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MCL coexpression mm9:958: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!1.78e-32!75;UBERON:0001017!4.38e-32!73;UBERON:0000073!4.41e-26!54;UBERON:0001049!1.01e-24!52;UBERON:0005068!1.01e-24!52;UBERON:0006241!1.01e-24!52;UBERON:0007135!1.01e-24!52;UBERON:0002020!3.98e-24!34;UBERON:0002346!6.84e-24!64;UBERON:0003075!6.84e-24!64;UBERON:0007284!6.84e-24!64;UBERON:0004121!9.13e-24!95;UBERON:0000924!9.13e-24!95;UBERON:0006601!9.13e-24!95;UBERON:0003080!7.39e-22!40;UBERON:0002780!3.68e-21!39;UBERON:0001890!3.68e-21!39;UBERON:0006240!3.68e-21!39;UBERON:0000955!5.79e-21!47;UBERON:0006238!5.79e-21!47;UBERON:0002616!3.04e-20!46;UBERON:0003528!3.69e-20!29;UBERON:0002791!3.69e-20!29;UBERON:0001893!3.69e-20!29;UBERON:0003056!4.78e-19!49;UBERON:0010371!5.19e-19!73;UBERON:0010314!4.35e-14!92;UBERON:0000956!5.20e-14!21;UBERON:0001869!5.20e-14!21;UBERON:0000203!5.20e-14!21;UBERON:0002619!2.36e-11!17;UBERON:0002021!2.54e-09!10;UBERON:0000411!2.54e-09!10;UBERON:0001950!2.54e-09!10;UBERON:0002420!2.32e-07!8;UBERON:0007245!2.32e-07!8;UBERON:0010009!2.32e-07!8;UBERON:0010011!2.32e-07!8;UBERON:0000454!2.32e-07!8
|ontology_enrichment_uberon=UBERON:0001016!1.78e-32!75;UBERON:0001017!4.38e-32!73;UBERON:0000073!4.41e-26!54;UBERON:0001049!1.01e-24!52;UBERON:0005068!1.01e-24!52;UBERON:0006241!1.01e-24!52;UBERON:0007135!1.01e-24!52;UBERON:0002020!3.98e-24!34;UBERON:0002346!6.84e-24!64;UBERON:0003075!6.84e-24!64;UBERON:0007284!6.84e-24!64;UBERON:0004121!9.13e-24!95;UBERON:0000924!9.13e-24!95;UBERON:0006601!9.13e-24!95;UBERON:0003080!7.39e-22!40;UBERON:0002780!3.68e-21!39;UBERON:0001890!3.68e-21!39;UBERON:0006240!3.68e-21!39;UBERON:0000955!5.79e-21!47;UBERON:0006238!5.79e-21!47;UBERON:0002616!3.04e-20!46;UBERON:0003528!3.69e-20!29;UBERON:0002791!3.69e-20!29;UBERON:0001893!3.69e-20!29;UBERON:0003056!4.78e-19!49;UBERON:0010371!5.19e-19!73;UBERON:0010314!4.35e-14!92;UBERON:0000956!5.20e-14!21;UBERON:0001869!5.20e-14!21;UBERON:0000203!5.20e-14!21;UBERON:0002619!2.36e-11!17;UBERON:0002021!2.54e-09!10;UBERON:0000411!2.54e-09!10;UBERON:0001950!2.54e-09!10;UBERON:0002420!2.32e-07!8;UBERON:0007245!2.32e-07!8;UBERON:0010009!2.32e-07!8;UBERON:0010011!2.32e-07!8;UBERON:0000454!2.32e-07!8
|tfbs_overrepresentation_for_novel_motifs=1.01838,0.289542,0.96259,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,0.386846,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.0622758,0.549359,0.717658,0.374936,1.41403,0.909128,0.469052,0.303071,0.757024,0.455168,0.843667,0.250677,0.136998,0.276324,0.0711618,0.678971,0.522578,0.221921,0.570041,0.256422,0.460258,0.0558565,0.761266,0.0824666,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.732634,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,1.9158,1.34113,0.922232,0.178433,0.872563,1.03623,0.140213,0.409836,0.136938,1.56933,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,0.108172,0.123242,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.62322,0.202284,0.982739,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.340849,0.333829,1.00333,0.96962,0.895335,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,1.35892,0.950857,0.427043,1.10792,0.570914,1.23736,4.28091,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.120154,2.79776,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0131724
|tfbs_overrepresentation_for_novel_motifs=1.01838,0.289542,0.96259,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,0.386846,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.0622758,0.549359,0.717658,0.374936,1.41403,0.909128,0.469052,0.303071,0.757024,0.455168,0.843667,0.250677,0.136998,0.276324,0.0711618,0.678971,0.522578,0.221921,0.570041,0.256422,0.460258,0.0558565,0.761266,0.0824666,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.732634,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,1.9158,1.34113,0.922232,0.178433,0.872563,1.03623,0.140213,0.409836,0.136938,1.56933,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,0.108172,0.123242,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.62322,0.202284,0.982739,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.340849,0.333829,1.00333,0.96962,0.895335,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,1.35892,0.950857,0.427043,1.10792,0.570914,1.23736,4.28091,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.120154,2.79776,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0131724
|tfbs_overrepresentation_jaspar=MA0003.1;0.127295,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.325341,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;0.685543,MA0050.1;0.472794,MA0051.1;2.44382,MA0052.1;0.890676,MA0055.1;0.282934,MA0056.1;0,MA0057.1;1.58436,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.638933,MA0063.1;0,MA0066.1;2.37953,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;10.8357,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.980744,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.49616,MA0089.1;0,MA0090.1;0.401197,MA0091.1;1.13691,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.41549,MA0106.1;0.626997,MA0107.1;0.814533,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;1.45892,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;1.63575,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;0.246409,MA0146.1;0.0169049,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.402847,MA0138.2;1.61926,MA0002.2;0.513194,MA0137.2;0.32312,MA0104.2;0.18504,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;0.100744,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;0.230918,MA0163.1;1.36861,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;3.21994,MA0102.2;1.59466,MA0258.1;2.51672,MA0259.1;0.643936,MA0442.1;0
}}
}}

