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MCL coexpression mm9:1903: Difference between revisions

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{{MCL_coexpression_mm9
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protein kinase complex;0.0349580978036032;19084!GO:0030552;cAMP binding;0.0349580978036032;19084!GO:0008603;cAMP-dependent protein kinase regulator activity;0.0349580978036032;19084!GO:0031594;neuromuscular junction;0.0349580978036032;19084!GO:0016208;AMP binding;0.0349580978036032;19084!GO:0030551;cyclic nucleotide binding;0.0349580978036032;19084!GO:0001707;mesoderm formation;0.0349580978036032;19084!GO:0048332;mesoderm morphogenesis;0.0349580978036032;19084!GO:0001704;formation of primary germ 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|ontology_enrichment_celltype=CL:0000055!1.64e-18!49;CL:0000393!1.92e-16!39;CL:0000211!1.92e-16!39;CL:0002319!4.40e-15!43;CL:0000221!5.47e-15!44;CL:0000133!5.47e-15!44;CL:0000540!4.55e-13!33;CL:0000047!4.55e-13!33;CL:0000031!4.55e-13!33;CL:0000404!4.55e-13!33;CL:0000117!9.59e-09!23;CL:0000337!9.59e-09!23;CL:0002321!4.14e-07!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!2.53e-30!75;UBERON:0001017!2.92e-30!73;UBERON:0004121!7.46e-30!95;UBERON:0000924!7.46e-30!95;UBERON:0006601!7.46e-30!95;UBERON:0010314!5.57e-24!92;UBERON:0002346!1.62e-23!64;UBERON:0003075!1.62e-23!64;UBERON:0007284!1.62e-23!64;UBERON:0010371!4.87e-22!73;UBERON:0000073!6.65e-21!54;UBERON:0001049!1.75e-19!52;UBERON:0005068!1.75e-19!52;UBERON:0006241!1.75e-19!52;UBERON:0007135!1.75e-19!52;UBERON:0000955!2.60e-17!47;UBERON:0006238!2.60e-17!47;UBERON:0002616!9.20e-17!46;UBERON:0003056!1.42e-16!49;UBERON:0002020!4.96e-15!34;UBERON:0003080!3.40e-14!40;UBERON:0002780!1.28e-13!39;UBERON:0001890!1.28e-13!39;UBERON:0006240!1.28e-13!39;UBERON:0003528!5.25e-13!29;UBERON:0002791!5.25e-13!29;UBERON:0001893!5.25e-13!29;UBERON:0000956!2.45e-09!21;UBERON:0001869!2.45e-09!21;UBERON:0000203!2.45e-09!21;UBERON:0002619!3.33e-08!17;UBERON:0000025!3.48e-08!114;UBERON:0004111!5.44e-08!122;UBERON:0002021!7.90e-08!10;UBERON:0000411!7.90e-08!10;UBERON:0001950!7.90e-08!10
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,0.483253,1.67884,0.803568,0.370124,1.76086,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,17.5639,0.290745,0.711848,1.12823,0.471365,0.854272,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,1.20358,0.717547,0.544696,1.26006,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,1.02399,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.864765,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,2.1607,1.34553,1.16494,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,1.41174,0.7614,1.51002,0.476467,0.869142,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,4.94449,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.79777,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,0.0824127
}}

Latest revision as of 17:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:67375223..67375240,-p4@Zfp365
Mm9::chr11:109510690..109510751,+p4@Prkar1a
Mm9::chr15:22478661..22478682,+p4@Cdh18
Mm9::chr18:13132927..13132946,+p@chr18:13132927..13132946
+


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:0005952cAMP-dependent protein kinase complex0.0349580978036032
GO:0030552cAMP binding0.0349580978036032
GO:0008603cAMP-dependent protein kinase regulator activity0.0349580978036032
GO:0031594neuromuscular junction0.0349580978036032
GO:0016208AMP binding0.0349580978036032
GO:0030551cyclic nucleotide binding0.0349580978036032
GO:0001707mesoderm formation0.0349580978036032
GO:0048332mesoderm morphogenesis0.0349580978036032
GO:0001704formation of primary germ layer0.0349580978036032



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
nervous system2.53e-3075
central nervous system2.92e-3073
ectoderm-derived structure7.46e-3095
ectoderm7.46e-3095
presumptive ectoderm7.46e-3095
structure with developmental contribution from neural crest5.57e-2492
neurectoderm1.62e-2364
neural plate1.62e-2364
presumptive neural plate1.62e-2364
ecto-epithelium4.87e-2273
regional part of nervous system6.65e-2154
neural tube1.75e-1952
neural rod1.75e-1952
future spinal cord1.75e-1952
neural keel1.75e-1952
brain2.60e-1747
future brain2.60e-1747
regional part of brain9.20e-1746
pre-chordal neural plate1.42e-1649
gray matter4.96e-1534
anterior neural tube3.40e-1440
regional part of forebrain1.28e-1339
forebrain1.28e-1339
future forebrain1.28e-1339
brain grey matter5.25e-1329
regional part of telencephalon5.25e-1329
telencephalon5.25e-1329
cerebral cortex2.45e-0921
cerebral hemisphere2.45e-0921
pallium2.45e-0921
regional part of cerebral cortex3.33e-0817
tube3.48e-08114
anatomical conduit5.44e-08122
occipital lobe7.90e-0810
visual cortex7.90e-0810
neocortex7.90e-0810


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)
MA0003.10.142214
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
MA0041.11.47002
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.790894
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
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.00221226
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
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
MA0106.13.43447
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.11.24367
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
MA0146.10.313734
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.238019
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.21.14524
MA0065.20.212467
MA0150.11.61189
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.704935
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.0234849
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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