Personal tools

MCL coexpression mm9:1052: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0001017!1.30e-36!73;UBERON:0001016!3.17e-35!75;UBERON:0000073!1.33e-32!54;UBERON:0002346!4.55e-32!64;UBERON:0003075!4.55e-32!64;UBERON:0007284!4.55e-32!64;UBERON:0004121!4.78e-32!95;UBERON:0000924!4.78e-32!95;UBERON:0006601!4.78e-32!95;UBERON:0001049!6.56e-30!52;UBERON:0005068!6.56e-30!52;UBERON:0006241!6.56e-30!52;UBERON:0007135!6.56e-30!52;UBERON:0002020!2.12e-28!34;UBERON:0010371!1.03e-27!73;UBERON:0010314!1.65e-23!92;UBERON:0000955!2.40e-23!47;UBERON:0006238!2.40e-23!47;UBERON:0002616!2.00e-22!46;UBERON:0003528!1.20e-21!29;UBERON:0002791!1.20e-21!29;UBERON:0001893!1.20e-21!29;UBERON:0003056!8.45e-21!49;UBERON:0003080!8.48e-20!40;UBERON:0002780!9.93e-19!39;UBERON:0001890!9.93e-19!39;UBERON:0006240!9.93e-19!39;UBERON:0000956!3.24e-12!21;UBERON:0001869!3.24e-12!21;UBERON:0000203!3.24e-12!21;UBERON:0002420!1.83e-11!8;UBERON:0007245!1.83e-11!8;UBERON:0010009!1.83e-11!8;UBERON:0010011!1.83e-11!8;UBERON:0000454!1.83e-11!8;UBERON:0003076!9.24e-11!12;UBERON:0003057!9.24e-11!12;UBERON:0002240!2.31e-09!6;UBERON:0005174!2.31e-09!6;UBERON:0001137!2.31e-09!6;UBERON:0002619!8.70e-09!17;UBERON:0001948!2.76e-08!5;UBERON:0002315!2.76e-08!5;UBERON:0000025!1.92e-07!114;UBERON:0000369!2.32e-07!5;UBERON:0002435!2.32e-07!5;UBERON:0000204!2.32e-07!5;UBERON:0010082!2.32e-07!5;UBERON:0002950!8.13e-07!4;UBERON:0001891!8.13e-07!4;UBERON:0009616!8.13e-07!4;UBERON:0010286!8.13e-07!4;UBERON:0004111!8.38e-07!122
|ontology_enrichment_uberon=UBERON:0001017!1.30e-36!73;UBERON:0001016!3.17e-35!75;UBERON:0000073!1.33e-32!54;UBERON:0002346!4.55e-32!64;UBERON:0003075!4.55e-32!64;UBERON:0007284!4.55e-32!64;UBERON:0004121!4.78e-32!95;UBERON:0000924!4.78e-32!95;UBERON:0006601!4.78e-32!95;UBERON:0001049!6.56e-30!52;UBERON:0005068!6.56e-30!52;UBERON:0006241!6.56e-30!52;UBERON:0007135!6.56e-30!52;UBERON:0002020!2.12e-28!34;UBERON:0010371!1.03e-27!73;UBERON:0010314!1.65e-23!92;UBERON:0000955!2.40e-23!47;UBERON:0006238!2.40e-23!47;UBERON:0002616!2.00e-22!46;UBERON:0003528!1.20e-21!29;UBERON:0002791!1.20e-21!29;UBERON:0001893!1.20e-21!29;UBERON:0003056!8.45e-21!49;UBERON:0003080!8.48e-20!40;UBERON:0002780!9.93e-19!39;UBERON:0001890!9.93e-19!39;UBERON:0006240!9.93e-19!39;UBERON:0000956!3.24e-12!21;UBERON:0001869!3.24e-12!21;UBERON:0000203!3.24e-12!21;UBERON:0002420!1.83e-11!8;UBERON:0007245!1.83e-11!8;UBERON:0010009!1.83e-11!8;UBERON:0010011!1.83e-11!8;UBERON:0000454!1.83e-11!8;UBERON:0003076!9.24e-11!12;UBERON:0003057!9.24e-11!12;UBERON:0002240!2.31e-09!6;UBERON:0005174!2.31e-09!6;UBERON:0001137!2.31e-09!6;UBERON:0002619!8.70e-09!17;UBERON:0001948!2.76e-08!5;UBERON:0002315!2.76e-08!5;UBERON:0000025!1.92e-07!114;UBERON:0000369!2.32e-07!5;UBERON:0002435!2.32e-07!5;UBERON:0000204!2.32e-07!5;UBERON:0010082!2.32e-07!5;UBERON:0002950!8.13e-07!4;UBERON:0001891!8.13e-07!4;UBERON:0009616!8.13e-07!4;UBERON:0010286!8.13e-07!4;UBERON:0004111!8.38e-07!122
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,1.47084,0.495263,0.587291,0.594722,0.215218,0.0609112,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.792229,0.19222,0.361892,0.978328,0.27937,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,0.344372,0.145661,0.50223,0.897561,0.289148,0.166577,0.316253,0.101236,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.0742755,0.317766,0.277561,0.469348,0.714592,0.532496,0.0609361,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,1.00328,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,0.580284,0.975495,0.0369809,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.589174,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.0501572,1.21618,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,1.19218,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,1.48714,0.278874,0.573477,0.0206035
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,1.47084,0.495263,0.587291,0.594722,0.215218,0.0609112,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.792229,0.19222,0.361892,0.978328,0.27937,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,0.344372,0.145661,0.50223,0.897561,0.289148,0.166577,0.316253,0.101236,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.0742755,0.317766,0.277561,0.469348,0.714592,0.532496,0.0609361,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,1.00328,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,0.580284,0.975495,0.0369809,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.589174,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.0501572,1.21618,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,1.19218,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,1.48714,0.278874,0.573477,0.0206035
|tfbs_overrepresentation_jaspar=MA0003.1;0.0286946,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;1.17655,MA0009.1;0.92425,MA0014.1;0.425579,MA0017.1;0.89657,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,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;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.362005,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,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;0.0004304,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.0841779,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;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.719313,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;1.04809,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.585936,MA0140.1;1.3943,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.0910975,MA0146.1;0.264322,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.014361,MA0138.2;0.727395,MA0002.2;1.11916,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.631649,MA0065.2;1.0577,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.792589,MA0155.1;0.336768,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.0312493,MA0163.1;0.28052,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.0190804,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;0.26402,MA0442.1;0
}}
}}

