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MCL coexpression mm9:1392: Difference between revisions

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{{MCL_coexpression_mm9
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neurocranium morphogenesis;0.0153391036659962;15531!GO:0051923;sulfation;0.0153391036659962;15531!GO:0006477;protein amino acid sulfation;0.0153391036659962;15531!GO:0048703;embryonic viscerocranium morphogenesis;0.0184049074230457;15531!GO:0015016;[heparan sulfate]-glucosamine N-sulfotransferase activity;0.0184049074230457;15531!GO:0048701;embryonic cranial skeleton morphogenesis;0.0230036132428184;15531!GO:0006476;protein amino acid deacetylation;0.026286962732604;15531!GO:0048704;embryonic skeletal morphogenesis;0.0272973368109995;15531!GO:0030901;midbrain development;0.0272973368109995;15531!GO:0008543;fibroblast growth factor receptor signaling pathway;0.0272973368109995;15531!GO:0048706;embryonic skeletal development;0.0272973368109995;15531!GO:0005794;Golgi apparatus;0.0272973368109995;15531,11778!GO:0006022;aminoglycan metabolic process;0.0272973368109995;15531!GO:0030203;glycosaminoglycan metabolic process;0.0272973368109995;15531!GO:0007585;respiratory gaseous exchange;0.0272973368109995;15531!GO:0000271;polysaccharide biosynthetic process;0.0272973368109995;15531!GO:0048705;skeletal morphogenesis;0.0290285459467753;15531!GO:0030119;AP-type membrane coat adaptor complex;0.0290285459467753;11778!GO:0030131;clathrin adaptor complex;0.0290285459467753;11778!GO:0007224;smoothened signaling pathway;0.0321662516056839;15531!GO:0005802;trans-Golgi network;0.0350032099612206;11778!GO:0030118;clathrin coat;0.0354965224870329;11778!GO:0008146;sulfotransferase activity;0.0439153450651711;15531!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0458913605078615;15531!GO:0030117;membrane coat;0.0458913605078615;11778!GO:0048475;coated 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|gostat_on_MCL_coexpression=GO:0048702;embryonic neurocranium morphogenesis;0.0153391036659962;15531!GO:0051923;sulfation;0.0153391036659962;15531!GO:0006477;protein amino acid sulfation;0.0153391036659962;15531!GO:0048703;embryonic viscerocranium morphogenesis;0.0184049074230457;15531!GO:0015016;[heparan sulfate]-glucosamine N-sulfotransferase activity;0.0184049074230457;15531!GO:0048701;embryonic cranial skeleton morphogenesis;0.0230036132428184;15531!GO:0006476;protein amino acid deacetylation;0.026286962732604;15531!GO:0048704;embryonic skeletal morphogenesis;0.0272973368109995;15531!GO:0030901;midbrain development;0.0272973368109995;15531!GO:0008543;fibroblast growth factor receptor signaling pathway;0.0272973368109995;15531!GO:0048706;embryonic skeletal development;0.0272973368109995;15531!GO:0005794;Golgi apparatus;0.0272973368109995;15531,11778!GO:0006022;aminoglycan metabolic process;0.0272973368109995;15531!GO:0030203;glycosaminoglycan metabolic process;0.0272973368109995;15531!GO:0007585;respiratory gaseous exchange;0.0272973368109995;15531!GO:0000271;polysaccharide biosynthetic process;0.0272973368109995;15531!GO:0048705;skeletal morphogenesis;0.0290285459467753;15531!GO:0030119;AP-type membrane coat adaptor complex;0.0290285459467753;11778!GO:0030131;clathrin adaptor complex;0.0290285459467753;11778!GO:0007224;smoothened signaling pathway;0.0321662516056839;15531!GO:0005802;trans-Golgi network;0.0350032099612206;11778!GO:0030118;clathrin coat;0.0354965224870329;11778!GO:0008146;sulfotransferase activity;0.0439153450651711;15531!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0458913605078615;15531!GO:0030117;membrane coat;0.0458913605078615;11778!GO:0048475;coated membrane;0.0458913605078615;11778!
|ontology_enrichment_celltype=CL:0000221!1.46e-14!44;CL:0000133!1.46e-14!44;CL:0002319!1.79e-14!43;CL:0000117!9.35e-14!23;CL:0000337!9.35e-14!23;CL:0000540!1.03e-13!33;CL:0000047!1.03e-13!33;CL:0000031!1.03e-13!33;CL:0000404!1.03e-13!33;CL:0000055!5.92e-12!49;CL:0000393!7.86e-11!39;CL:0000211!7.86e-11!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.09e-33!73;UBERON:0001016!1.19e-31!75;UBERON:0004121!3.99e-30!95;UBERON:0000924!3.99e-30!95;UBERON:0006601!3.99e-30!95;UBERON:0002346!1.66e-29!64;UBERON:0003075!1.66e-29!64;UBERON:0007284!1.66e-29!64;UBERON:0000073!1.76e-27!54;UBERON:0001049!1.51e-26!52;UBERON:0005068!1.51e-26!52;UBERON:0006241!1.51e-26!52;UBERON:0007135!1.51e-26!52;UBERON:0010371!4.48e-26!73;UBERON:0010314!2.14e-23!92;UBERON:0003056!4.00e-23!49;UBERON:0000955!4.82e-23!47;UBERON:0006238!4.82e-23!47;UBERON:0002616!1.79e-22!46;UBERON:0003080!1.93e-20!40;UBERON:0002780!7.48e-20!39;UBERON:0001890!7.48e-20!39;UBERON:0006240!7.48e-20!39;UBERON:0002020!1.58e-18!34;UBERON:0003528!2.52e-15!29;UBERON:0002791!2.52e-15!29;UBERON:0001893!2.52e-15!29;UBERON:0000956!2.26e-11!21;UBERON:0001869!2.26e-11!21;UBERON:0000203!2.26e-11!21;UBERON:0000468!1.47e-10!333;UBERON:0000025!4.40e-10!114;UBERON:0004111!2.07e-09!122;UBERON:0002619!4.84e-09!17;UBERON:0000922!4.08e-07!320;UBERON:0000479!4.55e-07!349
}}

