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MCL coexpression mm9:1975: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005178!2.95e-09!17;UBERON:0005181!2.95e-09!17;UBERON:0002224!2.95e-09!17;UBERON:0000915!2.95e-09!17;UBERON:0008947!2.95e-09!17;UBERON:0003258!2.95e-09!17;UBERON:0002048!1.82e-08!14;UBERON:0000117!1.82e-08!14;UBERON:0000171!1.82e-08!14;UBERON:0000170!1.82e-08!14;UBERON:0005597!1.82e-08!14;UBERON:0000118!1.82e-08!14;UBERON:0005153!4.03e-07!17;UBERON:0000464!6.07e-07!57
|ontology_enrichment_uberon=UBERON:0005178!2.95e-09!17;UBERON:0005181!2.95e-09!17;UBERON:0002224!2.95e-09!17;UBERON:0000915!2.95e-09!17;UBERON:0008947!2.95e-09!17;UBERON:0003258!2.95e-09!17;UBERON:0002048!1.82e-08!14;UBERON:0000117!1.82e-08!14;UBERON:0000171!1.82e-08!14;UBERON:0000170!1.82e-08!14;UBERON:0005597!1.82e-08!14;UBERON:0000118!1.82e-08!14;UBERON:0005153!4.03e-07!17;UBERON:0000464!6.07e-07!57
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,1.21364,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.683591,0.570433,1.08884,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,1.26006,0.325217,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.882473,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,1.74615,0.593145,1.32691,0.323563,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,0.40635,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,1.40021,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.293812,0.184289,1.27621,0.416214,1.95555,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,2.65001
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,1.21364,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.683591,0.570433,1.08884,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,1.26006,0.325217,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.882473,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,1.74615,0.593145,1.32691,0.323563,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,0.40635,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,1.40021,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.293812,0.184289,1.27621,0.416214,1.95555,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,2.65001
|tfbs_overrepresentation_jaspar=MA0003.1;2.33202,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;1.61215,MA0009.1;1.15569,MA0014.1;2.62764,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;1.4388,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;1.86956,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,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;0.112167,MA0074.1;1.86824,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;0.582815,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;3.20215,MA0106.1;0.899777,MA0107.1;1.3208,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;1.14526,MA0146.1;2.82479,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;1.47117,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;1.14524,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;0.346529,MA0163.1;1.11502,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;1.59291,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:09, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:59104248..59104260,-p1@Wnt3a
Mm9::chr1:162181568..162181612,-p@chr1:162181568..162181612
-
Mm9::chr2:25312350..25312370,+p1@Clic3
Mm9::chr5:23979973..23980002,+p@chr5:23979973..23980002
+


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:0048342paraxial mesodermal cell differentiation0.0106004162834652
GO:0048343paraxial mesodermal cell fate commitment0.0106004162834652
GO:0001710mesodermal cell fate commitment0.0106004162834652
GO:0048333mesodermal cell differentiation0.0106004162834652
GO:0048341paraxial mesoderm formation0.0141327267521486
GO:0048103somatic stem cell division0.0141327267521486
GO:0017145stem cell division0.0158980107671366
GO:0048340paraxial mesoderm morphogenesis0.0158980107671366
GO:0048339paraxial mesoderm development0.017661552343417
GO:0001947heart looping0.017661552343417
GO:0005247voltage-gated chloride channel activity0.017661552343417
GO:0022844voltage-gated anion channel activity0.017661552343417
GO:0007223Wnt receptor signaling pathway, calcium modulating pathway0.0217343166641928
GO:0030879mammary gland development0.0221988350799632
GO:0001707mesoderm formation0.0224331808841688
GO:0048332mesoderm morphogenesis0.0224331808841688
GO:0001704formation of primary germ layer0.0224331808841688
GO:0001756somitogenesis0.0224660190724778
GO:0007368determination of left/right symmetry0.0224660190724778
GO:0003007heart morphogenesis0.0224660190724778
GO:0009799determination of symmetry0.0224660190724778
GO:0009855determination of bilateral symmetry0.0224660190724778
GO:0035282segmentation0.0257821332254141
GO:0007498mesoderm development0.027313195137404
GO:0031404chloride ion binding0.027313195137404
GO:0043168anion binding0.027313195137404
GO:0042472inner ear morphogenesis0.027313195137404
GO:0005254chloride channel activity0.027313195137404
GO:0006821chloride transport0.027313195137404
GO:0042471ear morphogenesis0.027313195137404
GO:0005253anion channel activity0.027313195137404
GO:0007369gastrulation0.0273401459490074
GO:0048839inner ear development0.0297785356500678
GO:0048732gland development0.0297785356500678
GO:0048729tissue morphogenesis0.0297785356500678
GO:0043583ear development0.0297785356500678
GO:0009952anterior/posterior pattern formation0.0358181979770001
GO:0045165cell fate commitment0.0370956030094531
GO:0008509anion transmembrane transporter activity0.0404684219415818
GO:0001701in utero embryonic development0.0415773641297031
GO:0016055Wnt receptor signaling pathway0.0415773641297031
GO:0015698inorganic anion transport0.0468974151382522
GO:0003002regionalization0.0468974151382522
GO:0045595regulation of cell differentiation0.0468974151382522
GO:0007409axonogenesis0.0468974151382522
GO:0048667neuron morphogenesis during differentiation0.0468974151382522
GO:0048812neurite morphogenesis0.0468974151382522
GO:0006820anion transport0.0468974151382522
GO:0022832voltage-gated channel activity0.0468974151382522
GO:0005244voltage-gated ion channel activity0.0468974151382522
GO:0007507heart development0.0468974151382522
GO:0000904cellular morphogenesis during differentiation0.0484393228132578
GO:0007423sensory organ development0.0484393228132578
GO:0048646anatomical structure formation0.0484393228132578
GO:0031175neurite development0.0498474753391753



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
thoracic cavity element2.95e-0917
thoracic segment organ2.95e-0917
thoracic cavity2.95e-0917
thoracic segment of trunk2.95e-0917
respiratory primordium2.95e-0917
endoderm of foregut2.95e-0917
lung1.82e-0814
respiratory tube1.82e-0814
respiration organ1.82e-0814
pair of lungs1.82e-0814
lung primordium1.82e-0814
lung bud1.82e-0814
epithelial bud4.03e-0717
anatomical space6.07e-0757


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)
MA0003.12.33202
MA0004.10.6888
MA0006.10.497533
MA0007.11.61215
MA0009.11.15569
MA0014.12.62764
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
MA0042.11.4388
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.86956
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
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
MA0073.10.112167
MA0074.11.86824
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
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
MA0105.13.20215
MA0106.10.899777
MA0107.11.3208
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
MA0145.11.14526
MA0146.12.82479
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.21.47117
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.21.14524
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
MA0162.10.346529
MA0163.11.11502
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.21.59291
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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