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MCL coexpression mm9:1920: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!9.27e-18!54;UBERON:0001017!7.25e-17!73;UBERON:0001016!9.69e-17!75;UBERON:0001049!1.17e-16!52;UBERON:0005068!1.17e-16!52;UBERON:0006241!1.17e-16!52;UBERON:0007135!1.17e-16!52;UBERON:0000955!5.84e-15!47;UBERON:0006238!5.84e-15!47;UBERON:0002616!1.45e-14!46;UBERON:0004121!3.38e-14!95;UBERON:0000924!3.38e-14!95;UBERON:0006601!3.38e-14!95;UBERON:0002020!2.71e-13!34;UBERON:0003080!3.05e-12!40;UBERON:0007023!4.39e-12!51;UBERON:0003528!6.83e-12!29;UBERON:0002791!6.83e-12!29;UBERON:0001893!6.83e-12!29;UBERON:0002780!1.12e-11!39;UBERON:0001890!1.12e-11!39;UBERON:0006240!1.12e-11!39;UBERON:0002346!1.50e-11!64;UBERON:0003075!1.50e-11!64;UBERON:0007284!1.50e-11!64;UBERON:0010371!1.28e-10!73;UBERON:0000956!8.35e-10!21;UBERON:0001869!8.35e-10!21;UBERON:0000203!8.35e-10!21;UBERON:0002619!5.10e-09!17;UBERON:0003056!1.89e-08!49;UBERON:0002021!1.07e-07!10;UBERON:0000411!1.07e-07!10;UBERON:0001950!1.07e-07!10
|ontology_enrichment_uberon=UBERON:0000073!9.27e-18!54;UBERON:0001017!7.25e-17!73;UBERON:0001016!9.69e-17!75;UBERON:0001049!1.17e-16!52;UBERON:0005068!1.17e-16!52;UBERON:0006241!1.17e-16!52;UBERON:0007135!1.17e-16!52;UBERON:0000955!5.84e-15!47;UBERON:0006238!5.84e-15!47;UBERON:0002616!1.45e-14!46;UBERON:0004121!3.38e-14!95;UBERON:0000924!3.38e-14!95;UBERON:0006601!3.38e-14!95;UBERON:0002020!2.71e-13!34;UBERON:0003080!3.05e-12!40;UBERON:0007023!4.39e-12!51;UBERON:0003528!6.83e-12!29;UBERON:0002791!6.83e-12!29;UBERON:0001893!6.83e-12!29;UBERON:0002780!1.12e-11!39;UBERON:0001890!1.12e-11!39;UBERON:0006240!1.12e-11!39;UBERON:0002346!1.50e-11!64;UBERON:0003075!1.50e-11!64;UBERON:0007284!1.50e-11!64;UBERON:0010371!1.28e-10!73;UBERON:0000956!8.35e-10!21;UBERON:0001869!8.35e-10!21;UBERON:0000203!8.35e-10!21;UBERON:0002619!5.10e-09!17;UBERON:0003056!1.89e-08!49;UBERON:0002021!1.07e-07!10;UBERON:0000411!1.07e-07!10;UBERON:0001950!1.07e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,1.65947,0.24402,0.570433,0.197567,1.90943,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.854272,0.503207,0.089443,2.02937,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.66772,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,1.35435,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.40635,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,1.70541,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,2.55912,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,1.56687,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.992915
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,1.65947,0.24402,0.570433,0.197567,1.90943,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.854272,0.503207,0.089443,2.02937,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.66772,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,1.35435,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.40635,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,1.70541,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,2.55912,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,1.56687,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.992915
|tfbs_overrepresentation_jaspar=MA0003.1;0.942378,MA0004.1;0.6888,MA0006.1;1.24418,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;1.46333,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;1.26991,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;0.735223,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.396346,MA0056.1;0,MA0057.1;0.251896,MA0058.1;1.4226,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;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.552621,MA0074.1;1.86824,MA0076.1;1.35592,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;1.5065,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;1.29026,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;2.74278,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;0.647546,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;2.34802,MA0035.2;0.788288,MA0039.2;4.7835,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,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;1.34071,MA0155.1;0.230016,MA0156.1;1.35382,MA0157.1;1.0083,MA0158.1;0,MA0159.1;1.1762,MA0160.1;0.71003,MA0161.1;0,MA0162.1;1.16288,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;1.32296,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;1.90618,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:04, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80204967..80205025,-p1@Ap3d1
Mm9::chr17:34742800..34742807,+p5@Agpat1
Mm9::chr2:152119567..152119597,+p2@Tbc1d20
Mm9::chr7:149088266..149088353,-p1@Tollip


