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MCL coexpression mm9:829: Difference between revisions

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{{MCL_coexpression_mm9
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body;0.0155878198391758;14961!GO:0042605;peptide antigen binding;0.0155878198391758;14961!GO:0042613;MHC class II protein complex;0.0155878198391758;14961!GO:0002495;antigen processing and presentation of peptide antigen via MHC class II;0.0155878198391758;14961!GO:0019886;antigen processing and presentation of exogenous peptide antigen via MHC class II;0.0155878198391758;14961!GO:0002478;antigen processing and presentation of exogenous peptide antigen;0.0155878198391758;14961!GO:0002504;antigen processing and presentation of peptide or polysaccharide antigen via MHC class II;0.0155878198391758;14961!GO:0005769;early endosome;0.0155878198391758;14961!GO:0019884;antigen processing and presentation of exogenous antigen;0.0155878198391758;14961!GO:0005770;late endosome;0.0155878198391758;14961!GO:0042611;MHC protein complex;0.0155878198391758;14961!GO:0048002;antigen processing and presentation of peptide antigen;0.0179898947319687;14961!GO:0019882;antigen processing and presentation;0.0278220089141987;14961!GO:0003823;antigen binding;0.047838884337837;14961!GO:0045786;negative regulation of progression through cell cycle;0.047838884337837;72568!GO:0042277;peptide binding;0.047838884337837;14961!GO:0006260;DNA replication;0.047838884337837;72568!GO:0009897;external side of plasma 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|gostat_on_MCL_coexpression=GO:0005771;multivesicular body;0.0155878198391758;14961!GO:0042605;peptide antigen binding;0.0155878198391758;14961!GO:0042613;MHC class II protein complex;0.0155878198391758;14961!GO:0002495;antigen processing and presentation of peptide antigen via MHC class II;0.0155878198391758;14961!GO:0019886;antigen processing and presentation of exogenous peptide antigen via MHC class II;0.0155878198391758;14961!GO:0002478;antigen processing and presentation of exogenous peptide antigen;0.0155878198391758;14961!GO:0002504;antigen processing and presentation of peptide or polysaccharide antigen via MHC class II;0.0155878198391758;14961!GO:0005769;early endosome;0.0155878198391758;14961!GO:0019884;antigen processing and presentation of exogenous antigen;0.0155878198391758;14961!GO:0005770;late endosome;0.0155878198391758;14961!GO:0042611;MHC protein complex;0.0155878198391758;14961!GO:0048002;antigen processing and presentation of peptide antigen;0.0179898947319687;14961!GO:0019882;antigen processing and presentation;0.0278220089141987;14961!GO:0003823;antigen binding;0.047838884337837;14961!GO:0045786;negative regulation of progression through cell cycle;0.047838884337837;72568!GO:0042277;peptide binding;0.047838884337837;14961!GO:0006260;DNA replication;0.047838884337837;72568!GO:0009897;external side of plasma membrane;0.047838884337837;14961!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!4.15e-21!48;UBERON:0002405!4.15e-21!48;UBERON:0002390!6.13e-18!45;UBERON:0003061!6.13e-18!45;UBERON:0004177!2.69e-14!29;UBERON:0005057!2.69e-14!29;UBERON:0000077!6.04e-12!35;UBERON:0000065!3.77e-11!41;UBERON:0001007!5.75e-11!116;UBERON:0001555!5.75e-11!116;UBERON:0007026!5.75e-11!116;UBERON:0006562!6.84e-11!24;UBERON:0001557!6.84e-11!24;UBERON:0001042!6.84e-11!24;UBERON:0008814!6.84e-11!24;UBERON:0009145!6.84e-11!24;UBERON:0001004!1.01e-10!42;UBERON:0004119!1.43e-10!118;UBERON:0000925!1.43e-10!118;UBERON:0006595!1.43e-10!118;UBERON:0002370!2.55e-10!23;UBERON:0000974!2.55e-10!23;UBERON:0004807!2.55e-10!23;UBERON:0005058!2.55e-10!23;UBERON:0003351!2.55e-10!23;UBERON:0009113!2.55e-10!23;UBERON:0003295!2.55e-10!23;UBERON:0009722!2.55e-10!23;UBERON:0005562!2.55e-10!23;UBERON:0007690!2.55e-10!23;UBERON:0004921!1.03e-09!114;UBERON:0003408!1.05e-09!24;UBERON:0000072!3.68e-09!27;UBERON:0001041!1.98e-08!80;UBERON:0000063!3.64e-07!35;UBERON:0003081!6.28e-07!87
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.227469,0.330161,1.02163,0.645379,0.40827,0.495658,0.146465,0.468136,0.133458,0.453212,0.484001,0.146657,0.507558,0.24249,0,0.696644,1.17871,0.829774,0.0703872,0.802917,0.403891,0.50668,1.20034,0.337218,0.534339,0.801525,0.428336,0.739731,0.0963992,0.414842,0.796599,1.82817,0.735537,0.242923,3.79213,0.210533,0.480503,0.559915,0.167387,0.224094,0.419787,2.49925,1.2686,0.317317,0.383899,0.618203,0.443479,0.904531,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,1.28038,0.279148,0.471658,1.25881,0.512521,0.776777,0.569793,0.952934,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.460931,0.191038,0.987652,0.116281,0.107966,0.113315,0.607043,0.759798,1.47357,0.152219,0.713779,0.568383,0.14134,0.873141,0.0800961,0.0211263,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.551605,0.515495,0.444003,0.812053,0.618454,0.585565,0.605162,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,2.6235,0.222515,0.496288,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,1.23559,0.90286,0.387557,1.05894,0.527782,1.18781,0.177062,2.55534,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,1.07771,0.621266,1.92834,0.364791,0.229209,1.10522,0.041769,0.938577,0.178329,1.3067,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,4.33966,0.345891,0.669337,0.519673,0.209556,0.482466,0.683949
|tfbs_overrepresentation_jaspar=MA0003.1;0.0854318,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;3.19463,MA0014.1;0.0421798,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.692501,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.281053,MA0050.1;1.93344,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.221677,MA0056.1;0,MA0057.1;0.0745664,MA0058.1;0.305206,MA0059.1;0.849123,MA0060.1;0.169058,MA0061.1;0.56663,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.077274,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;1.92922,MA0073.1;0.00359098,MA0074.1;0.488775,MA0076.1;1.40007,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.897217,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.18495,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.35523,MA0106.1;0.582805,MA0107.1;1.35172,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;1.36684,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.867077,MA0140.1;1.20128,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.442138,MA0146.1;0.30073,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.738221,MA0035.2;0.482026,MA0039.2;0.043355,MA0138.2;0.630612,MA0002.2;0.447007,MA0137.2;0.783415,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.200175,MA0065.2;0.44341,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.581988,MA0155.1;0.226288,MA0156.1;0.763978,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.614411,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0143037,MA0163.1;0.0124565,MA0164.1;0.508398,MA0080.2;0.737531,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.000746166,MA0102.2;1.5442,MA0258.1;0.533988,MA0259.1;0.196451,MA0442.1;0
}}

