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MCL coexpression mm9:1661: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.749484749564373,0,0,0,0,0,0,0,0.0215489710494058,0,0,0,0,0,0,0,0,0,0,0,0.279861112062358,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0939036784206324,0.0872004331952016,0.104376848465594,1.48053201464612,0.297588351271036,0.918276613729044,1.0385016927778,1.09934461594207,0.67343175300822,0,0,0,0,0,0,0.623423703856061,0.606004520226781,0.725233468576698,1.02752058112369,1.27177658398003,0,0,0,0.936606828538206,0.893932852350843,0.406344191827532,0.392820329034968,0.411849951255441,0.393863470857367,0.422241566619074,0.157320083371159,0.228075801515011,0.181231738828597,0.391802669100403,0.522900663478156,0.401577834184896,1.00041002339324,1.10400240417331,1.01215742130269,0.478333864871846,0.396770342928593,0.517332634180475,0.514532933493103,0.499771211944417,0.622057285408293,0.108695652924206,0.143097898616902,0,0,0,0,0,0,0.118156949352509,0,0,0,0.134485549733331,0,0,0,0,0,0,0.0505418237368047,0,0.0120218238822,0.0138955327120455,0,0.0360489519589911,0,0,0,0,0,0,0,0,0,0,1.13390906383163,1.14561658677587,0,0,0,0,0.424518321431224,0.453463619968952,0.326602205826783,0.431343875182545,0.328084481723575,0.557740879041715,0.469168320590355,0.00842365674734102,0,0,0.151193542793892,0.570406469842373,0.426322189502793,0.504748592086331,0.45677106522575,0.498423745920274,0.415085071551046,0.478542677088365,0.310160490125005,0.590195999336396,0.390168808163855,0.243342874882006,0.143422122491795,0.0597165754397842,0.0978194453764078,0.0879545103752686,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.455016219705889,0.739599606703127,0,0,0,0,0.0105285910075999,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0150722621482758,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.43996831156504,0.423106445101373,0,0,0,0,0,0,0,0,0,0,0,0.588978613212759,0,0,0,0,0,0,0,0,0.0224742000359274,0,0,0,0,0,0,0,0.0705567514818088,0.64199460662754,0.72514932801085,0.685194531372846,0.679763898883752,0.799668129063246,0.616494897359036,0.510464723188677,0.0183102993199983,0,0,0.0439978072508772,0.0260023651116661,0.019532287555174,0,0.0132011095126881,0,0.355267117720455,0,0,0,0,0,0,0,0,0,0,0.0890632907208169,0,0,0,0.0343106184397177,0,0.0068978932917068,0,0,0,0,0.0121030453696687,0,0,0.0105510834322885,0.0135596422127217,0.00963840937126184,0.0106313975787212,0.00866139862179864,0,0,0,0,0,0,0,0,0.00985876082734042,0,0.00835481695976514,0,0,0,0,0,0,0.427808963205389,0.563973636486927,0.27581228863512,0,0,0,0,0,0.180395257187065,0.236972700309992,0.229692739311546,0.334791168041013,0.0906484693834816,0.249716165829837,0.119019364751072,0.220672995635257,0.289555393091344,0.183471165844846,0.567266797169378,0.467749986758138,0.419944893280978,0.309078295907822,0.362652023774368,0.23638696082109,0.287238259031487,0.215279058474979,0.235367072073697,0.204233418286662,0.192419418115929,0.267380350767943,0.284259645209069,0.329718410939333,0.331831126671663,0.228182892432858,0.311776026123353,0.231335112191592,0.187073146083346,0.262191990839168,0.145968571097416,0.187165751693537,0.260264560823872,0.258956829569938,0.194786569405062,0.26527553050005,0.24161183929839,0.159560444466239,0.289934488247973,0.253330078481407,0.257038382947846,0.256515956929726,0.266659714327891,0.23822795293961,0.195228714010501,0.536018119017093,0.236066643964888,0.226585765253813,0.181077540170765,0.116369266941668,0.0512053545100115|coexpression_dpi_cluster_scores_median=0.510824244082147,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202843190349958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0975327392940296,0,0,1.40233244054464,0.157169655903251,0.938970616713988,1.05326229372246,0.738746122005671,0.829310372422698,0,0,0,0,0,0,0.345157758033838,0.493592419892616,0.62004825170176,0.871458866273337,1.0990184190822,0,0,0,0.784845567325522,0.830157019553306,0.23699733111204,0.257687123905543,0.265124516696068,0.385294277714033,0.274959667229359,0.0501827898833331,0.0761636383140293,0,0.322458878535173,0.58082481854121,0.49837830748604,0.769362010722669,0.864074633699696,0.945158291458137,0.470451800356371,0.327466262382121,0.31588384183826,0.338160423388235,0.384481874606599,0.456972173289286,0.0612459843014792,0.0316393102377815,0,0,0,0,0,0,0.0570741246689917,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.24044252434001,1.25946557724611,0,0,0,0,0.161179842546876,0.451786805560604,0.302165236663908,0.310256870570088,0.305966219492192,0.568347784343862,0.444771224149836,0,0,0,0.0829439327499637,0.361955201335006,0.0898705446131073,0.187573281223881,0.243911736413968,0.275190262573239,0.0990682757404326,0.265599679938124,0.249469886918853,0.270043106933592,0.244629442017072,0.130945290313773,0.0860734338295156,0,0.12977112683364,0.0812688455295622,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.393053673693912,0.565318781032302,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.29298744963777,0.336883187795113,0,0,0,0,0,0,0,0,0,0,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during