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MCL coexpression mm9:155: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002384!4.03e-10!46;UBERON:0002390!5.14e-09!45;UBERON:0003061!5.14e-09!45;UBERON:0002193!9.81e-09!48;UBERON:0002405!9.81e-09!48;UBERON:0004177!3.67e-07!29;UBERON:0005057!3.67e-07!29
|ontology_enrichment_uberon=UBERON:0002384!4.03e-10!46;UBERON:0002390!5.14e-09!45;UBERON:0003061!5.14e-09!45;UBERON:0002193!9.81e-09!48;UBERON:0002405!9.81e-09!48;UBERON:0004177!3.67e-07!29;UBERON:0005057!3.67e-07!29
|tfbs_overrepresentation_for_novel_motifs=1.67218,0.798761,1.4764,0.107778,0.0330129,0.121302,0.43144,0.679706,0.201894,1.09863,1.1989,0.0828532,1.31279,1.08797,0.0930402,0,0.966374,0.0290369,0.137749,0.125862,0.0897051,0.973409,6.93552,0.139535,0.139667,0.522591,0.0372582,0.757472,0.547524,1.17753,0.704978,0.124072,1.12737,0.132784,1.3558,0.0333481,3.41306,0.971158,0.015876,0.511055,0.135321,1.02853,0.0696442,0.0158354,0.855749,2.343,0.421869,0.319718,0.215708,0.560083,0.915373,1.32698,0.45114,1.11255,1.15519,1.52789,0.0284166,2.16485,0.340883,1.1098,0.739728,1.83975,0.0883417,0.239977,2.06047,0.594885,0.307518,0.589877,0.360768,0.464798,1.33944,0.118968,5.52115,0.665474,1.31398,0.258993,0.682935,0.710405,0.106229,0.0383216,0.121337,2.07552,0.60804,1.01342,2.18541,3.1718,0.107751,0.195724,0.754219,0.734853,0.944652,1.54506,0.130522,0.080852,0.654823,0.106166,0.103209,1.3268,0.189615,0.0478438,0.00790021,0.39164,0.562883,0.538349,0.251407,2.21093,2.85083,0.528648,0.0989187,0.181236,0.286323,0.565488,0.187405,2.06288,0.364879,0.34905,0.457342,1.61977,0.970211,0.183675,0.673794,0.0605122,0.118917,0.178038,0.407157,0.349892,0.0955753,0.796753,0.306417,0.263415,0.1827,0.216324,0.285246,0.50668,0.38158,0.037352,0.0797499,0.475134,0.343906,1.08119,0.705903,0.310944,0.0313611,0.405531,0.895345,1.0307,0.19231,1.04312,0.026894,1.83034,0.518988,8.94632,0.590836,0.427058,0.271017,0.25788,0.13902,0.196646,0.0231171,3.04605,1.65524,1.52564,0.108148,0.680542,0.0682834,0.487254,0.109066,0.401915,0.0642238
|tfbs_overrepresentation_for_novel_motifs=1.67218,0.798761,1.4764,0.107778,0.0330129,0.121302,0.43144,0.679706,0.201894,1.09863,1.1989,0.0828532,1.31279,1.08797,0.0930402,0,0.966374,0.0290369,0.137749,0.125862,0.0897051,0.973409,6.93552,0.139535,0.139667,0.522591,0.0372582,0.757472,0.547524,1.17753,0.704978,0.124072,1.12737,0.132784,1.3558,0.0333481,3.41306,0.971158,0.015876,0.511055,0.135321,1.02853,0.0696442,0.0158354,0.855749,2.343,0.421869,0.319718,0.215708,0.560083,0.915373,1.32698,0.45114,1.11255,1.15519,1.52789,0.0284166,2.16485,0.340883,1.1098,0.739728,1.83975,0.0883417,0.239977,2.06047,0.594885,0.307518,0.589877,0.360768,0.464798,1.33944,0.118968,5.52115,0.665474,1.31398,0.258993,0.682935,0.710405,0.106229,0.0383216,0.121337,2.07552,0.60804,1.01342,2.18541,3.1718,0.107751,0.195724,0.754219,0.734853,0.944652,1.54506,0.130522,0.080852,0.654823,0.106166,0.103209,1.3268