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MCL coexpression mm9:992: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002346!5.47e-18!64;UBERON:0003075!5.47e-18!64;UBERON:0007284!5.47e-18!64;UBERON:0003056!6.43e-18!49;UBERON:0010371!1.21e-13!73;UBERON:0000073!3.45e-13!54;UBERON:0001049!2.26e-12!52;UBERON:0005068!2.26e-12!52;UBERON:0006241!2.26e-12!52;UBERON:0007135!2.26e-12!52;UBERON:0003080!3.24e-12!40;UBERON:0000955!3.76e-12!47;UBERON:0006238!3.76e-12!47;UBERON:0002780!1.28e-11!39;UBERON:0001890!1.28e-11!39;UBERON:0006240!1.28e-11!39;UBERON:0002616!1.49e-11!46;UBERON:0004121!1.52e-10!95;UBERON:0000924!1.52e-10!95;UBERON:0006601!1.52e-10!95;UBERON:0002021!1.78e-10!10;UBERON:0000411!1.78e-10!10;UBERON:0001950!1.78e-10!10;UBERON:0001017!3.23e-10!73;UBERON:0001016!1.45e-09!75;UBERON:0002020!2.63e-09!34;UBERON:0003528!3.69e-09!29;UBERON:0002791!3.69e-09!29;UBERON:0001893!3.69e-09!29;UBERON:0010314!1.89e-08!92;UBERON:0002619!7.56e-08!17;UBERON:0002048!2.31e-07!14;UBERON:0000117!2.31e-07!14;UBERON:0000171!2.31e-07!14;UBERON:0000170!2.31e-07!14;UBERON:0005597!2.31e-07!14;UBERON:0000118!2.31e-07!14;UBERON:0000025!2.59e-07!114;UBERON:0000970!3.17e-07!9;UBERON:0000019!3.17e-07!9;UBERON:0000047!3.17e-07!9;UBERON:0010312!3.17e-07!9;UBERON:0004088!3.17e-07!9;UBERON:0002104!3.17e-07!9;UBERON:0001456!3.17e-07!9;UBERON:0003072!3.17e-07!9;UBERON:0004128!3.17e-07!9;UBERON:0003071!3.17e-07!9
|ontology_enrichment_uberon=UBERON:0002346!5.47e-18!64;UBERON:0003075!5.47e-18!64;UBERON:0007284!5.47e-18!64;UBERON:0003056!6.43e-18!49;UBERON:0010371!1.21e-13!73;UBERON:0000073!3.45e-13!54;UBERON:0001049!2.26e-12!52;UBERON:0005068!2.26e-12!52;UBERON:0006241!2.26e-12!52;UBERON:0007135!2.26e-12!52;UBERON:0003080!3.24e-12!40;UBERON:0000955!3.76e-12!47;UBERON:0006238!3.76e-12!47;UBERON:0002780!1.28e-11!39;UBERON:0001890!1.28e-11!39;UBERON:0006240!1.28e-11!39;UBERON:0002616!1.49e-11!46;UBERON:0004121!1.52e-10!95;UBERON:0000924!1.52e-10!95;UBERON:0006601!1.52e-10!95;UBERON:0002021!1.78e-10!10;UBERON:0000411!1.78e-10!10;UBERON:0001950!1.78e-10!10;UBERON:0001017!3.23e-10!73;UBERON:0001016!1.45e-09!75;UBERON:0002020!2.63e-09!34;UBERON:0003528!3.69e-09!29;UBERON:0002791!3.69e-09!29;UBERON:0001893!3.69e-09!29;UBERON:0010314!1.89e-08!92;UBERON:0002619!7.56e-08!17;UBERON:0002048!2.31e-07!14;UBERON:0000117!2.31e-07!14;UBERON:0000171!2.31e-07!14;UBERON:0000170!2.31e-07!14;UBERON:0005597!2.31e-07!14;UBERON:0000118!2.31e-07!14;UBERON:0000025!2.59e-07!114;UBERON:0000970!3.17e-07!9;UBERON:0000019!3.17e-07!9;UBERON:0000047!3.17e-07!9;UBERON:0010312!3.17e-07!9;UBERON:0004088!3.17e-07!9;UBERON:0002104!3.17e-07!9;UBERON:0001456!3.17e-07!9;UBERON:0003072!3.17e-07!9;UBERON:0004128!3.17e-07!9;UBERON:0003071!3.17e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.181564,0.170907,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.0887261,0.883862,0.223663,0.549359,0.717658,0.374936,0.577606,0.909128,0.469052,0.303071,0.376624,0.455168,0.843667,0.250677,0.136998,0.276324,0.0153121,0.242032,0.522578,0.631914,0.195877,1.31403,0.460258,0.784847,0.761266,0.209497,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.844204,0.513517,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.140213,0.131016,0.136938,0.651651,0.806481,0.336166,0.530481,0.759925,1.48701,0.167672,0.920903,0.025519,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,0.202284,0.510015,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,1.47241,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,1.38244,0.240994,0.524587,0.0131724
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.181564,0.170907,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.0887261,0.883862,0.223663,0.549359,0.717658,0.374936,0.577606,0.909128,0.469052,0.303071,0.376624,0.455168,0.843667,0.250677,0.136998,0.276324,0.0153121,0.242032,0.522578,0.631914,0.195877,1.31403,0.460258,0.784847,0.761266,0.209497,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.844204,0.513517,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.140213,0.131016,0.136938,0.651651,0.806481,0.336166,0.530481,0.759925,1.48701,0.167672,0.920903,0.025519,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,0.202284,0.510015,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.143112,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,1.47241,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,1.38244,0.240994,0.524587,0.0131724
