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MCL coexpression mm9:969: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002346!9.67e-30!64;UBERON:0003075!9.67e-30!64;UBERON:0007284!9.67e-30!64;UBERON:0000073!2.99e-25!54;UBERON:0003056!7.32e-25!49;UBERON:0010371!8.72e-24!73;UBERON:0001049!1.73e-23!52;UBERON:0005068!1.73e-23!52;UBERON:0006241!1.73e-23!52;UBERON:0007135!1.73e-23!52;UBERON:0004121!1.35e-21!95;UBERON:0000924!1.35e-21!95;UBERON:0006601!1.35e-21!95;UBERON:0001017!2.56e-20!73;UBERON:0002020!3.50e-20!34;UBERON:0001016!2.53e-19!75;UBERON:0000955!2.54e-19!47;UBERON:0006238!2.54e-19!47;UBERON:0002616!1.94e-18!46;UBERON:0003080!9.25e-17!40;UBERON:0010314!5.91e-16!92;UBERON:0003528!5.98e-16!29;UBERON:0002791!5.98e-16!29;UBERON:0001893!5.98e-16!29;UBERON:0002780!6.87e-16!39;UBERON:0001890!6.87e-16!39;UBERON:0006240!6.87e-16!39;UBERON:0000956!4.12e-12!21;UBERON:0001869!4.12e-12!21;UBERON:0000203!4.12e-12!21;UBERON:0002021!1.08e-11!10;UBERON:0000411!1.08e-11!10;UBERON:0001950!1.08e-11!10;UBERON:0002619!4.64e-10!17;UBERON:0000970!1.38e-09!9;UBERON:0000019!1.38e-09!9;UBERON:0000047!1.38e-09!9;UBERON:0010312!1.38e-09!9;UBERON:0004088!1.38e-09!9;UBERON:0002104!1.38e-09!9;UBERON:0001456!1.38e-09!9;UBERON:0003072!1.38e-09!9;UBERON:0004128!1.38e-09!9;UBERON:0003071!1.38e-09!9;UBERON:0003076!2.10e-07!12;UBERON:0003057!2.10e-07!12;UBERON:0001444!2.59e-07!11
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.0293268,0.96259,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,0.170907,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.938682,0.29826,0.332107,0.223663,0.549359,0.258745,0.374936,0.577606,0.153291,1.18318,0.818708,0.118137,1.15331,0.843667,0.250677,0.136998,0.276324,0.363049,1.26012,0.522578,1.1836,0.570041,0.256422,0.460258,0.0558565,2.13761,0.0183213,0.423266,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.732634,0.985264,1.00271,1.37128,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.853709,0.409836,0.136938,0.651651,0.806481,0.336166,1.01677,0.759925,0.612313,1.54237,0.920903,0.025519,0.0299392,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.982739,0.859272,0.663249,0.101559,0.242106,0.843387,2.22052,0.725721,0.724668,0.459825,0.784351,0.480639,1.61924,0.333829,0.386136,0.96962,0.337254,1.24884,1.21576,0.708441,0.143112,0.437894,0.743872,0.238599,1.04163,2.78555,0.579418,0.650748,2.83289,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,1.44306,0.854131,0.718197,1.16523,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.0131724
|tfbs_overrepresentation_jaspar=MA0003.1;0.016751,MA0004.1;0.434673,MA0006.1;0.747445,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.012738,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;0.282934,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;1.86175,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;1.1212e-05,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;1.82869,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.950493,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;1.47808,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;0.0169049,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;1.30087,MA0039.2;0.027551,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.863775,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.247168,MA0150.1;0.419883,MA0151.1;0,MA0152.1;2.41287,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.0804339,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0925951,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 16:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:75092778..75092797,-p@chr16:75092778..75092797
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Mm9::chr16:75092941..75092951,-p@chr16:75092941..75092951
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Mm9::chr16:75092999..75093018,-p@chr16:75092999..75093018
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Mm9::chr16:75093062..75093088,-p@chr16:75093062..75093088
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Mm9::chr19:19185697..19185711,-p2@Rorb
Mm9::chr3:25739800..25739804,-p@chr3:25739800..25739804
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Mm9::chr3:26052879..26052916,-p@chr3:26052879..26052916
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Mm9::chr3:26052917..26052928,-p@chr3:26052917..26052928
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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

no results for this coexpression

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)1.23e-1223
neuroblast (sensu Vertebrata)1.23e-1223
neuron7.06e-0733
neuronal stem cell7.06e-0733
neuroblast7.06e-0733
electrically signaling cell7.06e-0733

Uber Anatomy
Ontology termp-valuen
neurectoderm9.67e-3064
neural plate9.67e-3064
presumptive neural plate9.67e-3064
regional part of nervous system2.99e-2554
pre-chordal neural plate7.32e-2549
ecto-epithelium8.72e-2473
neural tube1.73e-2352
neural rod1.73e-2352
future spinal cord1.73e-2352
neural keel1.73e-2352
ectoderm-derived structure1.35e-2195
ectoderm1.35e-2195
presumptive ectoderm1.35e-2195
central nervous system2.56e-2073
gray matter3.50e-2034
nervous system2.53e-1975
brain2.54e-1947
future brain2.54e-1947
regional part of brain1.94e-1846
anterior neural tube9.25e-1740
structure with developmental contribution from neural crest5.91e-1692
brain grey matter5.98e-1629
regional part of telencephalon5.98e-1629
telencephalon5.98e-1629
regional part of forebrain6.87e-1639
forebrain6.87e-1639
future forebrain6.87e-1639
cerebral cortex4.12e-1221
cerebral hemisphere4.12e-1221
pallium4.12e-1221
occipital lobe1.08e-1110
visual cortex1.08e-1110
neocortex1.08e-1110
regional part of cerebral cortex4.64e-1017
eye1.38e-099
camera-type eye1.38e-099
simple eye1.38e-099
immature eye1.38e-099
ocular region1.38e-099
visual system1.38e-099
face1.38e-099
optic cup1.38e-099
optic vesicle1.38e-099
eye primordium1.38e-099
posterior neural tube2.10e-0712
chordal neural plate2.10e-0712
subdivision of head2.59e-0711


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
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.012738
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
MA0055.10.282934
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.11.86175
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.11.1212e-05
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
MA0090.11.82869
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.950493
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.11.47808
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
MA0146.10.0169049
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.21.30087
MA0039.20.027551
MA0138.20.675599
MA0002.20.172399
MA0137.20.863775
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.12.41287
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0925951
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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