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MCL coexpression mm9:864: Difference between revisions

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{{MCL_coexpression_mm9
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regulation of oligodendrocyte differentiation;0.0158608441727178;235402!GO:0048713;regulation of oligodendrocyte differentiation;0.0158608441727178;235402!GO:0014014;negative regulation of gliogenesis;0.0158608441727178;235402!GO:0045686;negative regulation of glial cell differentiation;0.0158608441727178;235402!GO:0005154;epidermal growth factor receptor binding;0.0158608441727178;235402!GO:0045685;regulation of glial cell differentiation;0.0158608441727178;235402!GO:0014013;regulation of gliogenesis;0.0158608441727178;235402!GO:0048709;oligodendrocyte differentiation;0.0158608441727178;235402!GO:0043491;protein kinase B signaling cascade;0.0158608441727178;235402!GO:0021954;central nervous system neuron development;0.0272368829429225;235402!GO:0021953;central nervous system neuron differentiation;0.0282934074455258;235402!GO:0010001;glial cell 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|gostat_on_MCL_coexpression=GO:0048715;negative regulation of oligodendrocyte differentiation;0.0158608441727178;235402!GO:0048713;regulation of oligodendrocyte differentiation;0.0158608441727178;235402!GO:0014014;negative regulation of gliogenesis;0.0158608441727178;235402!GO:0045686;negative regulation of glial cell differentiation;0.0158608441727178;235402!GO:0005154;epidermal growth factor receptor binding;0.0158608441727178;235402!GO:0045685;regulation of glial cell differentiation;0.0158608441727178;235402!GO:0014013;regulation of gliogenesis;0.0158608441727178;235402!GO:0048709;oligodendrocyte differentiation;0.0158608441727178;235402!GO:0043491;protein kinase B signaling cascade;0.0158608441727178;235402!GO:0021954;central nervous system neuron development;0.0272368829429225;235402!GO:0021953;central nervous system neuron differentiation;0.0282934074455258;235402!GO:0010001;glial cell differentiation;0.040860385301581;235402!GO:0042063;gliogenesis;0.040860385301581;235402!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000955!8.33e-17!47;UBERON:0006238!8.33e-17!47;UBERON:0000073!4.45e-16!54;UBERON:0002616!5.89e-16!46;UBERON:0001049!3.58e-14!52;UBERON:0005068!3.58e-14!52;UBERON:0006241!3.58e-14!52;UBERON:0007135!3.58e-14!52;UBERON:0002021!9.36e-14!10;UBERON:0000411!9.36e-14!10;UBERON:0001950!9.36e-14!10;UBERON:0003080!1.32e-13!40;UBERON:0002780!9.94e-13!39;UBERON:0001890!9.94e-13!39;UBERON:0006240!9.94e-13!39;UBERON:0001017!4.77e-11!73;UBERON:0001016!1.76e-10!75;UBERON:0003528!5.87e-10!29;UBERON:0002791!5.87e-10!29;UBERON:0001893!5.87e-10!29;UBERON:0002619!6.91e-10!17;UBERON:0002346!8.80e-10!64;UBERON:0003075!8.80e-10!64;UBERON:0007284!8.80e-10!64;UBERON:0003056!1.12e-09!49;UBERON:0000956!7.57e-09!21;UBERON:0001869!7.57e-09!21;UBERON:0000203!7.57e-09!21;UBERON:0010371!3.94e-08!73;UBERON:0002020!1.04e-07!34;UBERON:0000025!1.93e-07!114;UBERON:0004121!9.04e-07!95;UBERON:0000924!9.04e-07!95;UBERON:0006601!9.04e-07!95
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,0.448401,0.538088,0.515265,0.535519,0.386846,0.494602,0.526159,0.173454,0.550255,0.756943,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.0622758,0.549359,0.258745,0.374936,0.577606,0.466037,0.469052,0.818708,0.118137,0.455168,0.843667,0.250677,0.136998,0.276324,0.185086,0.242032,0.522578,0.631914,0.195877,0.712303,0.460258,0.450632,0.761266,0.0824666,1.08432,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.50864,1.03623,0.140213,0.131016,0.136938,0.651651,0.806481,1.60272,1.01677,0.759925,0.612313,0.167672,0.920903,0.789543,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,1.34857,0.218233,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,2.22052,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.708441,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,0.447587,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.166768
|tfbs_overrepresentation_jaspar=MA0003.1;0.016751,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;1.07722,MA0009.1;0.870101,MA0014.1;0.162935,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.0283571,MA0056.1;0,MA0057.1;0.0935008,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.000129679,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.064239,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.827743,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.0701568,MA0146.1;0.198184,MA0147.1;0.236889,MA0148.1;1.14345,MA0149.1;0.367458,MA0062.2;0.426733,MA0035.2;0.524137,MA0039.2;0.00752803,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.0704227,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.230918,MA0163.1;0.0186439,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.00265486,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}