|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;0.012738,MA0017.1;0.804572,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;2.54725,MA0042.1;1.64499,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;2.06291,MA0055.1;0.0283571,MA0056.1;0,MA0057.1;0.0935008,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;0.577203,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;2.21686,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.064239,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;0.307078,MA0105.1;0.41549,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;0.633896,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;0.527241,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;0.144815,MA0138.2;0.675599,MA0002.2;0.513194,MA0137.2;0.32312,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.2464,MA0065.2;0.247168,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.579465,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;1.35808,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.431684,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:38, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr3:28981461..28981512,+p1@Egfem1
Mm9::chr3:29008723..29008729,+p@chr3:29008723..29008729
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Mm9::chr3:29053140..29053148,+p@chr3:29053140..29053148
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Mm9::chr3:29097690..29097692,+p@chr3:29097690..29097692
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Mm9::chr3:29134849..29134853,+p@chr3:29134849..29134853
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Mm9::chr3:29159921..29159925,+p@chr3:29159921..29159925
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Mm9::chr3:29276778..29276782,+p@chr3:29276778..29276782
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Mm9::chr3:29440815..29440817,+p@chr3:29440815..29440817
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neurectoderm5.47e-1864
neural plate5.47e-1864
presumptive neural plate5.47e-1864
pre-chordal neural plate6.43e-1849
ecto-epithelium1.21e-1373
regional part of nervous system3.45e-1354
neural tube2.26e-1252
neural rod2.26e-1252
future spinal cord2.26e-1252
neural keel2.26e-1252
anterior neural tube3.24e-1240
brain3.76e-1247
future brain3.76e-1247
regional part of forebrain1.28e-1139
forebrain1.28e-1139
future forebrain1.28e-1139
regional part of brain1.49e-1146
ectoderm-derived structure1.52e-1095
ectoderm1.52e-1095
presumptive ectoderm1.52e-1095
occipital lobe1.78e-1010
visual cortex1.78e-1010
neocortex1.78e-1010
central nervous system3.23e-1073
nervous system1.45e-0975
gray matter2.63e-0934
brain grey matter3.69e-0929
regional part of telencephalon3.69e-0929
telencephalon3.69e-0929
structure with developmental contribution from neural crest1.89e-0892
regional part of cerebral cortex7.56e-0817
lung2.31e-0714
respiratory tube2.31e-0714
respiration organ2.31e-0714
pair of lungs2.31e-0714
lung primordium2.31e-0714
lung bud2.31e-0714
tube2.59e-07114
eye3.17e-079
camera-type eye3.17e-079
simple eye3.17e-079
immature eye3.17e-079
ocular region3.17e-079
visual system3.17e-079
face3.17e-079
optic cup3.17e-079
optic vesicle3.17e-079
eye primordium3.17e-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)
MA0003.10.127295
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.012738
MA0017.10.804572
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
MA0041.12.54725
MA0042.11.64499
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.12.06291
MA0055.10.0283571
MA0056.10
MA0057.10.0935008
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
MA0073.10.577203
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.12.21686
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.633896
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
MA0145.10.527241
MA0146.10.0169049
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.144815
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.2464
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.579465
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.11.36861
MA0164.11.35808
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.431684
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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