,0.189615,0.0478438,0.00790021,0.39164,0.562883,0.538349,0.251407,2.21093,2.85083,0.528648,0.0989187,0.181236,0.286323,0.565488,0.187405,2.06288,0.364879,0.34905,0.457342,1.61977,0.970211,0.183675,0.673794,0.0605122,0.118917,0.178038,0.407157,0.349892,0.0955753,0.796753,0.306417,0.263415,0.1827,0.216324,0.285246,0.50668,0.38158,0.037352,0.0797499,0.475134,0.343906,1.08119,0.705903,0.310944,0.0313611,0.405531,0.895345,1.0307,0.19231,1.04312,0.026894,1.83034,0.518988,8.94632,0.590836,0.427058,0.271017,0.25788,0.13902,0.196646,0.0231171,3.04605,1.65524,1.52564,0.108148,0.680542,0.0682834,0.487254,0.109066,0.401915,0.0642238
|tfbs_overrepresentation_jaspar=MA0003.1;3.2964,MA0004.1;2.44894,MA0006.1;3.09178,MA0007.1;0.365969,MA0009.1;0.137565,MA0014.1;1.78353,MA0017.1;0.0576737,MA0019.1;0.0588475,MA0024.1;1.222,MA0025.1;0.282065,MA0027.1;1.56857,MA0028.1;12.5599,MA0029.1;0.105371,MA0030.1;0.351128,MA0031.1;0.308469,MA0038.1;0.522404,MA0040.1;0.144181,MA0041.1;0.00252973,MA0042.1;0.00205235,MA0043.1;1.06796,MA0046.1;0.156939,MA0048.1;0.128959,MA0050.1;0.146538,MA0051.1;0.295556,MA0052.1;0.148517,MA0055.1;0.288374,MA0056.1;0,MA0057.1;0.0970412,MA0058.1;1.97665,MA0059.1;2.9438,MA0060.1;1.63614,MA0061.1;0.0849529,MA0063.1;0,MA0066.1;0.0259328,MA0067.1;0.363901,MA0068.1;0.315448,MA0069.1;0.454571,MA0070.1;0.143488,MA0071.1;0.145644,MA0072.1;0.139001,MA0073.1;0.000199984,MA0074.1;0.216729,MA0076.1;17.7815,MA0077.1;0.127837,MA0078.1;0.150459,MA0081.1;1.53932,MA0083.1;0.191806,MA0084.1;0.637349,MA0087.1;0.498602,MA0088.1;1.19595,MA0089.1;0,MA0090.1;0.176187,MA0091.1;0.0427098,MA0092.1;0.0799772,MA0093.1;2.53737,MA0095.1;0,MA0098.1;0,MA0100.1;1.74594,MA0101.1;0.590319,MA0103.1;0.0255075,MA0105.1;0.645571,MA0106.1;0.645595,MA0107.1;0.127792,MA0108.2;0.509763,MA0109.1;0,MA0111.1;0.560854,MA0113.1;0.574532,MA0114.1;0.238773,MA0115.1;0.565506,MA0116.1;0.163922,MA0117.1;0.174766,MA0119.1;0.2364,MA0122.1;0.186489,MA0124.1;0.323825,MA0125.1;0.270734,MA0130.1;0,MA0131.1;2.24263,MA0132.1;0,MA0133.1;0,MA0135.1;0.214898,MA0136.1;1.49234,MA0139.1;4.22676,MA0140.1;0.201721,MA0141.1;0.652668,MA0142.1;0.0863477,MA0143.1;0.0371917,MA0144.1;0.247755,MA0145.1;0.093031,MA0146.1;3.984,MA0147.1;7.76057,MA0148.1;0.256362,MA0149.1;0.406861,MA0062.2;22.0544,MA0035.2;0.0816244,MA0039.2;1.67011,MA0138.2;0.0547361,MA0002.2;0.26171,MA0137.2;1.14867,MA0104.2;8.08443,MA0047.2;0.116955,MA0112.2;0.193997,MA0065.2;0.0941152,MA0150.1;0.204799,MA0151.1;0,MA0152.1;0.117033,MA0153.1;0.640472,MA0154.1;0.348726,MA0155.1;0.362756,MA0156.1;3.77915,MA0157.1;0.0735967,MA0158.1;0,MA0159.1;0.202755,MA0160.1;0.261608,MA0161.1;0,MA0162.1;2.66367,MA0163.1;1.14213,MA0164.1;0.745201,MA0080.2;1.28199,MA0018.2;1.54617,MA0099.2;0.052724,MA0079.2;0.166561,MA0102.2;1.63717,MA0258.1;0.00370057,MA0259.1;3.53761,MA0442.1;0
}}
}}

Revision as of 11:16, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79755198..79755240,+p1@LOC100046223
p1@Rps15