Latest revision as of 16:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:4978013..4978035,+p14@Syne1
Mm9::chr10:4978043..4978055,+p17@Syne1
Mm9::chr10:4978078..4978090,+p22@Syne1
Mm9::chr10:4978881..4978904,+p16@Syne1
Mm9::chr10:5007643..5007657,+p@chr10:5007643..5007657
+
Mm9::chr19:29038341..29038367,+p3@Ppapdc2
Mm9::chr9:56482905..56482942,-p2@Lingo1
Mm9::chrX:164857590..164857595,-p@chrX:164857590..164857595
-


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:0048715negative regulation of oligodendrocyte differentiation0.0158608441727178
GO:0048713regulation of oligodendrocyte differentiation0.0158608441727178
GO:0014014negative regulation of gliogenesis0.0158608441727178
GO:0045686negative regulation of glial cell differentiation0.0158608441727178
GO:0005154epidermal growth factor receptor binding0.0158608441727178
GO:0045685regulation of glial cell differentiation0.0158608441727178
GO:0014013regulation of gliogenesis0.0158608441727178
GO:0048709oligodendrocyte differentiation0.0158608441727178
GO:0043491protein kinase B signaling cascade0.0158608441727178
GO:0021954central nervous system neuron development0.0272368829429225
GO:0021953central nervous system neuron differentiation0.0282934074455258
GO:0010001glial cell differentiation0.040860385301581
GO:0042063gliogenesis0.040860385301581



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
brain8.33e-1747
future brain8.33e-1747
regional part of nervous system4.45e-1654
regional part of brain5.89e-1646
neural tube3.58e-1452
neural rod3.58e-1452
future spinal cord3.58e-1452
neural keel3.58e-1452
occipital lobe9.36e-1410
visual cortex9.36e-1410
neocortex9.36e-1410
anterior neural tube1.32e-1340
regional part of forebrain9.94e-1339
forebrain9.94e-1339
future forebrain9.94e-1339
central nervous system4.77e-1173
nervous system1.76e-1075
brain grey matter5.87e-1029
regional part of telencephalon5.87e-1029
telencephalon5.87e-1029
regional part of cerebral cortex6.91e-1017
neurectoderm8.80e-1064
neural plate8.80e-1064
presumptive neural plate8.80e-1064
pre-chordal neural plate1.12e-0949
cerebral cortex7.57e-0921
cerebral hemisphere7.57e-0921
pallium7.57e-0921
ecto-epithelium3.94e-0873
gray matter1.04e-0734
tube1.93e-07114
ectoderm-derived structure9.04e-0795
ectoderm9.04e-0795
presumptive ectoderm9.04e-0795


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)
MA0003.10.016751
MA0004.10.434673
MA0006.10.271714
MA0007.11.07722
MA0009.10.870101
MA0014.10.162935
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.000129679
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.827743
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.10.198184
MA0147.10.236889
MA0148.11.14345
MA0149.10.367458
MA0062.20.426733
MA0035.20.524137
MA0039.20.00752803
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.0186439
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.00265486
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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