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MCL coexpression mm9:1260: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002346!4.98e-19!64;UBERON:0003075!4.98e-19!64;UBERON:0007284!4.98e-19!64;UBERON:0000073!2.27e-18!54;UBERON:0003056!9.05e-18!49;UBERON:0001049!1.90e-17!52;UBERON:0005068!1.90e-17!52;UBERON:0006241!1.90e-17!52;UBERON:0007135!1.90e-17!52;UBERON:0001017!2.36e-17!73;UBERON:0010371!4.37e-17!73;UBERON:0000955!3.57e-16!47;UBERON:0006238!3.57e-16!47;UBERON:0001016!4.63e-16!75;UBERON:0003080!5.45e-16!40;UBERON:0004121!6.04e-16!95;UBERON:0000924!6.04e-16!95;UBERON:0006601!6.04e-16!95;UBERON:0002616!1.64e-15!46;UBERON:0002780!1.89e-15!39;UBERON:0001890!1.89e-15!39;UBERON:0006240!1.89e-15!39;UBERON:0002020!1.18e-14!34;UBERON:0010314!2.37e-14!92;UBERON:0003528!2.81e-13!29;UBERON:0002791!2.81e-13!29;UBERON:0001893!2.81e-13!29;UBERON:0000956!6.44e-10!21;UBERON:0001869!6.44e-10!21;UBERON:0000203!6.44e-10!21;UBERON:0002021!6.52e-08!10;UBERON:0000411!6.52e-08!10;UBERON:0001950!6.52e-08!10;UBERON:0002619!7.94e-08!17
|ontology_enrichment_uberon=UBERON:0002346!4.98e-19!64;UBERON:0003075!4.98e-19!64;UBERON:0007284!4.98e-19!64;UBERON:0000073!2.27e-18!54;UBERON:0003056!9.05e-18!49;UBERON:0001049!1.90e-17!52;UBERON:0005068!1.90e-17!52;UBERON:0006241!1.90e-17!52;UBERON:0007135!1.90e-17!52;UBERON:0001017!2.36e-17!73;UBERON:0010371!4.37e-17!73;UBERON:0000955!3.57e-16!47;UBERON:0006238!3.57e-16!47;UBERON:0001016!4.63e-16!75;UBERON:0003080!5.45e-16!40;UBERON:0004121!6.04e-16!95;UBERON:0000924!6.04e-16!95;UBERON:0006601!6.04e-16!95;UBERON:0002616!1.64e-15!46;UBERON:0002780!1.89e-15!39;UBERON:0001890!1.89e-15!39;UBERON:0006240!1.89e-15!39;UBERON:0002020!1.18e-14!34;UBERON:0010314!2.37e-14!92;UBERON:0003528!2.81e-13!29;UBERON:0002791!2.81e-13!29;UBERON:0001893!2.81e-13!29;UBERON:0000956!6.44e-10!21;UBERON:0001869!6.44e-10!21;UBERON:0000203!6.44e-10!21;UBERON:0002021!6.52e-08!10;UBERON:0000411!6.52e-08!10;UBERON:0001950!6.52e-08!10;UBERON:0002619!7.94e-08!17
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,1.46067,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.86893,0.426133,0.35122,2.67147,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,1.0231,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.871288,0.629145,0.303703,0.752287,0.342638,0.56353,0.0995018,0.366415,0.368882,0.524258,1.82546,1.43855,0.0835644,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,1.50238,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,1.62226,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,1.77235,1.156,0.599223,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,1.25583,1.03903,2.18121,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,1.67297,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,1.03315,2.22804,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.30995
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,1.46067,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.86893,0.426133,0.35122,2.67147,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,1.0231,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.871288,0.629145,0.303703,0.752287,0.342638,0.56353,0.0995018,0.366415,0.368882,0.524258,1.82546,1.43855,0.0835644,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,1.50238,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,1.62226,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,1.77235,1.156,0.599223,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,1.25583,1.03903,2.18121,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,1.67297,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,1.03315,2.22804,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.30995
|tfbs_overrepresentation_jaspar=MA0003.1;2.22936,MA0004.1;0.536396,MA0006.1;0.945134,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.558098,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;0.486223,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;0.827788,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;3.23551,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;2.36749,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;1.16089,MA0103.1;0.398766,MA0105.1;0.57901,MA0106.1;1.74856,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;0.944657,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;1.8691,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;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;0.591842,MA0035.2;0.630778,MA0039.2;2.17024,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;1.06926,MA0104.2;1.33199,MA0047.2;0.685741,MA0112.2;0.76177,MA0065.2;0.380324,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;2.04167,MA0163.1;0.372305,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;4.55588,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}
}}

Revision as of 13:03, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:93498473..93498514,-p1@Vezt
Mm9::chr13:70776647..70776703,-p1@BC018507
Mm9::chr16:96303996..96304088,-p1@Brwd1
Mm9::chr18:7868821..7868860,+p1@Wac
Mm9::chr3:108013356..108013420,-p1@Atxn7l2
Mm9::chr8:114167393..114167440,+p1@Zfp1


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

no results for this coexpression

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
CNS neuron (sensu Vertebrata)1.36e-1023
neuroblast (sensu Vertebrata)1.36e-1023
neuron5.08e-1033
neuronal stem cell5.08e-1033
neuroblast5.08e-1033
electrically signaling cell5.08e-1033

Uber Anatomy
Ontology termp-valuen
neurectoderm4.98e-1964
neural plate4.98e-1964
presumptive neural plate4.98e-1964
regional part of nervous system2.27e-1854
pre-chordal neural plate9.05e-1849
neural tube1.90e-1752
neural rod1.90e-1752
future spinal cord1.90e-1752
neural keel1.90e-1752
central nervous system2.36e-1773
ecto-epithelium4.37e-1773
brain3.57e-1647
future brain3.57e-1647
nervous system4.63e-1675
anterior neural tube5.45e-1640
ectoderm-derived structure6.04e-1695
ectoderm6.04e-1695
presumptive ectoderm6.04e-1695
regional part of brain1.64e-1546
regional part of forebrain1.89e-1539
forebrain1.89e-1539
future forebrain1.89e-1539
gray matter1.18e-1434
structure with developmental contribution from neural crest2.37e-1492
brain grey matter2.81e-1329
regional part of telencephalon2.81e-1329
telencephalon2.81e-1329
cerebral cortex6.44e-1021
cerebral hemisphere6.44e-1021
pallium6.44e-1021
occipital lobe6.52e-0810
visual cortex6.52e-0810
neocortex6.52e-0810
regional part of cerebral cortex7.94e-0817


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
MA0004.10.536396
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.558098
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
MA0048.10.486223
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
MA0061.10.827788
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.13.23551
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.12.36749
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.10.57901
MA0106.11.74856
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.944657
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.11.8691
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.682297
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
MA0062.20.591842
MA0035.20.630778
MA0039.22.17024
MA0138.20.788113
MA0002.20.246463
MA0137.21.06926
MA0104.21.33199
MA0047.20.685741
MA0112.20.76177
MA0065.20.380324
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
MA0162.12.04167
MA0163.10.372305
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.24.55588
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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