Mm9::chr10:80040030..80040072,-p1@Klf16
Mm9::chr11:101303726..101303753,+p2@Gm6341
p2@Rpl27
Mm9::chr11:116532972..116533008,+p1@1810032O08Rik
Mm9::chr11:120319407..120319461,+p1@Ccdc137
Mm9::chr11:120459828..120459832,-p2@Alyref
Mm9::chr11:51433233..51433315,+p1@Nhp2
Mm9::chr11:6428710..6428783,-p1@ENSMUST00000134527
p1@ENSMUST00000147762
p1@uc007hyu.1
Mm9::chr11:70468590..70468607,+p@chr11:70468590..70468607
+
Mm9::chr11:70796449..70796487,-p1@C1qbp
Mm9::chr11:82721862..82721902,-p1@Nle1
Mm9::chr11:93746585..93746603,+p@chr11:93746585..93746603
+
Mm9::chr11:97888297..97888306,+p4@LOC100045367
p4@LOC100505098
p4@Rpl19
Mm9::chr12:29320732..29320752,-p2@Rps7
Mm9::chr12:85291584..85291655,+p1@2410016O06Rik
Mm9::chr12:88784750..88784800,-p1@Alkbh1
Mm9::chr13:38750860..38750907,-p1@Eef1e1
Mm9::chr14:115440183..115440200,+p@chr14:115440183..115440200
+
Mm9::chr15:76199314..76199366,+p1@Fam203a
Mm9::chr15:76307669..76307689,-p1@Bop1
Mm9::chr16:43889614..43889620,-p@chr16:43889614..43889620
-
Mm9::chr17:26389860..26389928,+p1@Luc7l
Mm9::chr17:27693450..27693456,-p@chr17:27693450..27693456
-
Mm9::chr17:36053285..36053356,-p1@Mrps18b
Mm9::chr17:46384918..46384949,-p1@Polr1c
Mm9::chr17:56752815..56752848,+p2@Gm13611
p2@Gm4604
p2@LOC637553
p2@Rpl36
Mm9::chr18:35713055..35713075,+p1@Mir1949
p1@Snhg4
p1@Snora74a
Mm9::chr18:35713090..35713099,+p2@Mir1949
p2@Snhg4
p2@Snora74a
Mm9::chr18:35713237..35713250,+p@chr18:35713237..35713250
+
Mm9::chr18:36919868..36919946,+p1@Wdr55
Mm9::chr18:75160169..75160213,+p1@Gm10294
p1@Rpl17
Mm9::chr19:8810298..8810354,+p1@Wdr74
Mm9::chr19:9028376..9028428,+p1@Tut1
Mm9::chr1:88339113..88339129,-p@chr1:88339113..88339129
-
Mm9::chr2:103636127..103636172,+p@chr2:103636127..103636172
+
Mm9::chr2:128926736..128926802,+p1@Polr1b
Mm9::chr2:130100160..130100171,+p2@Nop56
Mm9::chr2:130100173..130100190,+p1@Nop56
Mm9::chr2:158187197..158187203,-p2@ENSMUST00000151331
Mm9::chr2:158187208..158187239,-p1@ENSMUST00000151331
Mm9::chr2:158187241..158187290,-p1@9430008C03Rik
Mm9::chr3:53267588..53267603,+p5@2810046L04Rik
Mm9::chr4:108520432..108520500,+p1@Kti12
Mm9::chr4:116793325..116793344,+p@chr4:116793325..116793344
+
Mm9::chr4:116828680..116828690,-p1@Gm10712
p1@Gm14438
p1@Gm15501
p1@Rps8
Mm9::chr4:117564599..117564645,-p1@Dph2
Mm9::chr4:131830192..131830242,-p@chr4:131830192..131830242
-
Mm9::chr4:131864583..131864603,+p1@Snhg12
Mm9::chr4:140255714..140255738,-p@chr4:140255714..140255738
-
Mm9::chr4:46402333..46402373,+p@chr4:46402333..46402373
+
Mm9::chr4:46465444..46465487,-p@chr4:46465444..46465487
-
Mm9::chr5:100858522..100858542,-p1@ENSMUST00000145557
p1@ENSMUST00000157057
Mm9::chr5:111082367..111082441,-p1@Noc4l
Mm9::chr5:121654525..121654565,+p1@Gm6136
p1@Rpl6
Mm9::chr5:77739074..77739119,-p1@Noa1
Mm9::chr6:124662056..124662089,-p1@Emg1
Mm9::chr6:124662297..124662371,+p1@Phb2
Mm9::chr7:134404134..134404190,-p1@Dctpp1
Mm9::chr7:26474167..26474188,-p@chr7:26474167..26474188
