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MCL coexpression mm9:931: Difference between revisions

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{{MCL_coexpression_mm9
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receptor metabolic process;0.0214694502798881;13405!GO:0001573;ganglioside metabolic process;0.0214694502798881;320910!GO:0046716;muscle maintenance;0.0214694502798881;13405!GO:0006687;glycosphingolipid metabolic process;0.0214694502798881;320910!GO:0005626;insoluble fraction;0.0214694502798881;13405!GO:0016010;dystrophin-associated glycoprotein complex;0.0214694502798881;13405!GO:0006664;glycolipid metabolic process;0.0220869754310361;320910!GO:0006672;ceramide metabolic process;0.0220869754310361;320910!GO:0043112;receptor metabolic process;0.0220869754310361;13405!GO:0046519;sphingoid metabolic process;0.0220869754310361;320910!GO:0005605;basal lamina;0.0220869754310361;13405!GO:0042383;sarcolemma;0.0220869754310361;13405!GO:0030018;Z disc;0.0220869754310361;13405!GO:0008305;integrin complex;0.0220869754310361;320910!GO:0031674;I band;0.0220869754310361;13405!GO:0045121;lipid raft;0.0220869754310361;13405!GO:0030055;cell-matrix 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|ontology_enrichment_celltype=CL:0000221!2.02e-15!44;CL:0000133!2.02e-15!44;CL:0002319!1.03e-14!43;CL:0000540!2.93e-12!33;CL:0000047!2.93e-12!33;CL:0000031!2.93e-12!33;CL:0000404!2.93e-12!33;CL:0000117!1.28e-11!23;CL:0000337!1.28e-11!23;CL:0000055!1.69e-11!49;CL:0000393!5.15e-09!39;CL:0000211!5.15e-09!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!1.51e-36!95;UBERON:0000924!1.51e-36!95;UBERON:0006601!1.51e-36!95;UBERON:0001016!3.93e-29!75;UBERON:0010371!5.89e-28!73;UBERON:0001017!1.69e-27!73;UBERON:0002346!3.22e-26!64;UBERON:0003075!3.22e-26!64;UBERON:0007284!3.22e-26!64;UBERON:0000073!4.39e-22!54;UBERON:0010314!6.60e-21!92;UBERON:0001049!9.69e-21!52;UBERON:0005068!9.69e-21!52;UBERON:0006241!9.69e-21!52;UBERON:0007135!9.69e-21!52;UBERON:0003056!1.30e-20!49;UBERON:0000955!1.27e-17!47;UBERON:0006238!1.27e-17!47;UBERON:0002616!5.02e-17!46;UBERON:0002020!3.20e-15!34;UBERON:0003080!3.69e-15!40;UBERON:0002780!1.67e-14!39;UBERON:0001890!1.67e-14!39;UBERON:0006240!1.67e-14!39;UBERON:0003528!2.21e-12!29;UBERON:0002791!2.21e-12!29;UBERON:0001893!2.21e-12!29;UBERON:0000956!2.09e-08!21;UBERON:0001869!2.09e-08!21;UBERON:0000203!2.09e-08!21;UBERON:0000020!4.03e-08!12;UBERON:0001032!4.03e-08!12;UBERON:0004456!4.03e-08!12;UBERON:0000468!7.58e-08!333;UBERON:0000033!1.57e-07!13;UBERON:0005085!9.15e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,0.448401,1.33049,0.173246,1.02512,0.170907,0.494602,1.30517,1.57591,0.550255,1.38589,0,0.742571,0.703873,0.483643,0.620214,0.332107,0.837949,0.549359,0.258745,0.374936,0.577606,0.153291,0.469052,0.303071,0.757024,1.15331,0.843667,0.699026,0.136998,0.276324,0.0153121,0.242032,0.522578,0.221921,0.195877,0.256422,0.460258,0.784847,0.27776,0.209497,0.423266,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,1.64913,0.178433,0.0665967,1.03623,0.140213,0.131016,1.35784,1.56933,0.806481,0.336166,0.530481,0.759925,0.612313,0.501608,0.920903,0.108172,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,1.34857,0.218233,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,1.72118,0.459825,0.784351,0.480639,0.340849,0.887702,3.65074,0.96962,0.337254,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,1.41785,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,2.0333,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,2.50508,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,1.30183,0.0131724
}}

