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MCL coexpression mm9:663: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!2.60e-16!95;UBERON:0000924!2.60e-16!95;UBERON:0006601!2.60e-16!95;UBERON:0010371!6.63e-16!73;UBERON:0000073!8.46e-16!54;UBERON:0002346!9.93e-15!64;UBERON:0003075!9.93e-15!64;UBERON:0007284!9.93e-15!64;UBERON:0001049!1.03e-14!52;UBERON:0005068!1.03e-14!52;UBERON:0006241!1.03e-14!52;UBERON:0007135!1.03e-14!52;UBERON:0001017!5.69e-14!73;UBERON:0001016!9.39e-14!75;UBERON:0002020!1.03e-13!34;UBERON:0000955!2.55e-12!47;UBERON:0006238!2.55e-12!47;UBERON:0003056!5.44e-12!49;UBERON:0002616!8.42e-12!46;UBERON:0003080!2.44e-11!40;UBERON:0003528!2.50e-11!29;UBERON:0002791!2.50e-11!29;UBERON:0001893!2.50e-11!29;UBERON:0002780!7.71e-11!39;UBERON:0001890!7.71e-11!39;UBERON:0006240!7.71e-11!39;UBERON:0010314!9.08e-11!92;UBERON:0002021!6.72e-08!10;UBERON:0000411!6.72e-08!10;UBERON:0001950!6.72e-08!10;UBERON:0000956!1.29e-07!21;UBERON:0001869!1.29e-07!21;UBERON:0000203!1.29e-07!21;UBERON:0002619!4.73e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.140695,0.7433,0.329881,0.176699,0.342839,0.425757,0.345089,0.112618,3.30828,0.385334,0.414631,1.16031,0.437133,0.555819,0,0.619876,0.170475,0.656134,0.387499,0.238546,0.281622,0.436294,0.175485,0.276437,0.4628,0.0908349,0.361771,1.15025,0.0650265,0.921513,0.717576,0.504188,0.570676,0.556756,0.308746,2.88023,0.411296,0.144953,0.391645,0.173534,0.931853,0.255102,0.191571,1.45562,0.319944,0.543674,0.376103,0.208261,0.215702,1.4677,1.22385,0.220536,0.855661,0.87275,1.9733,0.223087,0.40287,0.288386,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,1.30396,0.355763,5.29776,0.905636,3.29689,0.932285,0.270351,0.532872,0.681539,0.242107,0.110993,0.636582,0.495545,0.333618,0.792744,10.3556,0.4982,0.231893,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.437593,0.129056,0.104462,0.732731,1.34284,0.764487,0.161581,0.717305,0.838603,0.603683,0.602672,2.51086,2.681,0.372438,0.246223,2.72214,0.781068,0.840348,0.243062,0.390066,1.0825,0.512539,2.01901,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,0.0275241,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,1.60254,2.39898,8.62531,0.857198,1.3356,0.455644,0.93735,0.488969,0.199652,0.290467,2.24847,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,0.160658,0.413167,4.33626
|tfbs_overrepresentation_jaspar=MA0003.1;10.0236,MA0004.1;0.330313,MA0006.1;3.94346,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;6.634,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;1.16958,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;3.241,MA0046.1;0.778239,MA0048.1;1.17627,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.735247,MA0056.1;0,MA0057.1;0.048013,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.395347,MA0061.1;0.451296,MA0063.1;0,MA0066.1;0.452472,MA0067.1;2.45116,MA0068.1;0.0500842,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.416236,MA0074.1;0.419185,MA0076.1;0.223625,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.534411,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;1.05226,MA0101.1;1.34597,MA0103.1;0.216742,MA0105.1;0.26272,MA0106.1;0.509454,MA0107.1;1.14406,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.446898,MA0115.1;0.84036,MA0116.1;0.546914,MA0117.1;0.808813,MA0119.1;0.733279,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;1.38377,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.338099,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.147954,MA0145.1;1.29899,MA0146.1;4.70423,MA0147.1;3.61873,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.271822,MA0035.2;0.412747,MA0039.2;1.11109,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;0.230686,MA0104.2;3.85819,MA0047.2;0.46201,MA0112.2;1.29895,MA0065.2;0.314773,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.195907,MA0155.1;0.637282,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.495113,MA0160.1;0.347545,MA0161.1;0,MA0162.1;6.97924,MA0163.1;2.27461,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;5.14811,MA0099.2;0.549696,MA0079.2;4.09415,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;2.05988,MA0442.1;0
}}

