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MCL coexpression mm9:159: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.064513712786576,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.179051645532617,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.675940999735182,0.760491754914107,0.681511539650463,0,0,0,0,0,0,0,0.150221463778622,0.147681830935052,0.122898517376903,0.877008478396901,0.842824499331024,0.276481849788278,0.282864857432175,0.28312448614836,0.877784039392966,0.794849055410241,0.844517856919114,0.73324286993079,0.724218554124095,0.651538698462017,0.779978241563323,0.858395864009762,0.845633272713636,0.898856889284108,0.821074351777541,0.724833668352426,0,0,0,0,0,0,0,0,0.0301583286619172,0,0,0,0.0626722748382988,0,0,0,0,0,0,0.00292210879839535,0,0.0568749727366705,0.0694776635602275,0.111584068254384,0.0423154657708865,0.06097065795378,0.0917293418104957,0,0,0,0,0,0,0,0,0.237886831843786,0.268647776772344,0,0,0,0,0.815299137565835,0.469607032052358,0.469376130431555,0.438288824846147,0.436437301610595,0.784105470891499,0.662553775625478,0,0,0,0.0829439327499637,0.0540832088517389,0.0997998355226637,0.134906098324995,0.162886375277492,0.207453528713667,0.179682427843873,0.193739510044836,0.181102009199648,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.408781082094384,0.335122014717603,0,0,0,0.021584016565783,0.0526332442203703,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.782244067430569,0.764968517387691,0,0,0.104130841177619,0,0.0847275925579778,0,0,0,0,0.10753161633046,0.010686784090611,0.466560377831798,0,0.00595453829624705,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.127508051874503,0.0719044921483595,0.142413261346553,0.0843392403965415,0.101297763209344,0.186138497248578,0.219635884762414,0.280157689426283,0,0,0,0,0,0,0,0,0,0.697733289957992,0,0,0,0,0,0,0,0,0,0,0.0637715600712905,0.0499201424910975,0.0441832952821187,0.0142200454582979,0,0.00356875530830709,0.0279421632588873,0,0,0,0,0,0,0.0446994780424601,0.00750586070323995,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.406380466917586,0.376754964798171,0.331587424856164,0.35904152682956,0.374778587894724,0.399810008829701,0.347733015792894,0.355426251657825,0.372806586713801,0.407098602473158,0.081914003768173,0.15091263877167,0.179609468438842,0.17208118264908,0.211878289366281,0.190760324464606,0.168571332836902,0.209006745960922,0.215330413983256,0.17765030293269,0.245620709720879,0.194758206527804,0.193639056320997,0.223225275270844,0.191064405934859,0.169172763866184,0.194871354222781,0.183587767881725,0.14986111676545,0.201068050435521,0.128033729919821,0.185379913858661,0.169342968499384,0.199037798091534,0.232418784975152,0.224511532029221,0.156791318503149,0.151241448900246,0.199132253957242,0.193442483447008,0.201382397922935,0.203085505727974,0.171559908186711,0.165781451382873,0.169417641246843,0.329015238880389,0.230907198759394,0.155257708002722,0.140689222355642,0.0865703124974023,0.0905641158318875
