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MCL coexpression mm9:2365: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004121!2.50e-25!95;UBERON:0000924!2.50e-25!95;UBERON:0006601!2.50e-25!95;UBERON:0001016!8.48e-22!75;UBERON:0001017!4.54e-21!73;UBERON:0010371!5.43e-18!73;UBERON:0002346!1.14e-14!64;UBERON:0003075!1.14e-14!64;UBERON:0007284!1.14e-14!64;UBERON:0003056!7.22e-13!49;UBERON:0000073!1.15e-12!54;UBERON:0010314!1.61e-12!92;UBERON:0002780!1.63e-12!39;UBERON:0001890!1.63e-12!39;UBERON:0006240!1.63e-12!39;UBERON:0003080!1.90e-12!40;UBERON:0001049!2.13e-12!52;UBERON:0005068!2.13e-12!52;UBERON:0006241!2.13e-12!52;UBERON:0007135!2.13e-12!52;UBERON:0000955!1.51e-11!47;UBERON:0006238!1.51e-11!47;UBERON:0002616!2.52e-11!46;UBERON:0002619!4.95e-11!17;UBERON:0002020!5.20e-10!34;UBERON:0003528!8.40e-09!29;UBERON:0002791!8.40e-09!29;UBERON:0001893!8.40e-09!29;UBERON:0000956!8.91e-09!21;UBERON:0001869!8.91e-09!21;UBERON:0000203!8.91e-09!21;UBERON:0002021!4.07e-08!10;UBERON:0000411!4.07e-08!10;UBERON:0001950!4.07e-08!10;UBERON:0000010!4.33e-07!11
|ontology_enrichment_uberon=UBERON:0004121!2.50e-25!95;UBERON:0000924!2.50e-25!95;UBERON:0006601!2.50e-25!95;UBERON:0001016!8.48e-22!75;UBERON:0001017!4.54e-21!73;UBERON:0010371!5.43e-18!73;UBERON:0002346!1.14e-14!64;UBERON:0003075!1.14e-14!64;UBERON:0007284!1.14e-14!64;UBERON:0003056!7.22e-13!49;UBERON:0000073!1.15e-12!54;UBERON:0010314!1.61e-12!92;UBERON:0002780!1.63e-12!39;UBERON:0001890!1.63e-12!39;UBERON:0006240!1.63e-12!39;UBERON:0003080!1.90e-12!40;UBERON:0001049!2.13e-12!52;UBERON:0005068!2.13e-12!52;UBERON:0006241!2.13e-12!52;UBERON:0007135!2.13e-12!52;UBERON:0000955!1.51e-11!47;UBERON:0006238!1.51e-11!47;UBERON:0002616!2.52e-11!46;UBERON:0002619!4.95e-11!17;UBERON:0002020!5.20e-10!34;UBERON:0003528!8.40e-09!29;UBERON:0002791!8.40e-09!29;UBERON:0001893!8.40e-09!29;UBERON:0000956!8.91e-09!21;UBERON:0001869!8.91e-09!21;UBERON:0000203!8.91e-09!21;UBERON:0002021!4.07e-08!10;UBERON:0000411!4.07e-08!10;UBERON:0001950!4.07e-08!10;UBERON:0000010!4.33e-07!11
|tfbs_overrepresentation_for_novel_motifs=0.641384,2.54893,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,1.72258,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,1.18815,1.54138,1.2563,4.18064,1.16474,0.786577,0.434783,4.81685,1.20358,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,2.48198,1.32691,3.2665,2.29987,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,3.9116,0.409166,0.961641,1.14445,0.938512,2.07187,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,1.42067,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,2.01759,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,1.4513,3.92024,1.27621,2.80848,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,3.32103
|tfbs_overrepresentation_for_novel_motifs=0.641384,2.54893,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,1.72258,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,1.18815,1.54138,1.2563,4.18064,1.16474,0.786577,0.434783,4.81685,1.20358,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,2.48198,1.32691,3.2665,2.29987,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,3.9116,0.409166,0.961641,1.14445,0.938512,2.07187,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,1.42067,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,2.01759,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,1.4513,3.92024,1.27621,2.80848,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,3.32103
|tfbs_overrepresentation_jaspar=MA0003.1;3.50387,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;2.01483,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;2.07944,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;6.60728,MA0056.1;0,MA0057.1;2.00447,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;1.04037,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.783927,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.608454,MA0146.1;1.07887,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;1.07321,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;1.0034,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;0.650923,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;2.31798,MA0163.1;0.672192,MA0164.1;1.91337,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;12.2643,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:45, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr3:143865264..143865309,-p3@Lmo4
Mm9::chr3:143865314..143865331,-p5@Lmo4
Mm9::chr3:143868129..143868172,-p1@Lmo4
Mm9::chr3:143868471..143868494,-p2@Lmo4


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
non-terminally differentiated cell3.12e-1349
ectodermal cell3.17e-1144
neurectodermal cell3.17e-1144
neural cell8.06e-1143
electrically responsive cell6.43e-0939
electrically active cell6.43e-0939
neuron9.74e-0733
neuronal stem cell9.74e-0733
neuroblast9.74e-0733
electrically signaling cell9.74e-0733

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.50e-2595
ectoderm2.50e-2595
presumptive ectoderm2.50e-2595
nervous system8.48e-2275
central nervous system4.54e-2173
ecto-epithelium5.43e-1873
neurectoderm1.14e-1464
neural plate1.14e-1464
presumptive neural plate1.14e-1464
pre-chordal neural plate7.22e-1349
regional part of nervous system1.15e-1254
structure with developmental contribution from neural crest1.61e-1292
regional part of forebrain1.63e-1239
forebrain1.63e-1239
future forebrain1.63e-1239
anterior neural tube1.90e-1240
neural tube2.13e-1252
neural rod2.13e-1252
future spinal cord2.13e-1252
neural keel2.13e-1252
brain1.51e-1147
future brain1.51e-1147
regional part of brain2.52e-1146
regional part of cerebral cortex4.95e-1117
gray matter5.20e-1034
brain grey matter8.40e-0929
regional part of telencephalon8.40e-0929
telencephalon8.40e-0929
cerebral cortex8.91e-0921
cerebral hemisphere8.91e-0921
pallium8.91e-0921
occipital lobe4.07e-0810
visual cortex4.07e-0810
neocortex4.07e-0810
peripheral nervous system4.33e-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)
MA0003.13.50387
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.12.01483
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.12.07944
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.16.60728
MA0056.10
MA0057.12.00447
MA0058.10.581673
MA0059.10.59559
MA0060.11.04037
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.783927
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.608454
MA0146.11.07887
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.21.07321
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.12.31798
MA0163.10.672192
MA0164.11.91337
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.212.2643
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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