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MCL coexpression mm9:535: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0.125727960712818,0.0455894054315693,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0834533319011762,0,0,0.145411995067922,0.0896964873768703,0,0,0,0.0755555083173967,0,0.0434877098916977,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0400093965272457,0.18440492317299,0,0,0,0,0,0,0,0,0,0,0.050354161091433,0.109123086691028,0.12277748593221,0,0.0198746585451445,0,0.505464404962115,0.441094405811093,0.573761976486374,0.123224102318956,0.176810392371935,0.0910522389263605,0.325665874540913,0.387626206214038,0.463739992732168,0.334151889143925,0.350443038236559,0,0,0,0,0,0,0,0,0,0.0570741246689917,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0,0.82667432380898,0.5954765028743,0.620997582955309,0.60942017110563,0.953566003289279,0.844913367525133,1.02597122581686,0,0,0,0,0,0,0,0.336684465725675,0.351591407788256,0.098801861608942,0,0,0,0.161179842546876,0.375206552143423,0.138922288373465,0.325071741860858,0.325564651783995,0.280983247977995,0.295225594521175,0,0,0,0.0829439327499637,0,0,0,0.0876889746819101,0.0912850895577325,0.116017654526984,0.197359136203057,0.21528594805925,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.427171743726688,0.116844694267823,0.0619941838335705,0,0,0,0,0,0.0872055405749939,0.0756292965920817,0.192229323691076,0.259125815764664,0.199780931006561,0.112141771333522,0.110173605842676,0,0.177778711459279,0.141145253644615,0,0.0893741091821246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.325880249222541,0.398043506535903,0,0,0,0,0,0,0,0,0,0,0,0.121008441369486,0,0,0,0,0,0.367753944609732,0.242861776507364,0.159585615253267,0.112371000179637,0.162278901062865,0.140386497797093,0.237309301365803,0.183087496210002,0.0596340098159245,0,0,1.01538871924657,0.0359522460741798,0.0528318955547673,0.149989869616679,0.273776089422403,0.441217467993999,0.580886290345964,0.440975900005688,0,0,0,0,0,0,0,0,0.236171262379892,0.164538360789739,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0428882730496471,0.054943952156948,0.034489466458534,0.100975358632432,0.0765177418984193,0,0,0,0,0,0,0,0,0,0,0,0.054962990285351,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.379358589281386,0.376754964798171,0.424496055335199,0.585145732503103,0.300699880676714,0.399810008829701,0.224020645200257,0.395499166636056,0.410954935295049,0.308675506925909,0,0,0.034229042449623,0,0,0,0,0,0,0.0489230553888678,0,0,0.0745542549075041,0.0523284672130554,0.0242538736058389,0,0.0452645736210068,0.03830369771457,0,0,0,0.0709519923534245,0,0.0294684307081759,0.0390607415003592,0.0339498293155746,0,0,0.0276517186754466,0,0.0243442052522616,0.0408018333703219,0,0.0625582350728301,0,0,0.0456455446387725,0,0,0,0
|gostat_on_MCL_coexpression=GO:0005615;extracellular space;0.0457800511785315;12653,12652!GO:0044421;extracellular region part;0.0457800511785315;12653,12652!
}}

Latest revision as of 15:28, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:97385255..97385260,-p@chr11:97385255..97385260
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Mm9::chr12:103793176..103793194,+p1@Chga
Mm9::chr12:103800161..103800196,-p@chr12:103800161..103800196
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Mm9::chr14:21216570..21216580,-p@chr14:21216570..21216580
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Mm9::chr17:87449988..87450015,-p@chr17:87449988..87450015
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Mm9::chr2:132607398..132607414,+p1@Chgb
Mm9::chr2:132618345..132618358,-p@chr2:132618345..132618358
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Mm9::chr2:132618359..132618393,-p@chr2:132618359..132618393
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Mm9::chr2:132618395..132618438,-p@chr2:132618395..132618438
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Mm9::chr2:132618548..132618617,-p@chr2:132618548..132618617
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Mm9::chr2:132618623..132618630,-p@chr2:132618623..132618630
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Mm9::chr2:132619066..132619119,-p@chr2:132619066..132619119
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Mm9::chr2:132619103..132619115,+p@chr2:132619103..132619115
+
Mm9::chr2:132619265..132619276,-p@chr2:132619265..132619276
-


