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MCL coexpression mm9:979: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004121!8.14e-38!95;UBERON:0000924!8.14e-38!95;UBERON:0006601!8.14e-38!95;UBERON:0001016!4.57e-35!75;UBERON:0001017!5.75e-34!73;UBERON:0002346!2.28e-29!64;UBERON:0003075!2.28e-29!64;UBERON:0007284!2.28e-29!64;UBERON:0010371!6.67e-28!73;UBERON:0010314!9.32e-24!92;UBERON:0000073!8.45e-23!54;UBERON:0003056!1.03e-22!49;UBERON:0001049!8.13e-22!52;UBERON:0005068!8.13e-22!52;UBERON:0006241!8.13e-22!52;UBERON:0007135!8.13e-22!52;UBERON:0000955!2.47e-19!47;UBERON:0006238!2.47e-19!47;UBERON:0002616!6.93e-19!46;UBERON:0003080!1.16e-17!40;UBERON:0002780!4.59e-17!39;UBERON:0001890!4.59e-17!39;UBERON:0006240!4.59e-17!39;UBERON:0002020!9.76e-16!34;UBERON:0003528!1.27e-13!29;UBERON:0002791!1.27e-13!29;UBERON:0001893!1.27e-13!29;UBERON:0000468!2.85e-10!333;UBERON:0000956!1.56e-09!21;UBERON:0001869!1.56e-09!21;UBERON:0000203!1.56e-09!21;UBERON:0000922!1.68e-08!320;UBERON:0000025!2.30e-08!114;UBERON:0000010!3.46e-08!11;UBERON:0004111!4.53e-08!122;UBERON:0002619!4.99e-08!17;UBERON:0002410!1.90e-07!9
|ontology_enrichment_uberon=UBERON:0004121!8.14e-38!95;UBERON:0000924!8.14e-38!95;UBERON:0006601!8.14e-38!95;UBERON:0001016!4.57e-35!75;UBERON:0001017!5.75e-34!73;UBERON:0002346!2.28e-29!64;UBERON:0003075!2.28e-29!64;UBERON:0007284!2.28e-29!64;UBERON:0010371!6.67e-28!73;UBERON:0010314!9.32e-24!92;UBERON:0000073!8.45e-23!54;UBERON:0003056!1.03e-22!49;UBERON:0001049!8.13e-22!52;UBERON:0005068!8.13e-22!52;UBERON:0006241!8.13e-22!52;UBERON:0007135!8.13e-22!52;UBERON:0000955!2.47e-19!47;UBERON:0006238!2.47e-19!47;UBERON:0002616!6.93e-19!46;UBERON:0003080!1.16e-17!40;UBERON:0002780!4.59e-17!39;UBERON:0001890!4.59e-17!39;UBERON:0006240!4.59e-17!39;UBERON:0002020!9.76e-16!34;UBERON:0003528!1.27e-13!29;UBERON:0002791!1.27e-13!29;UBERON:0001893!1.27e-13!29;UBERON:0000468!2.85e-10!333;UBERON:0000956!1.56e-09!21;UBERON:0001869!1.56e-09!21;UBERON:0000203!1.56e-09!21;UBERON:0000922!1.68e-08!320;UBERON:0000025!2.30e-08!114;UBERON:0000010!3.46e-08!11;UBERON:0004111!4.53e-08!122;UBERON:0002619!4.99e-08!17;UBERON:0002410!1.90e-07!9
|tfbs_overrepresentation_for_novel_motifs=1.01838,1.66496,0.367606,0.434198,0.260188,0.448401,1.33049,0.173246,1.02512,2.00573,1.23792,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.620214,0.332107,0.0622758,1.35437,0.258745,0.374936,0.577606,0.153291,1.18318,0.818708,0.376624,0.455168,0.843667,0.250677,0.425071,1.38756,0.0711618,1.26012,1.29755,0.631914,1.08217,0.256422,0.460258,0.204736,0.27776,1.7835,1.08432,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,1.37128,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.560836,0.713876,1.39465,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.527912,1.31587,1.03623,3.4185,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,5.69681,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,2.07611,0.62322,0.202284,0.1711,0.859272,0.663249,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,1.61924,0.333829,0.386136,0.96962,0.895335,0.499714,1.21576,0.254749,4.16154,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,2.85877,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,4.84212,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,1.76938,0.714896,0.562634,0.676555,0.524587,0.331912
|tfbs_overrepresentation_for_novel_motifs=1.01838,1.66496,0.367606,0.434198,0.260188,0.448401,1.33049,0.173246,1.02512,2.00573,1.23792,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.620214,0.332107,0.0622758,1.35437,0.258745,0.374936,0.577606,0.153291,1.18318,0.818708,0.376624,0.455168,0.843667,0.250677,0.425071,1.38756,0.0711618,1.26012,1.29755,0.631914,1.08217,0.256422,0.460258,0.204736,0.27776,1.7835,1.08432,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,1.37128,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.560836,0.713876,1.39465,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.527912,1.31587,1.03623,3.4185,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,5.69681,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,2.07611,0.62322,0.202284,0.1711,0.859272,0.663249,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,1.61924,0.333829,0.386136,0.96962,0.895335,0.499714,1.21576,0.254749,4.16154,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,2.85877,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,4.84212,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,1.76938,0.714896,0.562634,0.676555,0.524587,0.331912
|tfbs_overrepresentation_jaspar=MA0003.1;4.08339,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;1.89281,MA0009.1;0.870101,MA0014.1;1.16295,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.769859,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;1.66702,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;2.12384,MA0056.1;0,MA0057.1;0.31126,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;0.657844,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;1.91384,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;0.229377,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;0.747001,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;2.22005,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.900473,MA0146.1;0.946874,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;1.07211,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;1.64215,MA0047.2;0.576767,MA0112.2;1.87605,MA0065.2;0.247168,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.330759,MA0155.1;0.978338,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;1.276,MA0160.1;0.453546,MA0161.1;0,MA0162.1;6.08859,MA0163.1;3.9264,MA0164.1;0.551114,MA0080.2;0.816435,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;3.21994,MA0102.2;1.59466,MA0258.1;1.78339,MA0259.1;0.643936,MA0442.1;0
}}
}}