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

GO IDGO nameFDR corrected p-value
GO:0048003antigen processing and presentation of lipid antigen via MHC class Ib0.0176731013834793
GO:0048007antigen processing and presentation, exogenous lipid antigen via MHC class Ib0.0176731013834793
GO:0002475antigen processing and presentation via MHC class Ib0.0176731013834793
GO:0051136regulation of NK T cell differentiation0.0176731013834793
GO:0001865NK T cell differentiation0.0176731013834793
GO:0051138positive regulation of NK T cell differentiation0.0176731013834793
GO:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.0340698345234604
GO:0016411acylglycerol O-acyltransferase activity0.0430463304984218
GO:0046632alpha-beta T cell differentiation0.0484853132184813
GO:0019884antigen processing and presentation of exogenous antigen0.0484853132184813
GO:0032313regulation of Rab GTPase activity0.0484853132184813
GO:0032483regulation of Rab protein signal transduction0.0484853132184813
GO:0032482Rab protein signal transduction0.0484853132184813
GO:0008374O-acyltransferase activity0.0484853132184813
GO:0046631alpha-beta T cell activation0.0484853132184813
GO:0005097Rab GTPase activator activity0.0484853132184813
GO:0005802trans-Golgi network0.0484853132184813
GO:0032318regulation of Ras GTPase activity0.0484853132184813



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 cell1.32e-0749

Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.27e-1854
central nervous system7.25e-1773
nervous system9.69e-1775
neural tube1.17e-1652
neural rod1.17e-1652
future spinal cord1.17e-1652
neural keel1.17e-1652
brain5.84e-1547
future brain5.84e-1547
regional part of brain1.45e-1446
ectoderm-derived structure3.38e-1495
ectoderm3.38e-1495
presumptive ectoderm3.38e-1495
gray matter2.71e-1334
anterior neural tube3.05e-1240
adult organism4.39e-1251
brain grey matter6.83e-1229
regional part of telencephalon6.83e-1229
telencephalon6.83e-1229
regional part of forebrain1.12e-1139
forebrain1.12e-1139
future forebrain1.12e-1139
neurectoderm1.50e-1164
neural plate1.50e-1164
presumptive neural plate1.50e-1164
ecto-epithelium1.28e-1073
cerebral cortex8.35e-1021
cerebral hemisphere8.35e-1021
pallium8.35e-1021
regional part of cerebral cortex5.10e-0917
pre-chordal neural plate1.89e-0849
occipital lobe1.07e-0710
visual cortex1.07e-0710
neocortex1.07e-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)
MA0003.10.942378
MA0004.10.6888
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.11.46333
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.11.26991
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
MA0048.10.735223
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.396346
MA0056.10
MA0057.10.251896
MA0058.11.4226
MA0059.10.59559
MA0060.11.04037
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.552621
MA0074.11.86824
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.11.5065
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.11.29026
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
MA0117.12.74278
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
MA0146.10.647546
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.22.34802
MA0035.20.788288
MA0039.24.7835
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.11.34071
MA0155.10.230016
MA0156.11.35382
MA0157.11.0083
MA0158.10
MA0159.11.1762
MA0160.10.71003
MA0161.10
MA0162.11.16288
MA0163.10.0996272
MA0164.10.817786
MA0080.21.32296
MA0018.20.828253
MA0099.20.944966
MA0079.21.90618
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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