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:0005615extracellular space0.0457800511785315
GO:0044421extracellular region part0.0457800511785315



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
CNS neuron (sensu Vertebrata)3.36e-0723
neuroblast (sensu Vertebrata)3.36e-0723

Uber Anatomy
Ontology termp-valuen
regional part of nervous system5.78e-2654
neural tube9.79e-2452
neural rod9.79e-2452
future spinal cord9.79e-2452
neural keel9.79e-2452
neurectoderm6.01e-2364
neural plate6.01e-2364
presumptive neural plate6.01e-2364
brain1.08e-2147
future brain1.08e-2147
regional part of brain3.88e-2146
pre-chordal neural plate2.02e-2049
anterior neural tube1.97e-1940
regional part of forebrain8.04e-1939
forebrain8.04e-1939
future forebrain8.04e-1939
central nervous system1.04e-1873
structure with developmental contribution from neural crest1.77e-1892
ecto-epithelium5.93e-1873
nervous system9.58e-1875
ectoderm-derived structure4.52e-1595
ectoderm4.52e-1595
presumptive ectoderm4.52e-1595
gray matter9.67e-1434
brain grey matter5.52e-1229
regional part of telencephalon5.52e-1229
telencephalon5.52e-1229
occipital lobe1.20e-0910
visual cortex1.20e-0910
neocortex1.20e-0910
adrenal gland1.21e-087
adrenal/interrenal gland1.21e-087
diencephalon3.50e-0810
future diencephalon3.50e-0810
regional part of cerebral cortex2.35e-0717
cerebral cortex4.55e-0721
cerebral hemisphere4.55e-0721
pallium4.55e-0721
pituitary gland8.68e-078
gland of diencephalon8.68e-078
neuroendocrine gland8.68e-078


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)
MA0003.10.0100854
MA0004.10.258473
MA0006.10.412095
MA0007.10.246385
MA0009.10.649874
MA0014.10.023905
MA0017.10.458117
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.430035
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.12.43453
MA0042.12.36259
MA0043.10.74191
MA0046.10.683926
MA0048.10.121113
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.45021
MA0056.10
MA0057.10.107353
MA0058.10.183941
MA0059.10.563468
MA0060.10.0819399
MA0061.10.32765
MA0063.10
MA0066.10.970926
MA0067.10.981551
MA0068.10.0266408
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.10.0104616
MA0074.10.340281
MA0076.10.491745
MA0077.10.632005
MA0078.10.418168
MA0081.11.14043
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.12.50348
MA0089.10
MA0090.13.50174
MA0091.10.269175
MA0092.10.653984
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.157724
MA0105.10.684733
MA0106.10.425111
MA0107.10.153373
MA0108.21.25225
MA0109.10
MA0111.10.679612
MA0113.10.400008
MA0114.10.0981613
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.231431
MA0140.10.330266
MA0141.11.56687
MA0142.10.547747
MA0143.10.414534
MA0144.11.64479
MA0145.10.189432
MA0146.10.662029
MA0147.10.107632
MA0148.10.747422
MA0149.10.204102
MA0062.20.177386
MA0035.20.33429
MA0039.20.000784583
MA0138.22.05815
MA0002.21.31437
MA0137.20.506794
MA0104.20.0740839
MA0047.20.380343
MA0112.20.0731504
MA0065.20.371748
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.0285118
MA0155.10.22104
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.365914
MA0160.10.753068
MA0161.10
MA0162.10.21028
MA0163.10.094989
MA0164.10.357779
MA0080.20.467794
MA0018.20.959515
MA0099.21.17093
MA0079.20.00744075
MA0102.21.35579
MA0258.10.0900907
MA0259.10.101001
MA0442.10
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