Revision as of 12:44, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:100215439..100215457,-p5@Hap1
Mm9::chr1:38851929..38851932,-p@chr1:38851929..38851932
-
Mm9::chr1:84367076..84367079,-p@chr1:84367076..84367079
-
Mm9::chr1:84577274..84577285,-p@chr1:84577274..84577285
-
Mm9::chr5:38550223..38550234,-p@chr5:38550223..38550234
-
Mm9::chr8:116813265..116813288,+p@chr8:116813265..116813288
+
Mm9::chr8:61392493..61392501,+p@chr8:61392493..61392501
+


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:0030503regulation of cell redox homeostasis0.0120518227025482
GO:0050780dopamine receptor binding0.0120518227025482
GO:0003906DNA-(apurinic or apyrimidinic site) lyase activity0.0140593041970687
GO:0007212dopamine receptor signaling pathway0.0271062004775957



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 system1.30e-3673
nervous system3.17e-3575
regional part of nervous system1.33e-3254
neurectoderm4.55e-3264
neural plate4.55e-3264
presumptive neural plate4.55e-3264
ectoderm-derived structure4.78e-3295
ectoderm4.78e-3295
presumptive ectoderm4.78e-3295
neural tube6.56e-3052
neural rod6.56e-3052
future spinal cord6.56e-3052
neural keel6.56e-3052
gray matter2.12e-2834
ecto-epithelium1.03e-2773
structure with developmental contribution from neural crest1.65e-2392
brain2.40e-2347
future brain2.40e-2347
regional part of brain2.00e-2246
brain grey matter1.20e-2129
regional part of telencephalon1.20e-2129
telencephalon1.20e-2129
pre-chordal neural plate8.45e-2149
anterior neural tube8.48e-2040
regional part of forebrain9.93e-1939
forebrain9.93e-1939
future forebrain9.93e-1939
cerebral cortex3.24e-1221
cerebral hemisphere3.24e-1221
pallium3.24e-1221
basal ganglion1.83e-118
nuclear complex of neuraxis1.83e-118
aggregate regional part of brain1.83e-118
collection of basal ganglia1.83e-118
cerebral subcortex1.83e-118
posterior neural tube9.24e-1112
chordal neural plate9.24e-1112
spinal cord2.31e-096
dorsal region element2.31e-096
dorsum2.31e-096
regional part of cerebral cortex8.70e-0917
regional part of spinal cord2.76e-085
gray matter of spinal cord2.76e-085
tube1.92e-07114
corpus striatum2.32e-075
striatum2.32e-075
ventral part of telencephalon2.32e-075
future corpus striatum2.32e-075
regional part of midbrain8.13e-074
midbrain8.13e-074
presumptive midbrain8.13e-074
midbrain neural tube8.13e-074
anatomical conduit8.38e-07122


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)
MA0003.10.0286946
MA0004.10.481116
MA0006.10.311391
MA0007.11.17655
MA0009.10.92425
MA0014.10.425579
MA0017.10.89657
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
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
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
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
MA0073.10.0004304
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.11.04809
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.585936
MA0140.11.3943
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.264322
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.014361
MA0138.20.727395
MA0002.21.11916
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.631649
MA0065.21.0577
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.792589
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.0312493
MA0163.10.28052
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.0190804
MA0102.21.65195
MA0258.10.688848
MA0259.10.26402
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1052&oldid=2574447"