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MCL coexpression mm9:609: Difference between revisions

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{{MCL_coexpression_mm9
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defense response;0.0108886210485948;18013!GO:0001662;behavioral fear response;0.0108886210485948;18013!GO:0008306;associative learning;0.0108886210485948;18013!GO:0042596;fear response;0.0108886210485948;18013!GO:0033555;multicellular organismal response to stress;0.0145181613981263;18013!GO:0007612;learning;0.023712996950273;18013!GO:0007611;learning and/or 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|ontology_enrichment_celltype=CL:0000117!2.10e-19!23;CL:0000337!2.10e-19!23;CL:0002319!1.85e-14!43;CL:0000221!6.93e-14!44;CL:0000133!6.93e-14!44;CL:0000540!9.97e-14!33;CL:0000047!9.97e-14!33;CL:0000031!9.97e-14!33;CL:0000404!9.97e-14!33;CL:0000055!2.10e-11!49;CL:0000393!2.79e-10!39;CL:0000211!2.79e-10!39;CL:0002609!5.47e-08!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!4.07e-33!73;UBERON:0002346!1.97e-32!64;UBERON:0003075!1.97e-32!64;UBERON:0007284!1.97e-32!64;UBERON:0001016!1.12e-31!75;UBERON:0000073!2.93e-31!54;UBERON:0002020!4.85e-31!34;UBERON:0001049!1.52e-30!52;UBERON:0005068!1.52e-30!52;UBERON:0006241!1.52e-30!52;UBERON:0007135!1.52e-30!52;UBERON:0004121!9.26e-29!95;UBERON:0000924!9.26e-29!95;UBERON:0006601!9.26e-29!95;UBERON:0003528!5.36e-27!29;UBERON:0002791!5.36e-27!29;UBERON:0001893!5.36e-27!29;UBERON:0000955!1.28e-26!47;UBERON:0006238!1.28e-26!47;UBERON:0010371!4.65e-26!73;UBERON:0002616!1.22e-25!46;UBERON:0003056!1.29e-25!49;UBERON:0003080!1.20e-22!40;UBERON:0002780!2.90e-22!39;UBERON:0001890!2.90e-22!39;UBERON:0006240!2.90e-22!39;UBERON:0000956!7.10e-21!21;UBERON:0001869!7.10e-21!21;UBERON:0000203!7.10e-21!21;UBERON:0010314!7.17e-17!92;UBERON:0002619!1.17e-16!17;UBERON:0002021!4.13e-11!10;UBERON:0000411!4.13e-11!10;UBERON:0001950!4.13e-11!10;UBERON:0003076!3.15e-08!12;UBERON:0003057!3.15e-08!12;UBERON:0002420!3.10e-07!8;UBERON:0007245!3.10e-07!8;UBERON:0010009!3.10e-07!8;UBERON:0010011!3.10e-07!8;UBERON:0000454!3.10e-07!8;UBERON:0001954!5.31e-07!7;UBERON:0003022!5.31e-07!7;UBERON:0002421!5.31e-07!7;UBERON:0000349!5.31e-07!7;UBERON:0002600!5.31e-07!7
|tfbs_overrepresentation_for_novel_motifs=0.737036,1.24506,0.245304,0.818969,0.1565,0.315748,0.396495,0.630239,0.320069,0.0641678,1.67609,0.385627,0.304329,1.05028,0.169024,0,0.587245,0.150639,0.0817508,0.602977,0.215242,0.235703,0.406794,0.471175,0.251585,0.432737,0.561494,0.334131,0.191143,1.17115,0.321757,0.683831,0.455295,0.0658632,0.169391,2.23468,0.862318,0.382372,0.398832,0.347926,0.153518,0.326286,0.407596,0.170547,0.283915,0.293566,1.27535,0.34807,0.0642028,0.19345,0.570705,0.457464,0.736781,0.82076,0.837732,0.414119,0.200484,0.37415,0.535132,0.412262,0.664611,0.46618,0.340458,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.229771,0.0945081,1.11546,0.870406,0.0680008,0.222652,0.0658238,0.50152,0.648171,0.624196,0.0952669,0.60374,0.464847,0.293128,0.758319,0.0325399,0.930456,0.198381,2.21622,1.47691,1.03946,1.80075,0.696137,0.16091,1.27589,0.360425,0.299765,0.698838,0.512384,0.379245,0.438441,0.683562,0.803823,0.571268,1.39856,0.3259,0.627019,0.344504,0.63348,0.216685,0.261228,0.805555,0.219561,0.361667,1.04639,0.152197,0.0493982,0.826326,0.58848,0.850885,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.95011,0.787341,0.804729,0.940498,0.426575,1.06766,0.231689,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,1.38563,0.326684,0.515065,1.80426,0.276297,0.157809,0.445509,0.0825345,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.265096,0.752802,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.141416,0.384198,0.0476708
}}

