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MCL coexpression mm9:558: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0030865;cortical cytoskeleton organization and biogenesis;0.0480374230474727;104027!GO:0043197;dendritic spine;0.0480374230474727;104027!GO:0050772;positive regulation of axonogenesis;0.0480374230474727;70083!GO:0050769;positive regulation of neurogenesis;0.0480374230474727;70083!
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|ontology_enrichment_uberon=UBERON:0001016!2.38e-35!75;UBERON:0001017!1.98e-34!73;UBERON:0004121!1.21e-33!95;UBERON:0000924!1.21e-33!95;UBERON:0006601!1.21e-33!95;UBERON:0002346!1.86e-25!64;UBERON:0003075!1.86e-25!64;UBERON:0007284!1.86e-25!64;UBERON:0010371!1.77e-21!73;UBERON:0000073!3.71e-20!54;UBERON:0010314!4.28e-19!92;UBERON:0001049!7.97e-19!52;UBERON:0005068!7.97e-19!52;UBERON:0006241!7.97e-19!52;UBERON:0007135!7.97e-19!52;UBERON:0000955!8.83e-16!47;UBERON:0006238!8.83e-16!47;UBERON:0003056!1.02e-15!49;UBERON:0002616!3.54e-15!46;UBERON:0003080!9.73e-12!40;UBERON:0002020!2.15e-11!34;UBERON:0002780!3.35e-11!39;UBERON:0001890!3.35e-11!39;UBERON:0006240!3.35e-11!39;UBERON:0003528!1.21e-08!29;UBERON:0002791!1.21e-08!29;UBERON:0001893!1.21e-08!29;UBERON:0003076!1.92e-08!12;UBERON:0003057!1.92e-08!12;UBERON:0000010!2.20e-08!11;UBERON:0002410!7.29e-08!9
|tfbs_overrepresentation_for_novel_motifs=0.684947,3.66275,0.223558,0.279403,0.138992,0.291576,0.370193,0.959416,0.283485,1.40965,0.883008,0.35958,0.567414,0.381063,0.15081,0,1.37184,0.416118,0.244912,0.286444,0.194751,0.944339,0.38026,0.427399,0.64994,0.405649,0.861345,0.309422,0.171781,1.05808,0.297405,2.65847,0.131928,0.202991,2.78029,0.73018,0.395883,0.356403,0.358188,0.640643,0.136186,0.301802,0.175756,0.152251,0.119688,0.270091,0.48361,0.863451,0.138343,0.994443,0.541299,0.429887,0.366754,0.788877,0.805733,0.387424,0.18067,0.348382,0.476143,0.385607,0.634076,0.438439,0.302747,1.31502,1.02791,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.277751,0.669459,0.838198,0.458017,1.14856,0.447182,0.473159,0.617814,0.575143,0.279684,0.573903,0.437131,0.0742829,0.72691,0.490197,0.00535506,0.170021,0.488122,1.44275,1.0064,0.731688,0.665283,0.143149,0.108477,0.321665,0.948949,0.667958,0.483845,1.34415,0.125632,0.652833,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,0.584153,1.08317,0.671624,0.773781,0.19888,0.893019,1.01331,0.134943,1.6023,2.16199,0.558838,0.123076,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.377415,0.658832,0.936732,2.02905,0.755703,0.273302,0.907893,0.399614,1.03449,0.0751544,0.700863,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,0.486482,1.76978,0.253405,0.140226,0.694195,0.173908,0.790393,0.331601,0.398786,0.869538,0.430798,0.159498,0.242603,0.700333,0.995609,0.726089,0.621734,1.24129,0.531751,0.392164,0.12482,0.358185,2.22458
|tfbs_overrepresentation_jaspar=MA0003.1;1.11461,MA0004.1;0.279808,MA0006.1;0.451962,MA0007.1;1.35441,MA0009.1;0.678286,MA0014.1;1.81873,MA0017.1;1.53792,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;0.155127,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.332541,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.776491,MA0056.1;0,MA0057.1;2.20915,MA0058.1;0.202403,MA0059.1;1.79197,MA0060.1;1.07734,MA0061.1;0.363764,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;0.0328198,MA0069.1;1.66641,MA0070.1;0.688999,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;3.35491,MA0074.1;0.363923,MA0076.1;0.181159,MA0077.1;0.660245,MA0078.1;0.443468,MA0081.1;0.651709,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.965806,MA0089.1;0,MA0090.1;0.700834,MA0091.1;0.290854,MA0092.1;0.251716,MA0093.1;0.161141,MA0095.1;0,MA0098.1;0,MA0100.1;0.353762,MA0101.1;0.219061,MA0103.1;0.174916,MA0105.1;0.434904,MA0106.1;1.14333,MA0107.1;0.508149,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.727672,MA0113.1;1.088,MA0114.1;2.37343,MA0115.1;0.773793,MA0116.1;0.147513,MA0117.1;0.742722,MA0119.1;0.219527,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.942843,MA0140.1;0.353662,MA0141.1;0.18979,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.737036,MA0145.1;1.02938,MA0146.1;4.38589,MA0147.1;0.773525,MA0148.1;0.293462,MA0149.1;0.223436,MA0062.2;0.0556611,MA0035.2;0.357786,MA0039.2;8.91824,MA0138.2;1.23931,MA0002.2;0.0773396,MA0137.2;0.55008,MA0104.2;0.605306,MA0047.2;0.404891,MA0112.2;1.02934,MA0065.2;1.03219,MA0150.1;0.267221,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.593208,MA0155.1;3.67183,MA0156.1;0.180505,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.803691,MA0160.1;1.45924,MA0161.1;0,MA0162.1;0.424868,MA0163.1;3.51192,MA0164.1;0.381832,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;3.99314,MA0102.2;1.38728,MA0258.1;0.687966,MA0259.1;0.367748,MA0442.1;0
}}