Latest revision as of 15:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:10526454..10526466,+p@chr16:10526454..10526466
+
Mm9::chr16:10526557..10526561,+p@chr16:10526557..10526561
+
Mm9::chr17:34404939..34404950,+p11@H2-Ab1
Mm9::chr17:34420121..34420133,-p@chr17:34420121..34420133
-
Mm9::chr18:60971994..60972007,+p@chr18:60971994..60972007
+
Mm9::chr18:60972021..60972032,+p@chr18:60972021..60972032
+
Mm9::chr1:87497610..87497645,+p1@Gm2427
p1@Sp140
Mm9::chr1:89549906..89549917,+p@chr1:89549906..89549917
+
Mm9::chr4:3502131..3502140,+p6@Tgs1


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:0005771multivesicular body0.0155878198391758
GO:0042605peptide antigen binding0.0155878198391758
GO:0042613MHC class II protein complex0.0155878198391758
GO:0002495antigen processing and presentation of peptide antigen via MHC class II0.0155878198391758
GO:0019886antigen processing and presentation of exogenous peptide antigen via MHC class II0.0155878198391758
GO:0002478antigen processing and presentation of exogenous peptide antigen0.0155878198391758
GO:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class II0.0155878198391758
GO:0005769early endosome0.0155878198391758
GO:0019884antigen processing and presentation of exogenous antigen0.0155878198391758
GO:0005770late endosome0.0155878198391758
GO:0042611MHC protein complex0.0155878198391758
GO:0048002antigen processing and presentation of peptide antigen0.0179898947319687
GO:0019882antigen processing and presentation0.0278220089141987
GO:0003823antigen binding0.047838884337837
GO:0045786negative regulation of progression through cell cycle0.047838884337837
GO:0042277peptide binding0.047838884337837
GO:0006260DNA replication0.047838884337837
GO:0009897external side of plasma membrane0.047838884337837



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.15e-2148
immune system4.15e-2148
hematopoietic system6.13e-1845
blood island6.13e-1845
hemopoietic organ2.69e-1429
immune organ2.69e-1429
mixed endoderm/mesoderm-derived structure6.04e-1235
respiratory tract3.77e-1141
digestive system5.75e-11116
digestive tract5.75e-11116
primitive gut5.75e-11116
pharynx6.84e-1124
upper respiratory tract6.84e-1124
chordate pharynx6.84e-1124
pharyngeal arch system6.84e-1124
pharyngeal region of foregut6.84e-1124
respiratory system1.01e-1042
endoderm-derived structure1.43e-10118
endoderm1.43e-10118
presumptive endoderm1.43e-10118
thymus2.55e-1023
neck2.55e-1023
respiratory system epithelium2.55e-1023
hemolymphoid system gland2.55e-1023
pharyngeal epithelium2.55e-1023
thymic region2.55e-1023
pharyngeal gland2.55e-1023
entire pharyngeal arch endoderm2.55e-1023
thymus primordium2.55e-1023
early pharyngeal endoderm2.55e-1023
subdivision of digestive tract1.03e-09114
gland of gut1.05e-0924
segment of respiratory tract3.68e-0927
foregut1.98e-0880
organ segment3.64e-0735
lateral plate mesoderm6.28e-0787


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)
MA0003.10.0854318
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.13.19463
MA0014.10.0421798
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.692501
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.11.93344
MA0051.10.542972
MA0052.10.84317
MA0055.10.221677
MA0056.10
MA0057.10.0745664
MA0058.10.305206
MA0059.10.849123
MA0060.10.169058
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.11.92922
MA0073.10.00359098
MA0074.10.488775
MA0076.11.40007
MA0077.10.804033
MA0078.10.575205
MA0081.10.897217
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.35523
MA0106.10.582805
MA0107.11.35172
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.11.36684
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.867077
MA0140.11.20128
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.442138
MA0146.10.30073
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.738221
MA0035.20.482026
MA0039.20.043355
MA0138.20.630612
MA0002.20.447007
MA0137.20.783415
MA0104.20.157347
MA0047.20.533516
MA0112.20.200175
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.226288
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.10.413266
MA0161.10
MA0162.10.0143037
MA0163.10.0124565
MA0164.10.508398
MA0080.20.737531
MA0018.20.51781
MA0099.20.624421
MA0079.20.000746166
MA0102.21.5442
MA0258.10.533988
MA0259.10.196451
MA0442.10
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