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MCL coexpression mm9:1410: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000221!1.52e-19!44;CL:0000133!1.52e-19!44;CL:0002319!4.18e-19!43;CL:0000540!2.78e-14!33;CL:0000047!2.78e-14!33;CL:0000031!2.78e-14!33;CL:0000404!2.78e-14!33;CL:0000117!6.16e-14!23;CL:0000337!6.16e-14!23;CL:0000055!6.45e-14!49;CL:0000393!1.68e-09!39;CL:0000211!1.68e-09!39;CL:0000723!3.98e-08!91;CL:0000048!3.98e-08!91;CL:0000034!6.93e-08!97
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!1.45e-26!75;UBERON:0001017!6.62e-26!73;UBERON:0004121!1.06e-20!95;UBERON:0000924!1.06e-20!95;UBERON:0006601!1.06e-20!95;UBERON:0002346!3.71e-20!64;UBERON:0003075!3.71e-20!64;UBERON:0007284!3.71e-20!64;UBERON:0000073!1.66e-19!54;UBERON:0001049!1.96e-18!52;UBERON:0005068!1.96e-18!52;UBERON:0006241!1.96e-18!52;UBERON:0007135!1.96e-18!52;UBERON:0000955!2.52e-15!47;UBERON:0006238!2.52e-15!47;UBERON:0002616!4.50e-15!46;UBERON:0010371!7.62e-15!73;UBERON:0010314!1.53e-14!92;UBERON:0003056!3.70e-14!49;UBERON:0002020!1.01e-13!34;UBERON:0003080!1.33e-12!40;UBERON:0002780!2.90e-12!39;UBERON:0001890!2.90e-12!39;UBERON:0006240!2.90e-12!39;UBERON:0003528!8.17e-11!29;UBERON:0002791!8.17e-11!29;UBERON:0001893!8.17e-11!29;UBERON:0000956!6.00e-07!21;UBERON:0001869!6.00e-07!21;UBERON:0000203!6.00e-07!21;UBERON:0003076!8.04e-07!12;UBERON:0003057!8.04e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,1.00112,0.599767,0.632897,1.28144,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.143775,0.426133,0.108444,1.58083,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,1.56842,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.174327,2.49807,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.740068,1.156,1.13013,1.08629,0.204132,0.763395,0.922432,0.430551,0.254777,2.03037,0.722675,0.676326,1.03903,0.439832,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.90315,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,1.6461,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,1.62768,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.540361,0.667976,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.5667
}}

Latest revision as of 16:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:35931330..35931364,+p2@Ube2d2
Mm9::chr5:138220099..138220163,+p1@Ppp1r35
Mm9::chr6:113573982..113574031,+p1@Vhl
Mm9::chr8:74763951..74764080,+p1@Ap1m1
Mm9::chr8:97190514..97190550,+p1@Arl2bp
Mm9::chr8:97190552..97190576,+p2@Arl2bp


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:0030163protein catabolic process0.0343445343924042
GO:0043534blood vessel endothelial cell migration0.0343445343924042
GO:0043285biopolymer catabolic process0.0343445343924042
GO:0009057macromolecule catabolic process0.0343445343924042
GO:0043542endothelial cell migration0.0343445343924042



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
nervous system1.45e-2675
central nervous system6.62e-2673
ectoderm-derived structure1.06e-2095
ectoderm1.06e-2095
presumptive ectoderm1.06e-2095
neurectoderm3.71e-2064
neural plate3.71e-2064
presumptive neural plate3.71e-2064
regional part of nervous system1.66e-1954
neural tube1.96e-1852
neural rod1.96e-1852
future spinal cord1.96e-1852
neural keel1.96e-1852
brain2.52e-1547
future brain2.52e-1547
regional part of brain4.50e-1546
ecto-epithelium7.62e-1573
structure with developmental contribution from neural crest1.53e-1492
pre-chordal neural plate3.70e-1449
gray matter1.01e-1334
anterior neural tube1.33e-1240
regional part of forebrain2.90e-1239
forebrain2.90e-1239
future forebrain2.90e-1239
brain grey matter8.17e-1129
regional part of telencephalon8.17e-1129
telencephalon8.17e-1129
cerebral cortex6.00e-0721
cerebral hemisphere6.00e-0721
pallium6.00e-0721
posterior neural tube8.04e-0712
chordal neural plate8.04e-0712


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)
MA0003.12.70639
MA0004.10.536396
MA0006.11.68531
MA0007.10.52077
MA0009.10.987341
MA0014.14.64288
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.11.72321
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.11.64201
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
MA0055.10.465302
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.11.38604
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
MA0073.10.00140584
MA0074.10.638014
MA0076.12.76767
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
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
MA0105.11.09694
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
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
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.11.24552
MA0146.11.41218
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.22.47808
MA0035.20.630778
MA0039.23.59125
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.21.81396
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.822245
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.70356
MA0163.10.0423021
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.911432
MA0102.21.7182
MA0258.10.790457
MA0259.10.833237
MA0442.10
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