:0031420alkali metal ion binding0.0471791609237227



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>

Uber Anatomy
Ontology termp-valuen
central nervous system1.40e-2873
nervous system1.50e-2875
ectoderm-derived structure2.96e-2695
ectoderm2.96e-2695
presumptive ectoderm2.96e-2695
neurectoderm1.53e-2464
neural plate1.53e-2464
presumptive neural plate1.53e-2464
structure with developmental contribution from neural crest8.33e-2292
regional part of nervous system2.08e-2154
ecto-epithelium1.19e-2073
neural tube3.93e-2052
neural rod3.93e-2052
future spinal cord3.93e-2052
neural keel3.93e-2052
pre-chordal neural plate1.27e-1749
brain2.08e-1747
future brain2.08e-1747
regional part of brain8.61e-1746
anterior neural tube2.77e-1540
regional part of forebrain1.10e-1439
forebrain1.10e-1439
future forebrain1.10e-1439
gray matter2.04e-1434
brain grey matter8.38e-1229
regional part of telencephalon8.38e-1229
telencephalon8.38e-1229
cerebral cortex5.75e-0921
cerebral hemisphere5.75e-0921
pallium5.75e-0921
regional part of cerebral cortex5.41e-0817
occipital lobe6.17e-0810
visual cortex6.17e-0810
neocortex6.17e-0810
multi-cellular organism7.83e-07333
autonomic nervous system9.36e-079


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)
MA0003.10.04894
MA0004.10.536396
MA0006.10.359699
MA0007.12.22952
MA0009.10.987341
MA0014.10.12867
MA0017.11.7816
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
MA0055.10.212634
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.12.1282
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.000157319
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
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.11.68825
MA0114.10.304661
MA0115.11.08851
MA0116.10.944657
MA0117.11.05576
MA0119.11.16221
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.13.36067
MA0143.11.72325
MA0144.10.307873
MA0145.11.24552
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.328366
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.70356
MA0163.10.664494
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.911432
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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