Latest revision as of 15:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:101758988..101759063,-p1@Ttc7b
Mm9::chr12:56922144..56922182,-p1@Ralgapa1
Mm9::chr15:36723350..36723392,-p1@Ywhaz
Mm9::chr15:76062984..76063064,-p7@Plec
Mm9::chr16:5013598..5013651,-p1@Rogdi
Mm9::chr1:59970327..59970380,+p@chr1:59970327..59970380
+
Mm9::chr3:137530722..137530761,+p1@Dnajb14
Mm9::chr5:33361418..33361419,+p7@Ywhah
Mm9::chr6:39675447..39675477,-p2@Braf
Mm9::chr9:54349372..54349451,-p1@Dmxl2
Mm9::chr9:54349454..54349490,-p2@Dmxl2


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:0019904protein domain specific binding0.0210612225400774



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>

Cell Type
Ontology termp-valuen
CNS neuron (sensu Vertebrata)5.98e-0923
neuroblast (sensu Vertebrata)5.98e-0923
neuron6.14e-0733
neuronal stem cell6.14e-0733
neuroblast6.14e-0733
electrically signaling cell6.14e-0733

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.60e-1695
ectoderm2.60e-1695
presumptive ectoderm2.60e-1695
ecto-epithelium6.63e-1673
regional part of nervous system8.46e-1654
neurectoderm9.93e-1564
neural plate9.93e-1564
presumptive neural plate9.93e-1564
neural tube1.03e-1452
neural rod1.03e-1452
future spinal cord1.03e-1452
neural keel1.03e-1452
central nervous system5.69e-1473
nervous system9.39e-1475
gray matter1.03e-1334
brain2.55e-1247
future brain2.55e-1247
pre-chordal neural plate5.44e-1249
regional part of brain8.42e-1246
anterior neural tube2.44e-1140
brain grey matter2.50e-1129
regional part of telencephalon2.50e-1129
telencephalon2.50e-1129
regional part of forebrain7.71e-1139
forebrain7.71e-1139
future forebrain7.71e-1139
structure with developmental contribution from neural crest9.08e-1192
occipital lobe6.72e-0810
visual cortex6.72e-0810
neocortex6.72e-0810
cerebral cortex1.29e-0721
cerebral hemisphere1.29e-0721
pallium1.29e-0721
regional part of cerebral cortex4.73e-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)
MA0003.110.0236
MA0004.10.330313
MA0006.13.94346
MA0007.10.316976
MA0009.10.743257
MA0014.16.634
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.11.16958
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.13.241
MA0046.10.778239
MA0048.11.17627
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.735247
MA0056.10
MA0057.10.048013
MA0058.10.246908
MA0059.10.257372
MA0060.10.395347
MA0061.10.451296
MA0063.10
MA0066.10.452472
MA0067.12.45116
MA0068.10.0500842
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.416236
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.534411
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.11.05226
MA0101.11.34597
MA0103.10.216742
MA0105.10.26272
MA0106.10.509454
MA0107.11.14406
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.446898
MA0115.10.84036
MA0116.10.546914
MA0117.10.808813
MA0119.10.733279
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.11.38377
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.338099
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.11.29899
MA0146.14.70423
MA0147.13.61873
MA0148.10.344843
MA0149.10.269772
MA0062.20.271822
MA0035.20.412747
MA0039.21.11109
MA0138.20.555696
MA0002.20.105469
MA0137.20.230686
MA0104.23.85819
MA0047.20.46201
MA0112.21.29895
MA0065.20.314773
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.195907
MA0155.10.637282
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.495113
MA0160.10.347545
MA0161.10
MA0162.16.97924
MA0163.12.27461
MA0164.10.437937
MA0080.20.212408
MA0018.25.14811
MA0099.20.549696
MA0079.24.09415
MA0102.21.45844
MA0258.10.135621
MA0259.12.05988
MA0442.10
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