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MCL coexpression mm9:2768: Difference between revisions

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{{MCL_coexpression_mm9
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of apoptosis;0.00691262605285871;11796,22031!GO:0043067;regulation of programmed cell death;0.00691262605285871;11796,22031!GO:0006915;apoptosis;0.00691262605285871;11796,22031!GO:0012501;programmed cell death;0.00691262605285871;11796,22031!GO:0008219;cell death;0.00691262605285871;11796,22031!GO:0016265;death;0.00691262605285871;11796,22031!GO:0048468;cell development;0.01785002838149;11796,22031!GO:0048869;cellular developmental process;0.0289969427809783;11796,22031!GO:0030154;cell differentiation;0.0289969427809783;11796,22031!GO:0006916;anti-apoptosis;0.0289969427809783;11796!GO:0008270;zinc ion binding;0.0311891338571884;11796,22031!GO:0046914;transition metal ion binding;0.0400161514098527;11796,22031!GO:0043066;negative regulation of apoptosis;0.0400161514098527;11796!GO:0043069;negative regulation of programmed cell 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|gostat_on_MCL_coexpression=GO:0042981;regulation of apoptosis;0.00691262605285871;11796,22031!GO:0043067;regulation of programmed cell death;0.00691262605285871;11796,22031!GO:0006915;apoptosis;0.00691262605285871;11796,22031!GO:0012501;programmed cell death;0.00691262605285871;11796,22031!GO:0008219;cell death;0.00691262605285871;11796,22031!GO:0016265;death;0.00691262605285871;11796,22031!GO:0048468;cell development;0.01785002838149;11796,22031!GO:0048869;cellular developmental process;0.0289969427809783;11796,22031!GO:0030154;cell differentiation;0.0289969427809783;11796,22031!GO:0006916;anti-apoptosis;0.0289969427809783;11796!GO:0008270;zinc ion binding;0.0311891338571884;11796,22031!GO:0046914;transition metal ion binding;0.0400161514098527;11796,22031!GO:0043066;negative regulation of apoptosis;0.0400161514098527;11796!GO:0043069;negative regulation of programmed cell death;0.0400161514098527;11796!
|ontology_enrichment_celltype=CL:0000838!1.72e-07!12;CL:0000988!2.90e-07!32;CL:0002032!2.90e-07!32;CL:0000037!2.90e-07!32;CL:0000566!2.90e-07!32;CL:0000837!2.90e-07!32;CL:0000084!7.63e-07!11;CL:0000827!7.63e-07!11
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!7.29e-21!118;UBERON:0000925!7.29e-21!118;UBERON:0006595!7.29e-21!118;UBERON:0001007!1.61e-20!116;UBERON:0001555!1.61e-20!116;UBERON:0007026!1.61e-20!116;UBERON:0004921!2.91e-19!114;UBERON:0003929!2.79e-11!55;UBERON:0000490!3.29e-11!66;UBERON:0002193!5.92e-11!48;UBERON:0002405!5.92e-11!48;UBERON:0005911!5.98e-11!69;UBERON:0004923!1.04e-09!24;UBERON:0001041!1.50e-09!80;UBERON:0002390!2.70e-09!45;UBERON:0003061!2.70e-09!45;UBERON:0005409!7.14e-09!47;UBERON:0000160!8.52e-09!31;UBERON:0000077!1.95e-08!35;UBERON:0000344!8.48e-08!15;UBERON:0004177!1.74e-07!29;UBERON:0005057!1.74e-07!29;UBERON:0000072!8.70e-07!27
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,1.05917,0.608816,0.444545,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,1.08907,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,3.02035,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.62246,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,1.31639,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,1.44008,0.38417,3.74474,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.421338
}}

Latest revision as of 19:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:112404696..112404731,+p3@Traf3
Mm9::chr9:7872814..7872876,-p1@Birc3
Mm9::chrX:34683959..34683976,+p@chrX:34683959..34683976
+


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:0042981regulation of apoptosis0.00691262605285871
GO:0043067regulation of programmed cell death0.00691262605285871
GO:0006915apoptosis0.00691262605285871
GO:0012501programmed cell death0.00691262605285871
GO:0008219cell death0.00691262605285871
GO:0016265death0.00691262605285871
GO:0048468cell development0.01785002838149
GO:0048869cellular developmental process0.0289969427809783
GO:0030154cell differentiation0.0289969427809783
GO:0006916anti-apoptosis0.0289969427809783
GO:0008270zinc ion binding0.0311891338571884
GO:0046914transition metal ion binding0.0400161514098527
GO:0043066negative regulation of apoptosis0.0400161514098527
GO:0043069negative regulation of programmed cell death0.0400161514098527



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
endoderm-derived structure7.29e-21118
endoderm7.29e-21118
presumptive endoderm7.29e-21118
digestive system1.61e-20116
digestive tract1.61e-20116
primitive gut1.61e-20116
subdivision of digestive tract2.91e-19114
gut epithelium2.79e-1155
unilaminar epithelium3.29e-1166
hemolymphoid system5.92e-1148
immune system5.92e-1148
endo-epithelium5.98e-1169
organ component layer1.04e-0924
foregut1.50e-0980
hematopoietic system2.70e-0945
blood island2.70e-0945
gastrointestinal system7.14e-0947
intestine8.52e-0931
mixed endoderm/mesoderm-derived structure1.95e-0835
mucosa8.48e-0815
hemopoietic organ1.74e-0729
immune organ1.74e-0729
segment of respiratory tract8.70e-0727


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)
MA0003.11.87396
MA0004.10.801718
MA0006.11.46714
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.11.5346
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.11.65098
MA0059.12.82482
MA0060.10.502699
MA0061.14.54623
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.908538
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.11.69369
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.11.40099
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.11.51475
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.12.85802
MA0103.10.647985
MA0105.12.75918
MA0106.11.01755
MA0107.13.81175
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.11.46662
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.11.16863
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.46063
MA0147.12.34772
MA0148.10.820161
MA0149.10.722227
MA0062.21.06145
MA0035.20.903829
MA0039.20.71803
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.22.10982
MA0047.20.962424
MA0112.20.794478
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.11.52001
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.12.19629
MA0163.10.927936
MA0164.10.933981
MA0080.22.62187
MA0018.20.944669
MA0099.21.06348
MA0079.21.16605
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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