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MCL coexpression mm9:1246: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0000073!2.69e-16!54;UBERON:0010371!5.13e-16!73;UBERON:0002346!1.09e-15!64;UBERON:0003075!1.09e-15!64;UBERON:0007284!1.09e-15!64;UBERON:0004121!2.60e-15!95;UBERON:0000924!2.60e-15!95;UBERON:0006601!2.60e-15!95;UBERON:0001017!2.69e-15!73;UBERON:0001049!4.22e-15!52;UBERON:0005068!4.22e-15!52;UBERON:0006241!4.22e-15!52;UBERON:0007135!4.22e-15!52;UBERON:0001016!2.20e-14!75;UBERON:0000955!1.16e-13!47;UBERON:0006238!1.16e-13!47;UBERON:0003056!1.86e-13!49;UBERON:0002616!4.22e-13!46;UBERON:0003080!4.89e-12!40;UBERON:0002780!1.56e-11!39;UBERON:0001890!1.56e-11!39;UBERON:0006240!1.56e-11!39;UBERON:0002020!3.23e-11!34;UBERON:0003528!7.92e-10!29;UBERON:0002791!7.92e-10!29;UBERON:0001893!7.92e-10!29;UBERON:0000064!9.92e-10!99;UBERON:0010314!3.20e-09!92;UBERON:0007811!5.36e-09!36;UBERON:0002370!5.31e-08!23;UBERON:0000974!5.31e-08!23;UBERON:0004807!5.31e-08!23;UBERON:0005058!5.31e-08!23;UBERON:0003351!5.31e-08!23;UBERON:0009113!5.31e-08!23;UBERON:0003295!5.31e-08!23;UBERON:0009722!5.31e-08!23;UBERON:0005562!5.31e-08!23;UBERON:0007690!5.31e-08!23;UBERON:0002021!5.95e-08!10;UBERON:0000411!5.95e-08!10;UBERON:0001950!5.95e-08!10;UBERON:0006562!1.30e-07!24;UBERON:0003408!1.30e-07!24;UBERON:0001557!1.30e-07!24;UBERON:0001042!1.30e-07!24;UBERON:0008814!1.30e-07!24;UBERON:0009145!1.30e-07!24;UBERON:0000153!1.46e-07!43;UBERON:0000956!2.85e-07!21;UBERON:0001869!2.85e-07!21;UBERON:0000203!2.85e-07!21;UBERON:0002619!5.20e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.491922,1.73744,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.257202,0.283981,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,1.72037,0.657163,0.345236,0.472505,0.686615,1.1909,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.326478,0.629145,0.820134,0.27383,0.342638,0.56353,0.327433,0.366415,0.659176,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,1.50238,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.599223,0.57254,0.589776,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.439832,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,1.30967,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,1.64681,0.540361,0.0987301,1.10596,1.42796,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,1.73883
|tfbs_overrepresentation_jaspar=MA0003.1;1.39154,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;2.76368,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;1.22706,MA0056.1;0,MA0057.1;0.895081,MA0058.1;0.436487,MA0059.1;1.14076,MA0060.1;0.275911,MA0061.1;2.28505,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;2.12135,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;3.05316,MA0089.1;0,MA0090.1;1.25093,MA0091.1;1.3559,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;2.43957,MA0106.1;1.74856,MA0107.1;1.79828,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.822296,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;0.761789,MA0146.1;0.635245,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.591842,MA0035.2;0.630778,MA0039.2;1.05907,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;0.380324,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;0.414701,MA0156.1;1.04798,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.881902,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.70356,MA0163.1;0.664494,MA0164.1;0.658997,MA0080.2;1.01893,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;2.73306,MA0102.2;1.7182,MA0258.1;0.790457,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:37, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:60638430..60638441,+p7@Tbata
Mm9::chr17:34767834..34767884,+p5@Prrt1
Mm9::chr17:57289056..57289060,-p1@Cd70
Mm9::chr18:33098795..33098859,+p2@Camk4
Mm9::chr4:63157016..63157067,-p1@Whrn
Mm9::chr7:36514763..36514812,-p2@Dpy19l3


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.69e-1654
ecto-epithelium5.13e-1673
neurectoderm1.09e-1564
neural plate1.09e-1564
presumptive neural plate1.09e-1564
ectoderm-derived structure2.60e-1595
ectoderm2.60e-1595
presumptive ectoderm2.60e-1595
central nervous system2.69e-1573
neural tube4.22e-1552
neural rod4.22e-1552
future spinal cord4.22e-1552
neural keel4.22e-1552
nervous system2.20e-1475
brain1.16e-1347
future brain1.16e-1347
pre-chordal neural plate1.86e-1349
regional part of brain4.22e-1346
anterior neural tube4.89e-1240
regional part of forebrain1.56e-1139
forebrain1.56e-1139
future forebrain1.56e-1139
gray matter3.23e-1134
brain grey matter7.92e-1029
regional part of telencephalon7.92e-1029
telencephalon7.92e-1029
organ part9.92e-1099
structure with developmental contribution from neural crest3.20e-0992
craniocervical region5.36e-0936
thymus5.31e-0823
neck5.31e-0823
respiratory system epithelium5.31e-0823
hemolymphoid system gland5.31e-0823
pharyngeal epithelium5.31e-0823
thymic region5.31e-0823
pharyngeal gland5.31e-0823
entire pharyngeal arch endoderm5.31e-0823
thymus primordium5.31e-0823
early pharyngeal endoderm5.31e-0823
occipital lobe5.95e-0810
visual cortex5.95e-0810
neocortex5.95e-0810
pharynx1.30e-0724
gland of gut1.30e-0724
upper respiratory tract1.30e-0724
chordate pharynx1.30e-0724
pharyngeal arch system1.30e-0724
pharyngeal region of foregut1.30e-0724
anterior region of body1.46e-0743
cerebral cortex2.85e-0721
cerebral hemisphere2.85e-0721
pallium2.85e-0721
regional part of cerebral cortex5.20e-0717


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)
MA0003.11.39154
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.12.76368
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
MA0055.11.22706
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.11.14076
MA0060.10.275911
MA0061.12.28505
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.12.12135
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.13.05316
MA0089.10
MA0090.11.25093
MA0091.11.3559
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.12.43957
MA0106.11.74856
MA0107.11.79828
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.822296
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
MA0145.10.761789
MA0146.10.635245
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.591842
MA0035.20.630778
MA0039.21.05907
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.37938
MA0065.20.380324
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.414701
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.881902
MA0160.10.556423
MA0161.10
MA0162.10.70356
MA0163.10.664494
MA0164.10.658997
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.22.73306
MA0102.21.7182
MA0258.10.790457
MA0259.10.309517
MA0442.10
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