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MCL coexpression mm9:620: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000055!1.01e-17!49;CL:0002319!1.05e-16!43;CL:0000221!1.35e-16!44;CL:0000133!1.35e-16!44;CL:0000393!2.71e-12!39;CL:0000211!2.71e-12!39;CL:0000117!5.02e-12!23;CL:0000337!5.02e-12!23;CL:0000540!2.62e-11!33;CL:0000047!2.62e-11!33;CL:0000031!2.62e-11!33;CL:0000404!2.62e-11!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!2.61e-33!75;UBERON:0001017!1.63e-32!73;UBERON:0004121!2.09e-29!95;UBERON:0000924!2.09e-29!95;UBERON:0006601!2.09e-29!95;UBERON:0002346!1.58e-27!64;UBERON:0003075!1.58e-27!64;UBERON:0007284!1.58e-27!64;UBERON:0000073!2.28e-27!54;UBERON:0001049!4.13e-26!52;UBERON:0005068!4.13e-26!52;UBERON:0006241!4.13e-26!52;UBERON:0007135!4.13e-26!52;UBERON:0010314!1.33e-23!92;UBERON:0000955!4.46e-23!47;UBERON:0006238!4.46e-23!47;UBERON:0010371!1.31e-22!73;UBERON:0002616!1.47e-22!46;UBERON:0003056!3.26e-20!49;UBERON:0002020!6.66e-20!34;UBERON:0003080!2.78e-19!40;UBERON:0002780!1.02e-18!39;UBERON:0001890!1.02e-18!39;UBERON:0006240!1.02e-18!39;UBERON:0003528!3.77e-17!29;UBERON:0002791!3.77e-17!29;UBERON:0001893!3.77e-17!29;UBERON:0000956!4.83e-13!21;UBERON:0001869!4.83e-13!21;UBERON:0000203!4.83e-13!21;UBERON:0002619!2.86e-11!17;UBERON:0000025!2.15e-09!114;UBERON:0004111!1.18e-08!122;UBERON:0002021!7.03e-08!10;UBERON:0000411!7.03e-08!10;UBERON:0001950!7.03e-08!10;UBERON:0003076!2.36e-07!12;UBERON:0003057!2.36e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.737036,1.61495,1.27243,0.303186,0.1565,0.315748,1.02601,0.303924,0.658686,2.01579,0.357058,0.385627,1.05446,0.407615,0.974258,0,0.587245,0.150639,0.279039,0.33293,0.215242,0.0948826,1.04849,0.471175,0.701128,0.432737,0.265362,0.888376,0.191143,0.198166,3.25516,0.683831,0.14899,1.308,2.21658,2.66261,4.24855,0.382372,0.398832,0.107198,0.153518,0.326286,0.0834993,0.170547,1.26221,0.293566,0.512146,2.48564,0.0135136,0.564214,0.570705,0.457464,0.0502729,0.82076,0.837732,1.06445,0.200484,0.37415,0.0716833,0.412262,0.664611,0.46618,1.68413,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.650349,0.0945081,2.4894,0.870406,6.01955,0.222652,0.0658238,0.50152,0.648171,0.218647,0.0952669,0.60374,0.464847,0.0868537,0.758319,6.16832,0.112936,0.053731,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,2.50467,0.11194,0.0892768,0.698838,0.512384,5.90911,0.142282,0.683562,0.803823,0.571268,0.57027,0.3259,0.627019,0.911463,2.60196,0.619563,0.261228,0.805555,0.219561,0.361667,1.04639,0.152197,8.35795,0.826326,0.58848,0.139554,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.95011,0.787341,0.296885,0.940498,0.426575,1.06766,0.0212043,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.276297,2.84471,0.445509,5.85703,0.822286,0.747142,0.425729,0.901933,0.458393,0.178202,0.265096,2.11874,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.141416,0.384198,3.9072
|tfbs_overrepresentation_jaspar=MA0003.1;15.1331,MA0004.1;0.303605,MA0006.1;0.496735,MA0007.1;0.290695,MA0009.1;0.709264,MA0014.1;4.37682,MA0017.1;2.34064,MA0019.1;0.535691,MA0024.1;0.667197,MA0025.1;0.936082,MA0027.1;2.34178,MA0028.1;0.173587,MA0029.1;0.64639,MA0030.1;0.65267,MA0031.1;0.618697,MA0038.1;0.432665,MA0040.1;0.721328,MA0041.1;0.239557,MA0042.1;0.228771,MA0043.1;0.802848,MA0046.1;0.743934,MA0048.1;0.680396,MA0050.1;0.337476,MA0051.1;0.440863,MA0052.1;0.729105,MA0055.1;0.0370218,MA0056.1;0,MA0057.1;0.350222,MA0058.1;0.223242,MA0059.1;0.658541,MA0060.1;0.713464,MA0061.1;0.40468,MA0063.1;0,MA0066.1;0.422624,MA0067.1;1.04514,MA0068.1;0.647449,MA0069.1;0.729433,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;0.00478565,MA0074.1;0.390075,MA0076.1;0.200996,MA0077.1;0.691048,MA0078.1;0.471303,MA0081.1;0.252371,MA0083.1;0.802078,MA0084.1;1.3693,MA0087.1;0.760279,MA0088.1;0.0227266,MA0089.1;0,MA0090.1;0.27428,MA0091.1;0.315003,MA0092.1;0.274547,MA0093.1;0.179936,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;0.675688,MA0103.1;0.19444,MA0105.1;0.0633795,MA0106.1;0.478503,MA0107.1;0.555009,MA0108.2;0.557195,MA0109.1;0,MA0111.1;0.286331,MA0113.1;0.452439,MA0114.1;2.54073,MA0115.1;0.805567,MA0116.1;2.91832,MA0117.1;4.38354,MA0119.1;7.5847,MA0122.1;0.793507,MA0124.1;0.992825,MA0125.1;0.920215,MA0130.1;0,MA0131.1;0.531427,MA0132.1;0,MA0133.1;0,MA0135.1;0.838263,MA0136.1;0.408073,MA0139.1;0.0883913,MA0140.1;1.75428,MA0141.1;0.210047,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;0.129525,MA0145.1;0.264944,MA0146.1;0.436286,MA0147.1;0.428193,MA0148.1;0.317692,MA0149.1;0.245177,MA0062.2;1.31267,MA0035.2;0.383789,MA0039.2;0.382143,MA0138.2;0.523978,MA0002.2;0.0901987,MA0137.2;0.207733,MA0104.2;1.1126,MA0047.2;0.431964,MA0112.2;0.494696,MA0065.2;0.265926,MA0150.1;0.290598,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;0.376318,MA0155.1;0.30272,MA0156.1;0.200311,MA0157.1;0.574484,MA0158.1;0,MA0159.1;0.446593,MA0160.1;0.320315,MA0161.1;0,MA0162.1;1.03289,MA0163.1;2.01048,MA0164.1;0.408402,MA0080.2;0.190316,MA0018.2;0.417217,MA0099.2;0.518072,MA0079.2;2.82599,MA0102.2;1.42135,MA0258.1;1.23793,MA0259.1;0.130633,MA0442.1;0
}}