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000117!6.49e-19!23;CL:0000337!6.49e-19!23;CL:0000540!1.10e-14!33;CL:0000047!1.10e-14!33;CL:0000031!1.10e-14!33;CL:0000404!1.10e-14!33;CL:0000393!8.78e-11!39;CL:0000211!8.78e-11!39;CL:0000221!4.71e-09!44;CL:0000133!4.71e-09!44;CL:0002319!7.47e-09!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!2.10e-33!64;UBERON:0003075!2.10e-33!64;UBERON:0007284!2.10e-33!64;UBERON:0000073!2.82e-32!54;UBERON:0001017!2.38e-30!73;UBERON:0001049!4.00e-30!52;UBERON:0005068!4.00e-30!52;UBERON:0006241!4.00e-30!52;UBERON:0007135!4.00e-30!52;UBERON:0001016!6.81e-29!75;UBERON:0010371!2.63e-28!73;UBERON:0004121!6.42e-27!95;UBERON:0000924!6.42e-27!95;UBERON:0006601!6.42e-27!95;UBERON:0003056!2.30e-26!49;UBERON:0000955!3.81e-25!47;UBERON:0006238!3.81e-25!47;UBERON:0002616!2.53e-24!46;UBERON:0003080!4.73e-23!40;UBERON:0002020!2.75e-22!34;UBERON:0010314!3.02e-22!92;UBERON:0002780!4.10e-22!39;UBERON:0001890!4.10e-22!39;UBERON:0006240!4.10e-22!39;UBERON:0003528!1.42e-17!29;UBERON:0002791!1.42e-17!29;UBERON:0001893!1.42e-17!29;UBERON:0000956!6.08e-11!21;UBERON:0001869!6.08e-11!21;UBERON:0000203!6.08e-11!21;UBERON:0002619!2.06e-09!17;UBERON:0002021!3.05e-08!10;UBERON:0000411!3.05e-08!10;UBERON:0001950!3.05e-08!10;UBERON:0002420!3.49e-08!8;UBERON:0007245!3.49e-08!8;UBERON:0010009!3.49e-08!8;UBERON:0010011!3.49e-08!8;UBERON:0000454!3.49e-08!8;UBERON:0003076!1.91e-07!12;UBERON:0003057!1.91e-07!12;UBERON:0002240!6.68e-07!6;UBERON:0005174!6.68e-07!6;UBERON:0001137!6.68e-07!6
|tfbs_overrepresentation_for_novel_motifs=1.82285,1.49607,0.959637,0.00888262,0.0155219,0.141691,0.771071,0.220346,0.509642,1.93731,0.631068,0.0960945,2.73698,0.811899,0.0203752,0,2.10149,0.0846981,0.381396,0.560097,0.109263,0.0602581,0.808867,0.0921416,0.72253,1.30232,0.798617,0.164923,2.13789,1.36988,0.512945,0.135777,0.395468,0.256915,0.940932,0.996131,0.713559,1.05843,0.180561,0.792828,0.0892053,1.92124,0.361216,0.0559589,1.56177,3.014,0.21056,0.183603,0.474423,0.282874,0.0807928,0.358322,0.313403,0.218428,0.229722,0.524656,0.0103861,1.404,0.300923,0.82912,0.789819,1.03531,0.292036,0.263878,0.300477,0.309939,0.868094,0.611288,0.123175,1.21717,4.65833,0.0889362,0.93455,0.252042,3.73378,1.86714,0.108957,2.18408,0.117024,0.792122,0.496499,0.652515,0.0422022,0.0363566,0.528748,1.79914,0.0368391,3.07109,0.215447,0.757302,0.378015,0.535906,0.142533,0.45797,0.9807,0.221133,1.21073,0.870036,0.0579033,0.891662,0.233994,0.421601,0.207371,0.582445,0.275862,1.12486,0.346084,0.588221,0.0508276,1.05034,0.772373,1.13166,0.563381,2.21479,0.383507,0.412018,4.21972,0.464142,0.619292,0.347998,2.02431,0.241307,0.135319,0.767238,1.09127,0.378421,0.110007,0.429992,0.865579,0.192221,0.196823,0.434468,0.302288,0.128584,0.400489,1.53315,0.0955038,0.314065,0.362159,1.10499,0.728176,0.328549,0.03658,1.38469,0.960414,1.50456,0.213666,1.06682,0.209408,0.177719,0.117054,1.74725,0.219435,1.67031,0.302927,0.27426,0.0402799,0.132442,0.0288269,0.578634,0.369481,0.178272,0.119046,0.762498,0.0767232,1.2346,0.230882,0.095045,0.0555954
}}

