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MCL coexpression mm9:964: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!4.08e-33!73;UBERON:0001016!4.11e-31!75;UBERON:0002346!9.78e-27!64;UBERON:0003075!9.78e-27!64;UBERON:0007284!9.78e-27!64;UBERON:0004121!4.15e-26!95;UBERON:0000924!4.15e-26!95;UBERON:0006601!4.15e-26!95;UBERON:0000073!8.96e-25!54;UBERON:0001049!2.50e-23!52;UBERON:0005068!2.50e-23!52;UBERON:0006241!2.50e-23!52;UBERON:0007135!2.50e-23!52;UBERON:0010371!7.20e-22!73;UBERON:0003056!2.60e-21!49;UBERON:0010314!7.26e-21!92;UBERON:0000955!3.19e-20!47;UBERON:0006238!3.19e-20!47;UBERON:0002616!8.89e-20!46;UBERON:0003080!8.56e-19!40;UBERON:0002780!3.25e-18!39;UBERON:0001890!3.25e-18!39;UBERON:0006240!3.25e-18!39;UBERON:0002020!4.68e-15!34;UBERON:0003528!5.20e-12!29;UBERON:0002791!5.20e-12!29;UBERON:0001893!5.20e-12!29;UBERON:0000956!1.21e-07!21;UBERON:0001869!1.21e-07!21;UBERON:0000203!1.21e-07!21;UBERON:0001894!1.93e-07!10;UBERON:0006222!1.93e-07!10
|ontology_enrichment_uberon=UBERON:0001017!4.08e-33!73;UBERON:0001016!4.11e-31!75;UBERON:0002346!9.78e-27!64;UBERON:0003075!9.78e-27!64;UBERON:0007284!9.78e-27!64;UBERON:0004121!4.15e-26!95;UBERON:0000924!4.15e-26!95;UBERON:0006601!4.15e-26!95;UBERON:0000073!8.96e-25!54;UBERON:0001049!2.50e-23!52;UBERON:0005068!2.50e-23!52;UBERON:0006241!2.50e-23!52;UBERON:0007135!2.50e-23!52;UBERON:0010371!7.20e-22!73;UBERON:0003056!2.60e-21!49;UBERON:0010314!7.26e-21!92;UBERON:0000955!3.19e-20!47;UBERON:0006238!3.19e-20!47;UBERON:0002616!8.89e-20!46;UBERON:0003080!8.56e-19!40;UBERON:0002780!3.25e-18!39;UBERON:0001890!3.25e-18!39;UBERON:0006240!3.25e-18!39;UBERON:0002020!4.68e-15!34;UBERON:0003528!5.20e-12!29;UBERON:0002791!5.20e-12!29;UBERON:0001893!5.20e-12!29;UBERON:0000956!1.21e-07!21;UBERON:0001869!1.21e-07!21;UBERON:0000203!1.21e-07!21;UBERON:0001894!1.93e-07!10;UBERON:0006222!1.93e-07!10
|tfbs_overrepresentation_for_novel_motifs=2.69985,0.534222,0.367606,0.434198,0.260188,0.448401,1.33049,0.515265,3.06731,0.687027,2.14309,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.620214,0.332107,0.223663,1.35437,0.258745,1.73827,0.577606,0.466037,1.18318,1.48474,0.757024,1.15331,0.843667,0.250677,0.839887,0.757987,0.0153121,0.242032,0.522578,0.221921,0.195877,0.256422,0.460258,1.19668,0.27776,0.0183213,0.423266,0.662995,0.484612,0.687215,0.825035,1.72213,0.604356,1.2032,0.985264,1.00271,0.557354,0.314394,1.27827,0.145699,0.555328,0.823643,2.53214,0.192045,1.6988,2.38538,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,1.37807,0.813951,0.136938,0.651651,0.806481,0.892913,0.179489,0.759925,0.612313,0.167672,0.920903,0.789543,0.540827,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,2.02719,0.784351,3.10425,0.340849,0.333829,0.386136,0.96962,1.60656,0.499714,1.21576,0.254749,3.5137,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,4.33735,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,1.83663,5.71866,0.120154,0.780212,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,1.76938,0.714896,0.562634,0.676555,0.524587,0.558175
|tfbs_overrepresentation_for_novel_motifs=2.69985,0.534222,0.367606,0.434198,0.260188,0.448401,1.33049,0.515265,3.06731,0.687027,2.14309,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.620214,0.332107,0.223663,1.35437,0.258745,1.73827,0.577606,0.466037,1.18318,1.48474,0.757024,1.15331,0.843667,0.250677,0.839887,0.757987,0.0153121,0.242032,0.522578,0.221921,0.195877,0.256422,0.460258,1.19668,0.27776,0.0183213,0.423266,0.662995,0.484612,0.687215,0.825035,1.72213,0.604356,1.2032,0.985264,1.00271,0.557354,0.314394,1.27827,0.145699,0.555328,0.823643,2.53214,0.192045,1.6988,2.38538,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,1.37807,0.813951,0.136938,0.651651,0.806481,0.892913,0.179489,0.759925,0.612313,0.167672,0.920903,0.789543,0.540827,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,2.02719,0.784351,3.10425,0.340849,0.333829,0.386136,0.96962,1.60656,0.499714,1.21576,0.254749,3.5137,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,4.33735,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,1.83663,5.71866,0.120154,0.780212,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,1.76938,0.714896,0.562634,0.676555,0.524587,0.558175