Latest revision as of 15:30, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:102807325..102807370,-p@chr11:102807325..102807370
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Mm9::chr11:102808015..102808039,-p1@C1ql1
Mm9::chr11:102808055..102808065,-p2@C1ql1
Mm9::chr11:102808083..102808092,-p3@C1ql1
Mm9::chr17:25932584..25932609,-p@chr17:25932584..25932609
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Mm9::chr17:25933909..25933926,-p1@Metrn
Mm9::chr17:25933977..25934020,-p2@Metrn
Mm9::chr18:60760090..60760115,-p9@Synpo
Mm9::chr1:137051218..137051263,+p@chr1:137051218..137051263
+
Mm9::chr2:30663055..30663094,-p@chr2:30663055..30663094
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Mm9::chr3:28164152..28164169,-p@chr3:28164152..28164169
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Mm9::chr7:4703765..4703780,-p@chr7:4703765..4703780
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Mm9::chr9:43880279..43880294,+p@chr9:43880279..43880294
+


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:0030865cortical cytoskeleton organization and biogenesis0.0480374230474727
GO:0043197dendritic spine0.0480374230474727
GO:0050772positive regulation of axonogenesis0.0480374230474727
GO:0050769positive regulation of neurogenesis0.0480374230474727



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 system2.38e-3575
central nervous system1.98e-3473
ectoderm-derived structure1.21e-3395
ectoderm1.21e-3395
presumptive ectoderm1.21e-3395
neurectoderm1.86e-2564
neural plate1.86e-2564
presumptive neural plate1.86e-2564
ecto-epithelium1.77e-2173
regional part of nervous system3.71e-2054
structure with developmental contribution from neural crest4.28e-1992
neural tube7.97e-1952
neural rod7.97e-1952
future spinal cord7.97e-1952
neural keel7.97e-1952
brain8.83e-1647
future brain8.83e-1647
pre-chordal neural plate1.02e-1549
regional part of brain3.54e-1546
anterior neural tube9.73e-1240
gray matter2.15e-1134
regional part of forebrain3.35e-1139
forebrain3.35e-1139
future forebrain3.35e-1139
brain grey matter1.21e-0829
regional part of telencephalon1.21e-0829
telencephalon1.21e-0829
posterior neural tube1.92e-0812
chordal neural plate1.92e-0812
peripheral nervous system2.20e-0811
autonomic nervous system7.29e-089


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)
MA0003.11.11461
MA0004.10.279808
MA0006.10.451962
MA0007.11.35441
MA0009.10.678286
MA0014.11.81873
MA0017.11.53792
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.332541
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.776491
MA0056.10
MA0057.12.20915
MA0058.10.202403
MA0059.11.79197
MA0060.11.07734
MA0061.10.363764
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.10.0328198
MA0069.11.66641
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.13.35491
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.651709
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.965806
MA0089.10
MA0090.10.700834
MA0091.10.290854
MA0092.10.251716
MA0093.10.161141
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.10.219061
MA0103.10.174916
MA0105.10.434904
MA0106.11.14333
MA0107.10.508149
MA0108.20.527977
MA0109.10
MA0111.10.727672
MA0113.11.088
MA0114.12.37343
MA0115.10.773793
MA0116.10.147513
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.942843
MA0140.10.353662
MA0141.10.18979
MA0142.10.575041
MA0143.10.439766
MA0144.10.737036
MA0145.11.02938
MA0146.14.38589
MA0147.10.773525
MA0148.10.293462
MA0149.10.223436
MA0062.20.0556611
MA0035.20.357786
MA0039.28.91824
MA0138.21.23931
MA0002.20.0773396
MA0137.20.55008
MA0104.20.605306
MA0047.20.404891
MA0112.21.02934
MA0065.21.03219
MA0150.10.267221
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.593208
MA0155.13.67183
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.803691
MA0160.11.45924
MA0161.10
MA0162.10.424868
MA0163.13.51192
MA0164.10.381832
MA0080.20.170995
MA0018.20.390455
MA0099.20.489441
MA0079.23.99314
MA0102.21.38728
MA0258.10.687966
MA0259.10.367748
MA0442.10
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