Latest revision as of 14:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:3557824..3557841,-p2@Oprm1
Mm9::chr10:79602092..79602115,-p1@Dos
Mm9::chr11:100217392..100217410,-p1@Hap1
Mm9::chr11:100217415..100217422,-p3@Hap1
Mm9::chr11:105881429..105881481,+p@chr11:105881429..105881481
+
Mm9::chr11:33743526..33743629,-p1@Kcnip1
Mm9::chr11:46048962..46048973,+p1@C030019I05Rik
Mm9::chr11:68760875..68760914,-p3@Arhgef15
Mm9::chr11:82201059..82201070,+p@chr11:82201059..82201070
+
Mm9::chr12:106575018..106575047,+p2@ENSMUST00000138649
p2@uc007oyg.1
Mm9::chr12:106575370..106575380,+p3@uc007oyh.1
Mm9::chr12:106575405..106575435,+p1@uc007oyh.1
Mm9::chr12:109843967..109844024,+p5@Evl
Mm9::chr12:82434116..82434207,-p1@Slc8a3
Mm9::chr13:111071094..111071114,-p5@Rab3c
Mm9::chr13:14615293..14615304,-p3@Hecw1
Mm9::chr14:76903992..76904056,+p6@Tsc22d1
Mm9::chr14:96918286..96918321,-p1@Klhl1
Mm9::chr16:20621503..20621520,-p4@Camk2n2
Mm9::chr17:24625528..24625611,+p1@Caskin1
Mm9::chr17:47825908..47825919,+p7@Frs3
Mm9::chr17:47825941..47825956,+p5@Frs3
Mm9::chr17:8533892..8533912,+p@chr17:8533892..8533912
+
Mm9::chr17:93598688..93598748,+p2@Adcyap1
Mm9::chr18:37460464..37460489,+p1@Pcdhb3
Mm9::chr18:86881030..86881042,+p3@Cbln2
Mm9::chr19:45886783..45886797,-p2@Kcnip2
Mm9::chr1:89052702..89052720,-p1@Ecel1
Mm9::chr2:120070791..120070807,-p4@Pla2g4e
Mm9::chr2:120070813..120070841,-p2@Pla2g4e
Mm9::chr2:164786309..164786333,+p4@Slc12a5
Mm9::chr2:164786346..164786363,+p3@Slc12a5
Mm9::chr2:171868546..171868561,-p1@Cbln4
Mm9::chr2:180773900..180773933,-p3@Chrna4
Mm9::chr2:180773937..180773987,-p1@Chrna4
Mm9::chr2:32597922..32597930,-p@chr2:32597922..32597930
-
Mm9::chr2:70400911..70400928,+p12@Gad1
Mm9::chr5:145497411..145497422,-p@chr5:145497411..145497422
-
Mm9::chr5:145522434..145522445,-p2@Tmem130
Mm9::chr5:145522447..145522500,-p1@Tmem130
Mm9::chr5:145522502..145522513,-p3@Tmem130
Mm9::chr5:27230997..27231021,+p9@Dpp6
Mm9::chr6:144997329..144997341,-p14@Bcat1
Mm9::chr6:82889628..82889646,-p3@Sema4f
Mm9::chr7:106416063..106416074,+p5@Mtap6
Mm9::chr7:134094351..134094362,+p8@Sez6l2
Mm9::chr7:16858609..16858680,-p1@Prr24
Mm9::chr7:54389067..54389090,-p5@Ptpn5
Mm9::chr7:57230598..57230710,+p1@Nell1
Mm9::chr7:58877250..58877261,+p9@Slc17a6
Mm9::chr7:58877364..58877383,+p5@Slc17a6
Mm9::chr7:58877403..58877419,+p2@Slc17a6
Mm9::chr7:88638750..88638757,-p6@Ap3b2
Mm9::chr8:111061744..111061761,-p@chr8:111061744..111061761
-
Mm9::chr8:116729490..116729542,+p1@Vat1l
Mm9::chr9:20842219..20842239,-p1@ENSMUST00000164156
Mm9::chr9:59437137..59437160,+p2@Celf6
Mm9::chrX:33735923..33735927,+p4@Zcchc12
Mm9::chrX:33735933..33735940,+p3@Zcchc12
Mm9::chrX:33735945..33735954,+p2@Zcchc12
Mm9::chrX:33735963..33735988,+p1@Zcchc12
Mm9::chrX:56387556..56387569,-p11@Fgf13
Mm9::chrX:56387570..56387597,-p7@Fgf13
Mm9::chrX:70070500..70070522,+p2@Gabrq
Mm9::chrX:70070529..70070552,+p1@Gabrq
Mm9::chrX:8469480..8469498,+p2@B630019K06Rik
Mm9::chrX:8469502..8469549,+p1@B630019K06Rik
Mm9::chrX:8469569..8469580,+p3@B630019K06Rik


