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MCL coexpression mm9:641: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!6.89e-21!75;UBERON:0001017!9.36e-21!73;UBERON:0004121!1.14e-17!95;UBERON:0000924!1.14e-17!95;UBERON:0006601!1.14e-17!95;UBERON:0004111!1.84e-16!122;UBERON:0000073!3.80e-16!54;UBERON:0001049!6.56e-15!52;UBERON:0005068!6.56e-15!52;UBERON:0006241!6.56e-15!52;UBERON:0007135!6.56e-15!52;UBERON:0000025!7.15e-15!114;UBERON:0010314!1.06e-13!92;UBERON:0002346!1.12e-12!64;UBERON:0003075!1.12e-12!64;UBERON:0007284!1.12e-12!64;UBERON:0000955!3.30e-12!47;UBERON:0006238!3.30e-12!47;UBERON:0002616!3.68e-12!46;UBERON:0010371!1.07e-11!73;UBERON:0003080!4.21e-10!40;UBERON:0002780!8.26e-10!39;UBERON:0001890!8.26e-10!39;UBERON:0006240!8.26e-10!39;UBERON:0002020!1.11e-09!34;UBERON:0000467!2.49e-08!308;UBERON:0000480!2.49e-08!308;UBERON:0003056!2.97e-08!49;UBERON:0003528!1.95e-07!29;UBERON:0002791!1.95e-07!29;UBERON:0001893!1.95e-07!29
|ontology_enrichment_uberon=UBERON:0001016!6.89e-21!75;UBERON:0001017!9.36e-21!73;UBERON:0004121!1.14e-17!95;UBERON:0000924!1.14e-17!95;UBERON:0006601!1.14e-17!95;UBERON:0004111!1.84e-16!122;UBERON:0000073!3.80e-16!54;UBERON:0001049!6.56e-15!52;UBERON:0005068!6.56e-15!52;UBERON:0006241!6.56e-15!52;UBERON:0007135!6.56e-15!52;UBERON:0000025!7.15e-15!114;UBERON:0010314!1.06e-13!92;UBERON:0002346!1.12e-12!64;UBERON:0003075!1.12e-12!64;UBERON:0007284!1.12e-12!64;UBERON:0000955!3.30e-12!47;UBERON:0006238!3.30e-12!47;UBERON:0002616!3.68e-12!46;UBERON:0010371!1.07e-11!73;UBERON:0003080!4.21e-10!40;UBERON:0002780!8.26e-10!39;UBERON:0001890!8.26e-10!39;UBERON:0006240!8.26e-10!39;UBERON:0002020!1.11e-09!34;UBERON:0000467!2.49e-08!308;UBERON:0000480!2.49e-08!308;UBERON:0003056!2.97e-08!49;UBERON:0003528!1.95e-07!29;UBERON:0002791!1.95e-07!29;UBERON:0001893!1.95e-07!29
|tfbs_overrepresentation_for_novel_motifs=0.29262,1.06312,0.7433,0.329881,0.52369,0.342839,0.425757,0.106126,0.362206,1.77702,0.385334,0.414631,0.345518,1.11437,0.189961,0,0.619876,0.170475,0.656134,0.387499,0.238546,0.521547,1.94803,0.175485,0.276437,0.4628,0.304017,0.361771,0.611503,1.29897,0.921513,0.717576,0.168723,0.270473,1.06026,0.0246631,0.486454,1.0583,0.445168,0.123934,0.173534,0.931853,0.104243,0.191571,0.557517,0.856658,0.543674,0.376103,0.401883,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,1.12875,0.223087,0.40287,0.60268,0.441884,0.698157,1.24284,0.120887,0.592318,1.15114,0.631188,1.00675,1.3527,0.693631,1.20659,2.01398,0.720972,0.299271,0.905636,2.01635,0.0742951,0.570456,0.532872,0.681539,0.242107,0.110993,0.636582,0.495545,0.682423,0.792744,2.598,0.291599,0.500771,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.694736,0.732731,1.34284,0.764487,0.161581,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,1.25266,0.781068,0.840348,0.681364,1.01194,1.0825,0.512539,1.58424,0.333247,1.50549,0.158673,0.910937,0.572279,1.17341,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,0.2772,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.93276,0.546641,1.84176,0.302077,1.01111,1.8264,0.475084,0.857198,0.415832,0.455644,0.93735,0.488969,0.199652,0.290467,0.811219,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.160658,0.413167,1.58524