Latest revision as of 15:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98190955..98190968,-p2@Neurod2
Mm9::chr13:83854880..83854907,+p@chr13:83854880..83854907
+
Mm9::chr13:83854957..83854966,+p@chr13:83854957..83854966
+
Mm9::chr13:83860754..83860760,-p@chr13:83860754..83860760
-
Mm9::chr13:83860934..83860949,+p2@ENSMUST00000131907
Mm9::chr13:83860962..83860989,+p1@ENSMUST00000131907
Mm9::chr13:84487489..84487511,-p@chr13:84487489..84487511
-
Mm9::chr16:6348617..6348642,+p14@Rbfox1
Mm9::chr19:4711995..4712008,+p5@Spnb3
Mm9::chr3:17954496..17954515,+p3@Bhlhe22
Mm9::chr3:88011177..88011227,+p1@uc008pug.1
Mm9::chr3:88016661..88016693,+p@chr3:88016661..88016693
+


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:0002209behavioral defense response0.0108886210485948
GO:0001662behavioral fear response0.0108886210485948
GO:0008306associative learning0.0108886210485948
GO:0042596fear response0.0108886210485948
GO:0033555multicellular organismal response to stress0.0145181613981263
GO:0007612learning0.023712996950273
GO:0007611learning and/or memory0.0282067135735026



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 system4.07e-3373
neurectoderm1.97e-3264
neural plate1.97e-3264
presumptive neural plate1.97e-3264
nervous system1.12e-3175
regional part of nervous system2.93e-3154
gray matter4.85e-3134
neural tube1.52e-3052
neural rod1.52e-3052
future spinal cord1.52e-3052
neural keel1.52e-3052
ectoderm-derived structure9.26e-2995
ectoderm9.26e-2995
presumptive ectoderm9.26e-2995
brain grey matter5.36e-2729
regional part of telencephalon5.36e-2729
telencephalon5.36e-2729
brain1.28e-2647
future brain1.28e-2647
ecto-epithelium4.65e-2673
regional part of brain1.22e-2546
pre-chordal neural plate1.29e-2549
anterior neural tube1.20e-2240
regional part of forebrain2.90e-2239
forebrain2.90e-2239
future forebrain2.90e-2239
cerebral cortex7.10e-2121
cerebral hemisphere7.10e-2121
pallium7.10e-2121
structure with developmental contribution from neural crest7.17e-1792
regional part of cerebral cortex1.17e-1617
occipital lobe4.13e-1110
visual cortex4.13e-1110
neocortex4.13e-1110
posterior neural tube3.15e-0812
chordal neural plate3.15e-0812
basal ganglion3.10e-078
nuclear complex of neuraxis3.10e-078
aggregate regional part of brain3.10e-078
collection of basal ganglia3.10e-078
cerebral subcortex3.10e-078
Ammon's horn5.31e-077
lobe parts of cerebral cortex5.31e-077
hippocampal formation5.31e-077
limbic system5.31e-077
limbic lobe5.31e-077


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)
MA0003.10.307389
MA0004.10.303605
MA0006.10.496735
MA0007.10.290695
MA0009.10.709264
MA0014.10.357292
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.516099
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.11.1047
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.680396
MA0050.10.895831
MA0051.10.440863
MA0052.10.729105
MA0055.10.89968
MA0056.10
MA0057.10.983678
MA0058.10.223242
MA0059.10.233271
MA0060.10.351437
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.11.00777
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.12.4416
MA0074.10.390075
MA0076.10.582294
MA0077.10.691048
MA0078.10.471303
MA0081.10.702944
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.0227266
MA0089.10
MA0090.10.753315
MA0091.10.845572
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.19444
MA0105.10.0633795
MA0106.10.478503
MA0107.10.189625
MA0108.21.37095
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.10.127366
MA0115.10.805567
MA0116.10.496352
MA0117.11.82371
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.12.26454
MA0132.10
MA0133.10
MA0135.11.95545
MA0136.10.408073
MA0139.11.03624
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.11.17991
MA0144.10.129525
MA0145.10.494714
MA0146.10.0195411
MA0147.10.845188
MA0148.10.317692
MA0149.10.245177
MA0062.20.0662974
MA0035.20.383789
MA0039.21.12665
MA0138.20.523978
MA0002.20.0901987
MA0137.20.207733
MA0104.21.1126
MA0047.20.431964
MA0112.20.793603
MA0065.20.265926
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.376318
MA0155.10.127763
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.85749
MA0161.10
MA0162.10.174027
MA0163.10.069011
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.20.349444
MA0102.21.42135
MA0258.10.756558
MA0259.10.130633
MA0442.10
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