Revision as of 12:35, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:77556637..77556650,+p2@Enox1
Mm9::chr1:160292549..160292559,+p9@Astn1
Mm9::chr3:118132959..118132992,+p@chr3:118132959..118132992
+
Mm9::chr3:118133217..118133286,+p@chr3:118133217..118133286
+
Mm9::chr3:118134337..118134383,+p@chr3:118134337..118134383
+
Mm9::chr3:118134411..118134437,+p@chr3:118134411..118134437
+
Mm9::chr3:118134444..118134456,+p@chr3:118134444..118134456
+
Mm9::chr6:138371615..138371665,-p3@Lmo3


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>

Uber Anatomy
Ontology termp-valuen
nervous system1.78e-3275
central nervous system4.38e-3273
regional part of nervous system4.41e-2654
neural tube1.01e-2452
neural rod1.01e-2452
future spinal cord1.01e-2452
neural keel1.01e-2452
gray matter3.98e-2434
neurectoderm6.84e-2464
neural plate6.84e-2464
presumptive neural plate6.84e-2464
ectoderm-derived structure9.13e-2495
ectoderm9.13e-2495
presumptive ectoderm9.13e-2495
anterior neural tube7.39e-2240
regional part of forebrain3.68e-2139
forebrain3.68e-2139
future forebrain3.68e-2139
brain5.79e-2147
future brain5.79e-2147
regional part of brain3.04e-2046
brain grey matter3.69e-2029
regional part of telencephalon3.69e-2029
telencephalon3.69e-2029
pre-chordal neural plate4.78e-1949
ecto-epithelium5.19e-1973
structure with developmental contribution from neural crest4.35e-1492
cerebral cortex5.20e-1421
cerebral hemisphere5.20e-1421
pallium5.20e-1421
regional part of cerebral cortex2.36e-1117
occipital lobe2.54e-0910
visual cortex2.54e-0910
neocortex2.54e-0910
basal ganglion2.32e-078
nuclear complex of neuraxis2.32e-078
aggregate regional part of brain2.32e-078
collection of basal ganglia2.32e-078
cerebral subcortex2.32e-078


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)
MA0003.10.127295
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.325341
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
MA0048.10.685543
MA0050.10.472794
MA0051.12.44382
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.11.58436
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.638933
MA0063.10
MA0066.12.37953
MA0067.11.21448
MA0068.10.657844
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.110.8357
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.11.13691
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.10.814533
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.11.45892
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
MA0131.11.63575
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
MA0145.10.246409
MA0146.10.0169049
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.402847
MA0138.21.61926
MA0002.20.513194
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.21.87605
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
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
MA0162.10.230918
MA0163.11.36861
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.23.21994
MA0102.21.59466
MA0258.12.51672
MA0259.10.643936
MA0442.10
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