Revision as of 12:37, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:50753132..50753192,-p1@Sorcs1
Mm9::chr19:50753202..50753223,-p2@Sorcs1
Mm9::chr1:168931170..168931202,+p1@Fam78b
Mm9::chr5:112658087..112658107,-p5@Miat
Mm9::chr7:38557752..38557793,-p3@Zfp536
Mm9::chr9:47338426..47338445,+p1@Cadm1
Mm9::chr9:62384812..62384823,-p8@Coro2b
Mm9::chr9:62384843..62384868,-p3@Coro2b


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:0042271susceptibility to natural killer cell mediated cytotoxicity0.0459669089702543
GO:0016338calcium-independent cell-cell adhesion0.0459669089702543
GO:0045954positive regulation of natural killer cell mediated cytotoxicity0.0459669089702543
GO:0030165PDZ domain binding0.0459669089702543
GO:0042269regulation of natural killer cell mediated cytotoxicity0.0459669089702543
GO:0001912positive regulation of leukocyte mediated cytotoxicity0.0459669089702543
GO:0008022protein C-terminus binding0.0459669089702543
GO:0042267natural killer cell mediated cytotoxicity0.0459669089702543
GO:0001910regulation of leukocyte mediated cytotoxicity0.0459669089702543
GO:0031341regulation of cell killing0.0459669089702543
GO:0002228natural killer cell mediated immunity0.0459669089702543
GO:0007416synaptogenesis0.0494115251264313
GO:0001906cell killing0.0494115251264313
GO:0007157heterophilic cell adhesion0.0494115251264313
GO:0001909leukocyte mediated cytotoxicity0.0494115251264313



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
ectoderm-derived structure8.14e-3895
ectoderm8.14e-3895
presumptive ectoderm8.14e-3895
nervous system4.57e-3575
central nervous system5.75e-3473
neurectoderm2.28e-2964
neural plate2.28e-2964
presumptive neural plate2.28e-2964
ecto-epithelium6.67e-2873
structure with developmental contribution from neural crest9.32e-2492
regional part of nervous system8.45e-2354
pre-chordal neural plate1.03e-2249
neural tube8.13e-2252
neural rod8.13e-2252
future spinal cord8.13e-2252
neural keel8.13e-2252
brain2.47e-1947
future brain2.47e-1947
regional part of brain6.93e-1946
anterior neural tube1.16e-1740
regional part of forebrain4.59e-1739
forebrain4.59e-1739
future forebrain4.59e-1739
gray matter9.76e-1634
brain grey matter1.27e-1329
regional part of telencephalon1.27e-1329
telencephalon1.27e-1329
multi-cellular organism2.85e-10333
cerebral cortex1.56e-0921
cerebral hemisphere1.56e-0921
pallium1.56e-0921
embryo1.68e-08320
tube2.30e-08114
peripheral nervous system3.46e-0811
anatomical conduit4.53e-08122
regional part of cerebral cortex4.99e-0817
autonomic nervous system1.90e-079


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)
MA0003.14.08339
MA0004.10.434673
MA0006.10.271714
MA0007.11.89281
MA0009.10.870101
MA0014.11.16295
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
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
MA0048.11.66702
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.12.12384
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.657844
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.11.91384
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
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
MA0116.10.747001
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
MA0139.12.22005
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.900473
MA0146.10.946874
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.21.07211
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.21.64215
MA0047.20.576767
MA0112.21.87605
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.978338
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.11.276
MA0160.10.453546
MA0161.10
MA0162.16.08859
MA0163.13.9264
MA0164.10.551114
MA0080.20.816435
MA0018.20.560731
MA0099.20.669311
MA0079.23.21994
MA0102.21.59466
MA0258.11.78339
MA0259.10.643936
MA0442.10
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