|tfbs_overrepresentation_for_novel_motifs=0.29262,1.06312,0.7433,0.329881,0.52369,0.342839,0.425757,0.106126,0.362206,1.77702,0.385334,0.414631,0.345518,1.11437,0.189961,0,0.619876,0.170475,0.656134,0.387499,0.238546,0.521547,1.94803,0.175485,0.276437,0.4628,0.304017,0.361771,0.611503,1.29897,0.921513,0.717576,0.168723,0.270473,1.06026,0.0246631,0.486454,1.0583,0.445168,0.123934,0.173534,0.931853,0.104243,0.191571,0.557517,0.856658,0.543674,0.376103,0.401883,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,1.12875,0.223087,0.40287,0.60268,0.441884,0.698157,1.24284,0.120887,0.592318,1.15114,0.631188,1.00675,1.3527,0.693631,1.20659,2.01398,0.720972,0.299271,0.905636,2.01635,0.0742951,0.570456,0.532872,0.681539,0.242107,0.110993,0.636582,0.495545,0.682423,0.792744,2.598,0.291599,0.500771,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.694736,0.732731,1.34284,0.764487,0.161581,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,1.25266,0.781068,0.840348,0.681364,1.01194,1.0825,0.512539,1.58424,0.333247,1.50549,0.158673,0.910937,0.572279,1.17341,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,0.2772,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.93276,0.546641,1.84176,0.302077,1.01111,1.8264,0.475084,0.857198,0.415832,0.455644,0.93735,0.488969,0.199652,0.290467,0.811219,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.160658,0.413167,1.58524
|tfbs_overrepresentation_jaspar=MA0003.1;0.774944,MA0004.1;0.879856,MA0006.1;0.186435,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;1.22114,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;1.69693,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.729572,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.440822,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.136328,MA0056.1;0,MA0057.1;0.181039,MA0058.1;1.27846,MA0059.1;0.714494,MA0060.1;2.51989,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;2.10988,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.0212456,MA0074.1;0.419185,MA0076.1;1.85487,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.760108,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.12124,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;1.47462,MA0093.1;1.73415,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.619698,MA0105.1;0.0759118,MA0106.1;0.509454,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.145642,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;0.265536,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,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;0.3137,MA0146.1;1.06665,MA0147.1;0.475899,MA0148.1;0.912216,MA0149.1;0.269772,MA0062.2;1.9926,MA0035.2;0.412747,MA0039.2;2.64798,MA0138.2;0.555696,MA0002.2;0.343346,MA0137.2;0.230686,MA0104.2;0.744492,MA0047.2;0.46201,MA0112.2;2.25739,MA0065.2;0.574339,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.195907,MA0155.1;0.354827,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.347545,MA0161.1;0,MA0162.1;1.19805,MA0163.1;0.355774,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;1.0633,MA0102.2;1.45844,MA0258.1;0.421574,MA0259.1;0.455671,MA0442.1;0
}}
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Revision as of 12:04, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79132158..79132204,+p@chr10:79132158..79132204
+
Mm9::chr11:78141927..78141974,+p1@Pigs
Mm9::chr2:131005721..131005828,-p1@Cenpb
Mm9::chr2:32837527..32837606,-p1@Slc2a8
Mm9::chr5:120953602..120953636,-p1@Plbd2
Mm9::chr5:24092539..24092612,+p1@Chpf2
Mm9::chr7:149573800..149573811,-p3@Ctsd
Mm9::chr7:52765770..52765783,-p2@Nucb1
Mm9::chr8:26127724..26127777,+p1@Tm2d2
Mm9::chr8:26127778..26127792,+p2@Tm2d2
Mm9::chrX:71638550..71638606,-p2@Fam3a


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:0005536glucose binding0.00542376595628116
GO:0015284fructose uniporter activity0.00542376595628116
GO:0015757galactose transport0.00542376595628116
GO:0004192cathepsin D activity0.00542376595628116
GO:0015755fructose transport0.00542376595628116
GO:0005354galactose transmembrane transporter activity0.00542376595628116
GO:0015292uniporter activity0.00542376595628116