-
Mm9::chr7:88490075..88490123,-p1@Gm12034
p1@Rps17
Mm9::chr8:109580770..109580813,+p1@Nip7
Mm9::chr8:109948929..109948956,-p1@Nob1
Mm9::chr8:112741848..112741904,+p1@Ftsjd1
Mm9::chr8:113580219..113580284,+p1@Exosc6
Mm9::chr8:125000096..125000123,+p2@Ctu2
Mm9::chr8:126544834..126544855,-p3@Taf5l
Mm9::chr8:126544943..126545006,-p2@Taf5l
Mm9::chr8:87380881..87380935,+p1@Farsa
Mm9::chr9:106379610..106379683,+p1@Rrp9
Mm9::chr9:20692685..20692727,+p1@Ppan
Mm9::chr9:20692734..20692739,+p3@Ppan
Mm9::chrX:71167178..71167255,-p1@Arhgap4
p1@Naa10


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:0042254ribosome biogenesis and assembly1.00013597454651e-12
GO:0022613ribonucleoprotein complex biogenesis and assembly3.61177819270213e-11
GO:0016072rRNA metabolic process1.62462010528162e-08
GO:0006364rRNA processing1.62462010528162e-08
GO:0005634nucleus4.56303732299683e-06
GO:0010467gene expression3.10161958225887e-05
GO:0003723RNA binding6.22388570224254e-05
GO:0030529ribonucleoprotein complex0.000170816863319853
GO:0006996organelle organization and biogenesis0.000170816863319853
GO:0043229intracellular organelle0.000171792290831652
GO:0043226organelle0.000171792290831652
GO:0006396RNA processing0.000392453499792763
GO:0006412translation0.00114282554772659
GO:0043231intracellular membrane-bound organelle0.00124496728621528
GO:0043227membrane-bound organelle0.00124496728621528
GO:0044424intracellular part0.0014898188539095
GO:0003735structural constituent of ribosome0.00179559093047457
GO:0005840ribosome0.00192713336044085
GO:0033279ribosomal subunit0.00192713336044085
GO:0016043cellular component organization and biogenesis0.00204234959259176
GO:0005622intracellular0.00238014475926356
GO:0016070RNA metabolic process0.00556516708943367
GO:0009059macromolecule biosynthetic process0.00564158888009098
GO:0005730nucleolus0.00731290439283323
GO:0015934large ribosomal subunit0.0120031896100776
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0132041180727467
GO:0043517positive regulation of DNA damage response, signal transduction by p53 class mediator0.0136787059307971
GO:0030490maturation of SSU-rRNA0.0136787059307971
GO:0050265RNA uridylyltransferase activity0.0136787059307971
GO:0043170macromolecule metabolic process0.0149370948646656
GO:0044249cellular biosynthetic process0.0159091344868345
GO:0005830cytosolic ribosome (sensu Eukaryota)0.0201417948554072
GO:0042274ribosomal small subunit biogenesis and assembly0.020313434972658
GO:0001826inner cell mass cell differentiation0.020313434972658
GO:0042273ribosomal large subunit biogenesis and assembly0.020313434972658
GO:0043516regulation of DNA damage response, signal transduction by p53 class mediator0.020313434972658
GO:0001560regulation of cell growth by extracellular stimulus0.020313434972658
GO:0032991macromolecular complex0.020313434972658
GO:0017101aminoacyl-tRNA synthetase multienzyme complex0.0270233926871202
