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MCL coexpression mm9:1294: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!5.54e-39!73;UBERON:0001016!2.32e-38!75;UBERON:0004121!3.19e-33!95;UBERON:0000924!3.19e-33!95;UBERON:0006601!3.19e-33!95;UBERON:0002346!5.02e-29!64;UBERON:0003075!5.02e-29!64;UBERON:0007284!5.02e-29!64;UBERON:0000073!3.80e-28!54;UBERON:0001049!1.37e-26!52;UBERON:0005068!1.37e-26!52;UBERON:0006241!1.37e-26!52;UBERON:0007135!1.37e-26!52;UBERON:0010371!4.42e-26!73;UBERON:0010314!2.30e-25!92;UBERON:0000955!5.67e-23!47;UBERON:0006238!5.67e-23!47;UBERON:0002616!1.27e-22!46;UBERON:0003056!8.14e-21!49;UBERON:0003080!4.33e-20!40;UBERON:0002020!6.90e-20!34;UBERON:0002780!1.04e-19!39;UBERON:0001890!1.04e-19!39;UBERON:0006240!1.04e-19!39;UBERON:0003528!1.95e-16!29;UBERON:0002791!1.95e-16!29;UBERON:0001893!1.95e-16!29;UBERON:0000956!8.99e-12!21;UBERON:0001869!8.99e-12!21;UBERON:0000203!8.99e-12!21;UBERON:0002619!1.01e-09!17;UBERON:0000025!1.67e-07!114;UBERON:0000468!3.66e-07!333;UBERON:0003076!5.21e-07!12;UBERON:0003057!5.21e-07!12;UBERON:0004111!5.64e-07!122
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.86893,0.426133,0.713088,0.657163,0.345236,0.472505,0.686615,0.63639,0.572827,0.394364,1.61954,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.871288,0.629145,0.303703,0.27383,0.342638,1.38433,0.327433,0.959963,0.368882,1.30113,0.77511,0.589246,0.0835644,0.397446,0.839084,1.69993,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,2.69138,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,4.64017,1.156,2.50016,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,2.03037,0.722675,0.240896,1.03903,2.7679,0.479018,0.181203,0.780154,1.77427,1.33021,2.37572,0.973447,0.35304,0.810643,0.281222,0.244935,2.23779,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,2.36799,0.8998,0.585058,1.11115,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,1.35637,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,1.83209,2.10357,1.25623,0.348692,0.183562,6.88983,1.10596,0.783181,0.678689,1.18867,0.71546,1.74506,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,1.56426,0.63125,0.131395
|tfbs_overrepresentation_jaspar=MA0003.1;1.79006,MA0004.1;0.536396,MA0006.1;1.68531,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;2.15574,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.807132,MA0056.1;0,MA0057.1;0.895081,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.757042,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;0.169297,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;1.19273,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;1.2824,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;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;1.814,MA0146.1;0.990842,MA0147.1;1.54778,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.525037,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;2.86466,MA0047.2;0.685741,MA0112.2;1.24549,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;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;1.08528,MA0163.1;2.50108,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;2.70938,MA0099.2;0.781628,MA0079.2;0.0520572,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;2.29705,MA0442.1;0
}}

Latest revision as of 16:42, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:58752353..58752425,-p1@Rnf187
Mm9::chr16:18348274..18348366,+p2@Arvcf
Mm9::chr2:155102075..155102086,+p8@Map1lc3a
Mm9::chr5:34326128..34326178,+p1@Gm1673
Mm9::chr5:34326186..34326197,+p2@Gm1673
Mm9::chr7:25292246..25292259,+p6@Zfp428


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:0005776autophagic vacuole0.0394261229544641
GO:0016339calcium-dependent cell-cell adhesion0.0394261229544641



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 system5.54e-3973
nervous system2.32e-3875
ectoderm-derived structure3.19e-3395
ectoderm3.19e-3395
presumptive ectoderm3.19e-3395
neurectoderm5.02e-2964
neural plate5.02e-2964
presumptive neural plate5.02e-2964
regional part of nervous system3.80e-2854
neural tube1.37e-2652
neural rod1.37e-2652
future spinal cord1.37e-2652
neural keel1.37e-2652
ecto-epithelium4.42e-2673
structure with developmental contribution from neural crest2.30e-2592
brain5.67e-2347
future brain5.67e-2347
regional part of brain1.27e-2246
pre-chordal neural plate8.14e-2149
anterior neural tube4.33e-2040
gray matter6.90e-2034
regional part of forebrain1.04e-1939
forebrain1.04e-1939
future forebrain1.04e-1939
brain grey matter1.95e-1629
regional part of telencephalon1.95e-1629
telencephalon1.95e-1629
cerebral cortex8.99e-1221
cerebral hemisphere8.99e-1221
pallium8.99e-1221
regional part of cerebral cortex1.01e-0917
tube1.67e-07114
multi-cellular organism3.66e-07333
posterior neural tube5.21e-0712
chordal neural plate5.21e-0712
anatomical conduit5.64e-07122


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)
MA0003.11.79006
MA0004.10.536396
MA0006.11.68531
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
MA0048.12.15574
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.807132
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.10.449345
MA0060.10.757042
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
MA0073.10.169297
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.11.19273
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
MA0111.11.2824
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
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.11.814
MA0146.10.990842
MA0147.11.54778
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.525037
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.22.86466
MA0047.20.685741
MA0112.21.24549
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.12.50108
MA0164.10.658997
MA0080.20.393257
MA0018.22.70938
MA0099.20.781628
MA0079.20.0520572
MA0102.21.7182
MA0258.10.290587
MA0259.12.29705
MA0442.10
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