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MCL coexpression mm9:1082: Difference between revisions

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{{MCL_coexpression_mm9
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replication;0.0296968162132516;114741,21975!GO:0006259;DNA metabolic process;0.0296968162132516;114741,230484,21975!GO:0003917;DNA topoisomerase type I activity;0.0296968162132516;21975!GO:0006281;DNA repair;0.0296968162132516;114741,230484!GO:0005832;chaperonin-containing T-complex;0.0296968162132516;12462!GO:0008641;small protein activating enzyme activity;0.0296968162132516;!GO:0003916;DNA topoisomerase activity;0.0296968162132516;21975!GO:0006974;response to DNA damage stimulus;0.0296968162132516;114741,230484!GO:0043170;macromolecule metabolic process;0.0296968162132516;114741,12462,230484,75062,21975!GO:0006265;DNA topological change;0.0296968162132516;21975!GO:0032392;DNA geometric change;0.0296968162132516;21975!GO:0006268;DNA unwinding during replication;0.0296968162132516;21975!GO:0032508;DNA duplex unwinding;0.0296968162132516;21975!GO:0009719;response to endogenous stimulus;0.0299976368010458;114741,230484!GO:0044424;intracellular part;0.0330601004047649;114741,12462,230484,51810,75062,21975!GO:0005622;intracellular;0.0393223373439133;114741,12462,230484,51810,75062,21975!GO:0006304;DNA modification;0.0402409540760293;21975!GO:0044238;primary metabolic process;0.0402409540760293;114741,12462,230484,75062,21975!GO:0044237;cellular metabolic process;0.0402409540760293;114741,12462,230484,75062,21975!GO:0005694;chromosome;0.0402409540760293;114741,21975!GO:0043283;biopolymer metabolic 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|gostat_on_MCL_coexpression=GO:0006260;DNA replication;0.0296968162132516;114741,21975!GO:0006259;DNA metabolic process;0.0296968162132516;114741,230484,21975!GO:0003917;DNA topoisomerase type I activity;0.0296968162132516;21975!GO:0006281;DNA repair;0.0296968162132516;114741,230484!GO:0005832;chaperonin-containing T-complex;0.0296968162132516;12462!GO:0008641;small protein activating enzyme activity;0.0296968162132516;!GO:0003916;DNA topoisomerase activity;0.0296968162132516;21975!GO:0006974;response to DNA damage stimulus;0.0296968162132516;114741,230484!GO:0043170;macromolecule metabolic process;0.0296968162132516;114741,12462,230484,75062,21975!GO:0006265;DNA topological change;0.0296968162132516;21975!GO:0032392;DNA geometric change;0.0296968162132516;21975!GO:0006268;DNA unwinding during replication;0.0296968162132516;21975!GO:0032508;DNA duplex unwinding;0.0296968162132516;21975!GO:0009719;response to endogenous stimulus;0.0299976368010458;114741,230484!GO:0044424;intracellular part;0.0330601004047649;114741,12462,230484,51810,75062,21975!GO:0005622;intracellular;0.0393223373439133;114741,12462,230484,51810,75062,21975!GO:0006304;DNA modification;0.0402409540760293;21975!GO:0044238;primary metabolic process;0.0402409540760293;114741,12462,230484,75062,21975!GO:0044237;cellular metabolic process;0.0402409540760293;114741,12462,230484,75062,21975!GO:0005694;chromosome;0.0402409540760293;114741,21975!GO:0043283;biopolymer metabolic process;0.0402409540760293;114741,230484,75062,21975!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000153!4.90e-10!43;UBERON:0001048!1.14e-08!134;UBERON:0004177!2.20e-08!29;UBERON:0005057!2.20e-08!29;UBERON:0007811!1.01e-07!36
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.215218,0.478312,1.34037,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.112498,0.374752,0.08187,1.45867,0.29769,0.419327,1.51917,0.184473,1.28465,0.344372,0.446946,0.50223,0.897561,0.78719,0.498917,0.848378,0.468714,2.14888,0.57142,0.717242,0.652422,0.295233,0.507468,0.0742755,0.317766,1.19315,0.469348,1.70029,0.532496,0.0609361,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,1.14464,2.08885,1.09164,0.507615,0.482617,0.166511,0.703064,0.859987,0.378988,0.610783,1.90329,0.663039,0.580284,0.975495,2.93639,0.374181,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,2.01867,0.237542,0.203879,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,1.74385,0.430942,1.02459,0.380122,1.35148,1.27206,0.293461,2.11126,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,1.5026,1.00568,0.473246,1.16374,0.620831,1.29374,0.979575,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.813943,0.886471,1.92168,1.04192,0.681896,0.619892,1.12411,0.655955,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.433127
|tfbs_overrepresentation_jaspar=MA0003.1;0.79075,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.694761,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;2.04116,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;3.25502,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.40238,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;1.0092,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;1.22438,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.121435,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.00782298,MA0074.1;0.580087,MA0076.1;3.47313,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;1.07783,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.285759,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.0468,MA0103.1;0.348572,MA0105.1;0.488671,MA0106.1;0.677988,MA0107.1;0.906859,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;1.74348,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.585936,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;1.33652,MA0145.1;0.631666,MA0146.1;0.493711,MA0147.1;0.753844,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;4.58642,MA0035.2;0.573016,MA0039.2;0.557969,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.957645,MA0104.2;0.624968,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.336768,MA0156.1;0.936991,MA0157.1;0.781683,MA0158.1;0,MA0159.1;1.4173,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.878466,MA0163.1;0.116706,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.16158,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:60590743..60590786,-p1@Top3a
Mm9::chr14:52816857..52816882,-p2@LOC100505120
p2@Supt16h
Mm9::chr1:180267837..180267864,-p2@Hnrnpu
Mm9::chr3:88101118..88101140,+p3@Cct3
Mm9::chr4:124392053..124392123,+p1@Sf3a3
Mm9::chr4:98590599..98590667,+p1@Usp1
Mm9::chr7:34953535..34953601,-p1@Uba2