GO:0006432phenylalanyl-tRNA aminoacylation0.0270233926871202
GO:0030684preribosome0.0270233926871202
GO:0004826phenylalanine-tRNA ligase activity0.0270233926871202
GO:0030685nucleolar preribosome0.0270233926871202
GO:0043526neuroprotection0.0352525252211054
GO:0001825blastocyst formation0.0418590485762787
GO:0043232intracellular non-membrane-bound organelle0.0418590485762787
GO:0043228non-membrane-bound organelle0.0418590485762787
GO:0003676nucleic acid binding0.0451472474732762
GO:0009058biosynthetic process0.0460364227298273
GO:0044445cytosolic part0.0496546276881865



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
connective tissue4.03e-1046
hematopoietic system5.14e-0945
blood island5.14e-0945
hemolymphoid system9.81e-0948
immune system9.81e-0948
hemopoietic organ3.67e-0729
immune organ3.67e-0729


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)
MA0003.13.2964
MA0004.12.44894
MA0006.13.09178
MA0007.10.365969
MA0009.10.137565
MA0014.11.78353
MA0017.10.0576737
MA0019.10.0588475
MA0024.11.222
MA0025.10.282065
MA0027.11.56857
MA0028.112.5599
MA0029.10.105371
MA0030.10.351128
MA0031.10.308469
MA0038.10.522404
MA0040.10.144181
MA0041.10.00252973
MA0042.10.00205235
MA0043.11.06796
MA0046.10.156939
MA0048.10.128959
MA0050.10.146538
MA0051.10.295556
MA0052.10.148517
MA0055.10.288374
MA0056.10
MA0057.10.0970412
MA0058.11.97665
MA0059.12.9438
MA0060.11.63614
MA0061.10.0849529
MA0063.10
MA0066.10.0259328
MA0067.10.363901
MA0068.10.315448
MA0069.10.454571
MA0070.10.143488
MA0071.10.145644
MA0072.10.139001
MA0073.10.000199984
MA0074.10.216729
MA0076.117.7815
MA0077.10.127837
MA0078.10.150459
MA0081.11.53932
MA0083.10.191806
MA0084.10.637349
MA0087.10.498602
MA0088.11.19595
MA0089.10
MA0090.10.176187
MA0091.10.0427098
MA0092.10.0799772
MA0093.12.53737
MA0095.10
MA0098.10
MA0100.11.74594
MA0101.10.590319
MA0103.10.0255075
MA0105.10.645571
MA0106.10.645595
MA0107.10.127792
MA0108.20.509763
MA0109.10
MA0111.10.560854
MA0113.10.574532
MA0114.10.238773
MA0115.10.565506
MA0116.10.163922
MA0117.10.174766
MA0119.10.2364
MA0122.10.186489
MA0124.10.323825
MA0125.10.270734
MA0130.10
MA0131.12.24263
MA0132.10
MA0133.10
MA0135.10.214898
MA0136.11.49234
MA0139.14.22676
MA0140.10.201721
MA0141.10.652668
MA0142.10.0863477
MA0143.10.0371917
MA0144.10.247755
MA0145.10.093031
MA0146.13.984
MA0147.17.76057
MA0148.10.256362
MA0149.10.406861
MA0062.222.0544
MA0035.20.0816244
MA0039.21.67011
MA0138.20.0547361
MA0002.20.26171
MA0137.21.14867
MA0104.28.08443
MA0047.20.116955
MA0112.20.193997
MA0065.20.0941152
MA0150.10.204799
MA0151.10
MA0152.10.117033
MA0153.10.640472
MA0154.10.348726
MA0155.10.362756
MA0156.13.77915
MA0157.10.0735967
MA0158.10
MA0159.10.202755
MA0160.10.261608
MA0161.10
MA0162.12.66367
MA0163.11.14213
MA0164.10.745201
MA0080.21.28199
MA0018.21.54617
MA0099.20.052724
MA0079.20.166561
MA0102.21.63717
MA0258.10.00370057
MA0259.13.53761
MA0442.10
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