Latest revision as of 16:51, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:23723181..23723236,-p1@Zfp13
Mm9::chr18:60907987..60908064,-p2@Ndst1
Mm9::chr2:130249978..130250029,-p1@Fam113a
Mm9::chr7:25858091..25858144,-p@chr7:25858091..25858144
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Mm9::chr7:25858149..25858183,-p@chr7:25858149..25858183
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Mm9::chr7:87065485..87065544,-p1@Ap3s2


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:0048702embryonic neurocranium morphogenesis0.0153391036659962
GO:0051923sulfation0.0153391036659962
GO:0006477protein amino acid sulfation0.0153391036659962
GO:0048703embryonic viscerocranium morphogenesis0.0184049074230457
GO:0015016[heparan sulfate]-glucosamine N-sulfotransferase activity0.0184049074230457
GO:0048701embryonic cranial skeleton morphogenesis0.0230036132428184
GO:0006476protein amino acid deacetylation0.026286962732604
GO:0048704embryonic skeletal morphogenesis0.0272973368109995
GO:0030901midbrain development0.0272973368109995
GO:0008543fibroblast growth factor receptor signaling pathway0.0272973368109995
GO:0048706embryonic skeletal development0.0272973368109995
GO:0005794Golgi apparatus0.0272973368109995
GO:0006022aminoglycan metabolic process0.0272973368109995
GO:0030203glycosaminoglycan metabolic process0.0272973368109995
GO:0007585respiratory gaseous exchange0.0272973368109995
GO:0000271polysaccharide biosynthetic process0.0272973368109995
GO:0048705skeletal morphogenesis0.0290285459467753
GO:0030119AP-type membrane coat adaptor complex0.0290285459467753
GO:0030131clathrin adaptor complex0.0290285459467753
GO:0007224smoothened signaling pathway0.0321662516056839
GO:0005802trans-Golgi network0.0350032099612206
GO:0030118clathrin coat0.0354965224870329
GO:0008146sulfotransferase activity0.0439153450651711
GO:0016782transferase activity, transferring sulfur-containing groups0.0458913605078615
GO:0030117membrane coat0.0458913605078615
GO:0048475coated membrane0.0458913605078615



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
central nervous system3.09e-3373
nervous system1.19e-3175
ectoderm-derived structure3.99e-3095
ectoderm3.99e-3095
presumptive ectoderm3.99e-3095
neurectoderm1.66e-2964
neural plate1.66e-2964
presumptive neural plate1.66e-2964
regional part of nervous system1.76e-2754
neural tube1.51e-2652
neural rod1.51e-2652
future spinal cord1.51e-2652
neural keel1.51e-2652
ecto-epithelium4.48e-2673
structure with developmental contribution from neural crest2.14e-2392
pre-chordal neural plate4.00e-2349
brain4.82e-2347
future brain4.82e-2347
regional part of brain1.79e-2246
anterior neural tube1.93e-2040
regional part of forebrain7.48e-2039
forebrain7.48e-2039
future forebrain7.48e-2039
gray matter1.58e-1834
brain grey matter2.52e-1529
regional part of telencephalon2.52e-1529
telencephalon2.52e-1529
cerebral cortex2.26e-1121
cerebral hemisphere2.26e-1121
pallium2.26e-1121
multi-cellular organism1.47e-10333
tube4.40e-10114
anatomical conduit2.07e-09122
regional part of cerebral cortex4.84e-0917
embryo4.08e-07320
tissue4.55e-07349


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)
MA0003.12.22936
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.11.71935
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.11.43735
MA0058.11.11298
MA0059.10.449345
MA0060.10.757042
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.116.0199
MA0074.10.638014
MA0076.11.85013
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.11.09694
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.11.24552
MA0146.10.153598
MA0147.10.320675
MA0148.10.553294
MA0149.114.8562
MA0062.21.11803
MA0035.20.630778
MA0039.20.0823004
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.76177
MA0065.20.380324
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.11.49271
MA0155.10.132921
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.11.95647
MA0164.10.658997
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.21.11318
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1392&oldid=3073391"