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MCL coexpression mm9:1420: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000055!6.94e-09!49;CL:0002319!6.92e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!8.07e-20!54;UBERON:0001016!1.99e-19!75;UBERON:0001017!4.02e-19!73;UBERON:0001049!2.21e-18!52;UBERON:0005068!2.21e-18!52;UBERON:0006241!2.21e-18!52;UBERON:0007135!2.21e-18!52;UBERON:0004121!3.39e-18!95;UBERON:0000924!3.39e-18!95;UBERON:0006601!3.39e-18!95;UBERON:0010314!2.27e-17!92;UBERON:0002346!2.74e-16!64;UBERON:0003075!2.74e-16!64;UBERON:0007284!2.74e-16!64;UBERON:0000955!5.27e-16!47;UBERON:0006238!5.27e-16!47;UBERON:0002616!1.69e-15!46;UBERON:0010371!2.64e-15!73;UBERON:0002020!6.10e-13!34;UBERON:0003080!4.79e-12!40;UBERON:0002780!1.88e-11!39;UBERON:0001890!1.88e-11!39;UBERON:0006240!1.88e-11!39;UBERON:0003056!2.03e-11!49;UBERON:0003528!9.53e-11!29;UBERON:0002791!9.53e-11!29;UBERON:0001893!9.53e-11!29;UBERON:0000956!4.78e-08!21;UBERON:0001869!4.78e-08!21;UBERON:0000203!4.78e-08!21;UBERON:0004111!9.09e-08!122;UBERON:0003076!1.79e-07!12;UBERON:0003057!1.79e-07!12;UBERON:0002619!2.20e-07!17;UBERON:0002021!2.79e-07!10;UBERON:0000411!2.79e-07!10;UBERON:0001950!2.79e-07!10;UBERON:0000025!3.45e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,1.48899,0.599767,0.632897,1.28144,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.713088,0.657163,0.345236,0.472505,1.64218,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,0.589948,3.52165,2.34972,4.26527,0.629145,0.303703,1.37841,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,1.50238,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,2.94103,0.253541,3.09546,1.156,1.7706,1.08629,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,12.633,0.0610418,0.534643,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,17.5049,0.281222,0.244935,0.976308,0.775372,7.29374,0.326561,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,7.50306,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,1.87959,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.540361,1.10885,1.10596,3.96147,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,6.876
}}

Latest revision as of 16:54, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:5424822..5424845,-p3@Drap1
Mm9::chr2:156301447..156301474,+p5@Epb4.1l1
Mm9::chr2:156301539..156301570,+p4@Epb4.1l1
Mm9::chr2:156301580..156301598,+p3@Epb4.1l1
Mm9::chr2:32462499..32462577,+p1@St6galnac6
Mm9::chr8:73397376..73397400,-p1@Ccdc124


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:0001665alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity0.0197130614772321
GO:0001574ganglioside biosynthetic process0.0197130614772321
GO:0006688glycosphingolipid biosynthetic process0.0197130614772321
GO:0001573ganglioside metabolic process0.0197130614772321
GO:0030866cortical actin cytoskeleton organization and biogenesis0.0197130614772321
GO:0009247glycolipid biosynthetic process0.0197130614772321
GO:0030865cortical cytoskeleton organization and biogenesis0.0197130614772321
GO:0006687glycosphingolipid metabolic process0.0197130614772321
GO:0030148sphingolipid biosynthetic process0.0252244233060822
GO:0006664glycolipid metabolic process0.0252244233060822
GO:0008373sialyltransferase activity0.0286578341591222
GO:0006672ceramide metabolic process0.0302051664628912
GO:0046519sphingoid metabolic process0.0303028649509956
GO:0006665sphingolipid metabolic process0.0472284331056137



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
non-terminally differentiated cell6.94e-0949
neural cell6.92e-0743

Uber Anatomy
Ontology termp-valuen
regional part of nervous system8.07e-2054
nervous system1.99e-1975
central nervous system4.02e-1973
neural tube2.21e-1852
neural rod2.21e-1852
future spinal cord2.21e-1852
neural keel2.21e-1852
ectoderm-derived structure3.39e-1895
ectoderm3.39e-1895
presumptive ectoderm3.39e-1895
structure with developmental contribution from neural crest2.27e-1792
neurectoderm2.74e-1664
neural plate2.74e-1664
presumptive neural plate2.74e-1664
brain5.27e-1647
future brain5.27e-1647
regional part of brain1.69e-1546
ecto-epithelium2.64e-1573
gray matter6.10e-1334
anterior neural tube4.79e-1240
regional part of forebrain1.88e-1139
forebrain1.88e-1139
future forebrain1.88e-1139
pre-chordal neural plate2.03e-1149
brain grey matter9.53e-1129
regional part of telencephalon9.53e-1129
telencephalon9.53e-1129
cerebral cortex4.78e-0821
cerebral hemisphere4.78e-0821
pallium4.78e-0821
anatomical conduit9.09e-08122
posterior neural tube1.79e-0712
chordal neural plate1.79e-0712
regional part of cerebral cortex2.20e-0717
occipital lobe2.79e-0710
visual cortex2.79e-0710
neocortex2.79e-0710
tube3.45e-07114


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)
MA0003.112.2549
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.16.06782
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
MA0055.10.807132
MA0056.10
MA0057.12.76847
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
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
MA0088.10.358337
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
MA0105.10.57901
MA0106.12.92793
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
MA0119.14.08252
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
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.761789
MA0146.15.71847
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.22.17024
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.25.57559
MA0065.20.380324
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.933846
MA0155.10.822245
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.15.28077
MA0163.13.09314
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.29.77592
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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