Latest revision as of 15:36, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:81575487..81575561,+p1@Zc3h7b
Mm9::chr2:27297977..27298090,+p1@uc008ixj.1
Mm9::chr3:57652002..57652020,-p4@Pfn2
Mm9::chr4:132833645..132833719,-p2@Tmem222
Mm9::chr9:56008747..56008775,-p2@Tspan3
Mm9::chr9:99336889..99336952,-p2@Mras
Mm9::chr9:99336967..99336981,-p6@Mras
Mm9::chr9:99337002..99337028,-p4@Mras
Mm9::chr9:99337032..99337041,-p8@Mras
Mm9::chr9:99337048..99337060,-p5@Mras
Mm9::chr9:99337066..99337100,-p3@Mras
Mm9::chr9:99337106..99337152,-p1@Mras


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>

Uber Anatomy
Ontology termp-valuen
nervous system2.61e-3375
central nervous system1.63e-3273
ectoderm-derived structure2.09e-2995
ectoderm2.09e-2995
presumptive ectoderm2.09e-2995
neurectoderm1.58e-2764
neural plate1.58e-2764
presumptive neural plate1.58e-2764
regional part of nervous system2.28e-2754
neural tube4.13e-2652
neural rod4.13e-2652
future spinal cord4.13e-2652
neural keel4.13e-2652
structure with developmental contribution from neural crest1.33e-2392
brain4.46e-2347
future brain4.46e-2347
ecto-epithelium1.31e-2273
regional part of brain1.47e-2246
pre-chordal neural plate3.26e-2049
gray matter6.66e-2034
anterior neural tube2.78e-1940
regional part of forebrain1.02e-1839
forebrain1.02e-1839
future forebrain1.02e-1839
brain grey matter3.77e-1729
regional part of telencephalon3.77e-1729
telencephalon3.77e-1729
cerebral cortex4.83e-1321
cerebral hemisphere4.83e-1321
pallium4.83e-1321
regional part of cerebral cortex2.86e-1117
tube2.15e-09114
anatomical conduit1.18e-08122
occipital lobe7.03e-0810
visual cortex7.03e-0810
neocortex7.03e-0810
posterior neural tube2.36e-0712
chordal neural plate2.36e-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)
MA0003.115.1331
MA0004.10.303605
MA0006.10.496735
MA0007.10.290695
MA0009.10.709264
MA0014.14.37682
MA0017.12.34064
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.680396
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.0370218
MA0056.10
MA0057.10.350222
MA0058.10.223242
MA0059.10.658541
MA0060.10.713464
MA0061.10.40468
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.647449
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.00478565
MA0074.10.390075
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.0227266
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.675688
MA0103.10.19444
MA0105.10.0633795
MA0106.10.478503
MA0107.10.555009
MA0108.20.557195
MA0109.10
MA0111.10.286331
MA0113.10.452439
MA0114.12.54073
MA0115.10.805567
MA0116.12.91832
MA0117.14.38354
MA0119.17.5847
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.0883913
MA0140.11.75428
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.264944
MA0146.10.436286
MA0147.10.428193
MA0148.10.317692
MA0149.10.245177
MA0062.21.31267
MA0035.20.383789
MA0039.20.382143
MA0138.20.523978
MA0002.20.0901987
MA0137.20.207733
MA0104.21.1126
MA0047.20.431964
MA0112.20.494696
MA0065.20.265926
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.376318
MA0155.10.30272
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.446593
MA0160.10.320315
MA0161.10
MA0162.11.03289
MA0163.12.01048
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.22.82599
MA0102.21.42135
MA0258.11.23793
MA0259.10.130633
MA0442.10
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