|tfbs_overrepresentation_jaspar=MA0003.1;0.848341,MA0004.1;0.434673,MA0006.1;0.747445,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;0.769859,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;0.335404,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;1.2091,MA0056.1;0,MA0057.1;0.643187,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;2.42557,MA0061.1;0.638933,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;1.09399,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;1.38205,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;1.03628,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;1.33477,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;0.27152,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;2.75555,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;1.55504,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;0.385068,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.84271,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;0.90045,MA0065.2;0.528619,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;2.00864,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.71453,MA0163.1;0.0836563,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.685525,MA0102.2;1.59466,MA0258.1;1.13923,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:35, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:75911305..75911323,-p2@Puf60
Mm9::chr15:84388184..84388203,-p3@Ldoc1l
Mm9::chr17:23923013..23923050,-p1@Flywch2
Mm9::chr4:155366713..155366783,-p1@B3galt6
Mm9::chr9:108480925..108480987,-p1@Wdr6
Mm9::chr9:108480988..108481006,-p2@Wdr6
Mm9::chr9:108481008..108481022,-p4@Wdr6
Mm9::chr9:108481032..108481052,-p3@Wdr6


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
central nervous system4.08e-3373
nervous system4.11e-3175
neurectoderm9.78e-2764
neural plate9.78e-2764
presumptive neural plate9.78e-2764
ectoderm-derived structure4.15e-2695
ectoderm4.15e-2695
presumptive ectoderm4.15e-2695
regional part of nervous system8.96e-2554
neural tube2.50e-2352
neural rod2.50e-2352
future spinal cord2.50e-2352
neural keel2.50e-2352
ecto-epithelium7.20e-2273
pre-chordal neural plate2.60e-2149
structure with developmental contribution from neural crest7.26e-2192
brain3.19e-2047
future brain3.19e-2047
regional part of brain8.89e-2046
anterior neural tube8.56e-1940
regional part of forebrain3.25e-1839
forebrain3.25e-1839
future forebrain3.25e-1839
gray matter4.68e-1534
brain grey matter5.20e-1229
regional part of telencephalon5.20e-1229
telencephalon5.20e-1229
cerebral cortex1.21e-0721
cerebral hemisphere1.21e-0721
pallium1.21e-0721
diencephalon1.93e-0710
future diencephalon1.93e-0710


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)
MA0003.10.848341
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.325341
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
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
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.2091
MA0056.10
MA0057.10.643187
MA0058.10.341628
MA0059.10.353484
MA0060.12.42557
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.11.09399
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.11.38205
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
MA0090.11.03628
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.11.33477
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.12.75555
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.11.55504
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.246409
MA0146.10.385068
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.84271
MA0035.20.524137
MA0039.20.144815
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.90045
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.12.00864
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.688775
MA0160.10.453546
MA0161.10
MA0162.10.71453
MA0163.10.0836563
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.685525
MA0102.21.59466
MA0258.11.13923
MA0259.10.227035
MA0442.10
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