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:0006260DNA replication0.0296968162132516
GO:0006259DNA metabolic process0.0296968162132516
GO:0003917DNA topoisomerase type I activity0.0296968162132516
GO:0006281DNA repair0.0296968162132516
GO:0005832chaperonin-containing T-complex0.0296968162132516
GO:0008641small protein activating enzyme activity0.0296968162132516
GO:0003916DNA topoisomerase activity0.0296968162132516
GO:0006974response to DNA damage stimulus0.0296968162132516
GO:0043170macromolecule metabolic process0.0296968162132516
GO:0006265DNA topological change0.0296968162132516
GO:0032392DNA geometric change0.0296968162132516
GO:0006268DNA unwinding during replication0.0296968162132516
GO:0032508DNA duplex unwinding0.0296968162132516
GO:0009719response to endogenous stimulus0.0299976368010458
GO:0044424intracellular part0.0330601004047649
GO:0005622intracellular0.0393223373439133
GO:0006304DNA modification0.0402409540760293
GO:0044238primary metabolic process0.0402409540760293
GO:0044237cellular metabolic process0.0402409540760293
GO:0005694chromosome0.0402409540760293
GO:0043283biopolymer metabolic process0.0402409540760293



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
anterior region of body4.90e-1043
primordium1.14e-08134
hemopoietic organ2.20e-0829
immune organ2.20e-0829
craniocervical region1.01e-0736


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)
MA0003.10.79075
MA0004.10.481116
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.10.694761
MA0017.10.337808
MA0019.10.740036
MA0024.12.04116
MA0025.11.15921
MA0027.12.57545
MA0028.13.25502
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.11.0092
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.11.22438
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.00782298
MA0074.10.580087
MA0076.13.47313
MA0077.10.905143
MA0078.10.670113
MA0081.11.07783
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.10.906859
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.11.74348
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.585936
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.11.33652
MA0145.10.631666
MA0146.10.493711
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.24.58642
MA0035.20.573016
MA0039.20.557969
MA0138.20.727395
MA0002.20.205289
MA0137.20.957645
MA0104.20.624968
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.336768
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.11.4173
MA0160.10.50056
MA0161.10
MA0162.10.878466
MA0163.10.116706
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.16158
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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