Latest revision as of 16:07, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:120476420..120476474,-p2@Itgb8
Mm9::chr12:120476479..120476491,-p14@Itgb8
Mm9::chr12:120476493..120476534,-p3@Itgb8
Mm9::chr12:120476537..120476565,-p7@Itgb8
Mm9::chr12:120476571..120476595,-p8@Itgb8
Mm9::chr13:78341625..78341649,+p1@ENSMUST00000123998
p1@uc007rhf.1
Mm9::chr18:31402796..31402840,-p@chr18:31402796..31402840
-
Mm9::chrX:82018139..82018149,+p28@Dmd


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:0045213neurotransmitter receptor metabolic process0.0214694502798881
GO:0001573ganglioside metabolic process0.0214694502798881
GO:0046716muscle maintenance0.0214694502798881
GO:0006687glycosphingolipid metabolic process0.0214694502798881
GO:0005626insoluble fraction0.0214694502798881
GO:0016010dystrophin-associated glycoprotein complex0.0214694502798881
GO:0006664glycolipid metabolic process0.0220869754310361
GO:0006672ceramide metabolic process0.0220869754310361
GO:0043112receptor metabolic process0.0220869754310361
GO:0046519sphingoid metabolic process0.0220869754310361
GO:0005605basal lamina0.0220869754310361
GO:0042383sarcolemma0.0220869754310361
GO:0030018Z disc0.0220869754310361
GO:0008305integrin complex0.0220869754310361
GO:0031674I band0.0220869754310361
GO:0045121lipid raft0.0220869754310361
GO:0030055cell-matrix junction0.0220869754310361
GO:0006665sphingolipid metabolic process0.0250271009001221
GO:0044459plasma membrane part0.0284517783662214
GO:0005604basement membrane0.0284517783662214
GO:0007160cell-matrix adhesion0.0284517783662214
GO:0030017sarcomere0.0284517783662214
GO:0043234protein complex0.0284517783662214
GO:0031589cell-substrate adhesion0.0284517783662214
GO:0044449contractile fiber part0.0284517783662214
GO:0016323basolateral plasma membrane0.0284517783662214
GO:0043235receptor complex0.0284517783662214
GO:0030016myofibril0.0284517783662214
GO:0043292contractile fiber0.0284517783662214
GO:0007229integrin-mediated signaling pathway0.0317880550489242
GO:0044420extracellular matrix part0.0317880550489242
GO:0007519skeletal muscle development0.0317962327730742
GO:0005886plasma membrane0.0318918771747741
GO:0032991macromolecular complex0.0333212854780622
GO:0014706striated muscle development0.0370887258834726
GO:0007275multicellular organismal development0.0370887258834726
GO:0006643membrane lipid metabolic process0.0430424443421253
GO:0005792microsome0.0430424443421253
GO:0042598vesicular fraction0.0430424443421253
GO:0007517muscle development0.0443611126509407
GO:0007268synaptic transmission0.0495036423669913



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
ectoderm-derived structure1.51e-3695
ectoderm1.51e-3695
presumptive ectoderm1.51e-3695
nervous system3.93e-2975
ecto-epithelium5.89e-2873
central nervous system1.69e-2773
neurectoderm3.22e-2664
neural plate3.22e-2664
presumptive neural plate3.22e-2664
regional part of nervous system4.39e-2254
structure with developmental contribution from neural crest6.60e-2192
neural tube9.69e-2152
neural rod9.69e-2152
future spinal cord9.69e-2152
neural keel9.69e-2152
pre-chordal neural plate1.30e-2049
brain1.27e-1747
future brain1.27e-1747
regional part of brain5.02e-1746
gray matter3.20e-1534
anterior neural tube3.69e-1540
regional part of forebrain1.67e-1439
forebrain1.67e-1439
future forebrain1.67e-1439
brain grey matter2.21e-1229
regional part of telencephalon2.21e-1229
telencephalon2.21e-1229
cerebral cortex2.09e-0821
cerebral hemisphere2.09e-0821
pallium2.09e-0821
sense organ4.03e-0812
sensory system4.03e-0812
entire sense organ system4.03e-0812
multi-cellular organism7.58e-08333
head1.57e-0713
ectodermal placode9.15e-0713


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)
MA0003.11.45843
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.829081
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.00886773
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.10.0771944
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.0706842
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.978338
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.71453
MA0163.10.991519
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.0265037
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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