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

no results for this coexpression

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>

Cell Type
Ontology termp-valuen
CNS neuron (sensu Vertebrata)6.49e-1923
neuroblast (sensu Vertebrata)6.49e-1923
neuron1.10e-1433
neuronal stem cell1.10e-1433
neuroblast1.10e-1433
electrically signaling cell1.10e-1433
electrically responsive cell8.78e-1139
electrically active cell8.78e-1139
ectodermal cell4.71e-0944
neurectodermal cell4.71e-0944
neural cell7.47e-0943

Uber Anatomy
Ontology termp-valuen
neurectoderm2.10e-3364
neural plate2.10e-3364
presumptive neural plate2.10e-3364
regional part of nervous system2.82e-3254
central nervous system2.38e-3073
neural tube4.00e-3052
neural rod4.00e-3052
future spinal cord4.00e-3052
neural keel4.00e-3052
nervous system6.81e-2975
ecto-epithelium2.63e-2873
ectoderm-derived structure6.42e-2795
ectoderm6.42e-2795
presumptive ectoderm6.42e-2795
pre-chordal neural plate2.30e-2649
brain3.81e-2547
future brain3.81e-2547
regional part of brain2.53e-2446
anterior neural tube4.73e-2340
gray matter2.75e-2234
structure with developmental contribution from neural crest3.02e-2292
regional part of forebrain4.10e-2239
forebrain4.10e-2239
future forebrain4.10e-2239
brain grey matter1.42e-1729
regional part of telencephalon1.42e-1729
telencephalon1.42e-1729
cerebral cortex6.08e-1121
cerebral hemisphere6.08e-1121
pallium6.08e-1121
regional part of cerebral cortex2.06e-0917
occipital lobe3.05e-0810
visual cortex3.05e-0810
neocortex3.05e-0810
basal ganglion3.49e-088
nuclear complex of neuraxis3.49e-088
aggregate regional part of brain3.49e-088
collection of basal ganglia3.49e-088
cerebral subcortex3.49e-088
posterior neural tube1.91e-0712
chordal neural plate1.91e-0712
spinal cord6.68e-076
dorsal region element6.68e-076
dorsum6.68e-076


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)
MA0003.12.56374
MA0004.10.263095
MA0006.11.17241
MA0007.10.415612
MA0009.10.894862
MA0014.14.79813
MA0017.10.0283029
MA0019.10.508551
MA0024.10.399217
MA0025.10.299033
MA0027.11.59306
MA0028.10.0590028
MA0029.10.371368
MA0030.10.379701
MA0031.10.102488
MA0038.10.314733
MA0040.10.156803
MA0041.10.00337066
MA0042.10.0553845
MA0043.10.206742
MA0046.10.170091
MA0048.12.59141
MA0050.10.0134646
MA0051.10.140991
MA0052.10.942575
MA0055.11.10834
MA0056.10
MA0057.12.60291
MA0058.10.384059
MA0059.10.42044
MA0060.10.315193
MA0061.10.0231162
MA0063.10
MA0066.10.547234
MA0067.10.382513
MA0068.10.057532
MA0069.10.486441
MA0070.10.15608
MA0071.10.16835
MA0072.10.151397
MA0073.10.33392
MA0074.10.747758
MA0076.10.0015666
MA0077.10.139722
MA0078.10.169181
MA0081.10.305571
MA0083.10.594808
MA0084.10.659146
MA0087.10.179974
MA0088.12.09621
MA0089.10
MA0090.10.205646
MA0091.10.0513933
MA0092.10.58063
MA0093.10.240778
MA0095.10
MA0098.10
MA0100.10.229158
MA0101.10.0647202
MA0103.10.646529
MA0105.10.338932
MA0106.10.0464356
MA0107.10.0764875
MA0108.20.552839
MA0109.10
MA0111.10.40249
MA0113.10.038551
MA0114.10.0526218
MA0115.10.60017
MA0116.10.907982
MA0117.10.188603
MA0119.10.14809
MA0122.10.200745
MA0124.10.341692
MA0125.10.287434
MA0130.10
MA0131.10.231424
MA0132.10
MA0133.10
MA0135.10.230079
MA0136.10.11333
MA0139.10.766799
MA0140.11.04515
MA0141.10.102147
MA0142.11.08989
MA0143.10.37661
MA0144.10.00772757
MA0145.10.848634
MA0146.10.631171
MA0147.10.495378
MA0148.10.144071
MA0149.19.4988
MA0062.20.0340781
MA0035.21.06514
MA0039.22.47647
MA0138.20.836845
MA0002.20.322235
MA0137.20.0118915
MA0104.20.906201
MA0047.20.1332
MA0112.20.447453
MA0065.20.703581
MA0150.10.112612
MA0151.10
MA0152.10.133285
MA0153.10.241059
MA0154.10.328485
MA0155.10.263276
MA0156.10.0103518
MA0157.10.280866
MA0158.10
MA0159.10.542829
MA0160.10.298337
MA0161.10
MA0162.15.06293
MA0163.12.58152
MA0164.10.113593
MA0080.20.156528
MA0018.20.0291998
MA0099.20.0599619
MA0079.224.742
MA0102.20.706336
MA0258.10.153154
MA0259.10.193476
MA0442.10
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