GO:0008516hexose uniporter activity0.00542376595628116
GO:0005353fructose transmembrane transporter activity0.00964092987743474
GO:0003923GPI-anchor transamidase activity0.0130134726345087
GO:0004194pepsin A activity0.0315262134324555
GO:0005355glucose transmembrane transporter activity0.0340455772610801
GO:0015145monosaccharide transmembrane transporter activity0.0340455772610801
GO:0015149hexose transmembrane transporter activity0.0340455772610801
GO:0004190aspartic-type endopeptidase activity0.0475920528897136
GO:0006506GPI anchor biosynthetic process0.0475920528897136
GO:0048029monosaccharide binding0.0475920528897136
GO:0046489phosphoinositide biosynthetic process0.0475920528897136
GO:0001666response to hypoxia0.0475920528897136
GO:0006505GPI anchor metabolic process0.0475920528897136
GO:0008286insulin receptor signaling pathway0.0484175615673511
GO:0015758glucose transport0.0484175615673511
GO:0044444cytoplasmic part0.0484175615673511
GO:0008645hexose transport0.0484175615673511
GO:0015749monosaccharide transport0.0484175615673511
GO:0046474glycerophospholipid biosynthetic process0.049867069573456



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 system6.89e-2175
central nervous system9.36e-2173
ectoderm-derived structure1.14e-1795
ectoderm1.14e-1795
presumptive ectoderm1.14e-1795
anatomical conduit1.84e-16122
regional part of nervous system3.80e-1654
neural tube6.56e-1552
neural rod6.56e-1552
future spinal cord6.56e-1552
neural keel6.56e-1552
tube7.15e-15114
structure with developmental contribution from neural crest1.06e-1392
neurectoderm1.12e-1264
neural plate1.12e-1264
presumptive neural plate1.12e-1264
brain3.30e-1247
future brain3.30e-1247
regional part of brain3.68e-1246
ecto-epithelium1.07e-1173
anterior neural tube4.21e-1040
regional part of forebrain8.26e-1039
forebrain8.26e-1039
future forebrain8.26e-1039
gray matter1.11e-0934
anatomical system2.49e-08308
anatomical group2.49e-08308
pre-chordal neural plate2.97e-0849
brain grey matter1.95e-0729
regional part of telencephalon1.95e-0729
telencephalon1.95e-0729


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)
MA0003.10.774944
MA0004.10.879856
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.11.22114
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.11.69693
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.729572
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.440822
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.136328
MA0056.10
MA0057.10.181039
MA0058.11.27846
MA0059.10.714494
MA0060.12.51989
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.12.10988
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.0212456
MA0074.10.419185
MA0076.11.85487
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.12124
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.11.47462
MA0093.11.73415
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.619698
MA0105.10.0759118
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.145642
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
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
MA0145.10.3137
MA0146.11.06665
MA0147.10.475899
MA0148.10.912216
MA0149.10.269772
MA0062.21.9926
MA0035.20.412747
MA0039.22.64798
MA0138.20.555696
MA0002.20.343346
MA0137.20.230686
MA0104.20.744492
MA0047.20.46201
MA0112.22.25739
MA0065.20.574339
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.195907
MA0155.10.354827
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.11.19805
MA0163.10.355774
MA0164.10.437937
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.21.0633
MA0102.21.45844
MA0258.10.421574
MA0259.10.455671
MA0442.10
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