development;0.0408015330915254;22772!GO:0001843;neural tube closure;0.0408015330915254;22772!GO:0014020;primary neural tube formation;0.0408015330915254;22772!GO:0001841;neural tube formation;0.0408015330915254;22772!GO:0001839;neural plate morphogenesis;0.0408015330915254;22772!GO:0001838;embryonic epithelial tube formation;0.0408015330915254;22772!GO:0001840;neural plate development;0.0408015330915254;22772!GO:0021915;neural tube development;0.0408015330915254;22772!GO:0016331;morphogenesis of embryonic epithelium;0.0408015330915254;22772!GO:0008270;zinc ion binding;0.0427512187222919;22772,22774!GO:0003677;DNA 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|gostat_on_MCL_coexpression=GO:0048066;pigmentation during development;0.0408015330915254;22772!GO:0001843;neural tube closure;0.0408015330915254;22772!GO:0014020;primary neural tube formation;0.0408015330915254;22772!GO:0001841;neural tube formation;0.0408015330915254;22772!GO:0001839;neural plate morphogenesis;0.0408015330915254;22772!GO:0001838;embryonic epithelial tube formation;0.0408015330915254;22772!GO:0001840;neural plate development;0.0408015330915254;22772!GO:0021915;neural tube development;0.0408015330915254;22772!GO:0016331;morphogenesis of embryonic epithelium;0.0408015330915254;22772!GO:0008270;zinc ion binding;0.0427512187222919;22772,22774!GO:0003677;DNA binding;0.0427512187222919;22772,22774!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!3.66e-32!75;UBERON:0001017!8.75e-32!73;UBERON:0000073!2.00e-30!54;UBERON:0002346!4.65e-30!64;UBERON:0003075!4.65e-30!64;UBERON:0007284!4.65e-30!64;UBERON:0004121!1.52e-29!95;UBERON:0000924!1.52e-29!95;UBERON:0006601!1.52e-29!95;UBERON:0001049!2.24e-28!52;UBERON:0005068!2.24e-28!52;UBERON:0006241!2.24e-28!52;UBERON:0007135!2.24e-28!52;UBERON:0010371!3.67e-25!73;UBERON:0000955!3.76e-25!47;UBERON:0006238!3.76e-25!47;UBERON:0002616!3.08e-24!46;UBERON:0003056!1.50e-23!49;UBERON:0003080!1.22e-19!40;UBERON:0002780!2.57e-19!39;UBERON:0001890!2.57e-19!39;UBERON:0006240!2.57e-19!39;UBERON:0002020!1.99e-16!34;UBERON:0010314!1.08e-15!92;UBERON:0003528!3.93e-13!29;UBERON:0002791!3.93e-13!29;UBERON:0001893!3.93e-13!29;UBERON:0003076!2.86e-09!12;UBERON:0003057!2.86e-09!12;UBERON:0000956!1.37e-07!21;UBERON:0001869!1.37e-07!21;UBERON:0000203!1.37e-07!21;UBERON:0002420!1.99e-07!8;UBERON:0007245!1.99e-07!8;UBERON:0010009!1.99e-07!8;UBERON:0010011!1.99e-07!8;UBERON:0000454!1.99e-07!8;UBERON:0001894!2.63e-07!10;UBERON:0006222!2.63e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.557864,2.0905,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,1.22306,0.668936,0.702872,1.47559,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,2.70973,0.253145,1.08876,4.8835,1.00043,0.699032,0.360612,3.29853,0.401916,0.631725,0.134724,0.426986,0.4934,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,2.19087,0.30684,0.904104,1.23259,0.714607,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.970369,0.297068,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.806207,1.05152,0.848095,2.47367,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,2.15911,0.491483,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,1.11665,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,2.2879,1.72039,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,1.5287,0.851091,2.18247,0.569503,0.408309,0.230371,1.93643,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,2.31811,0.90208,0.741834,0.997706,0.701187,0.191104
|tfbs_overrepresentation_jaspar=MA0003.1;0.6678,MA0004.1;0.603793,MA0006.1;1.07705,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.736185,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;1.12075,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;1.68574,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.881183,MA0061.1;0.364227,MA0063.1;0,MA0066.1;1.76548,MA0067.1;1.41352,MA0068.1;1.71065,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;1.13827,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;1.33193,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.453686,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.693075,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;1.30068,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.8026,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;0.21827,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.749235,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.845917,MA0047.2;0.75686,MA0112.2;0.47695,MA0065.2;0.929207,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;2.45609,MA0163.1;1.79895,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;16.6343,MA0102.2;1.79669,MA0258.1;0.91616,MA0259.1;1.71005,MA0442.1;0
}}

Latest revision as of 17:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:122873999..122874022,+p@chr14:122873999..122874022
+
Mm9::chr14:122874619..122874634,+p1@Zic2
Mm9::chr14:122874718..122874729,+p3@Zic2
Mm9::chr9:91260797..91260807,+p@chr9:91260797..91260807
+
Mm9::chr9:91263649..91263666,+p3@Zic4


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:0048066pigmentation during development0.0408015330915254
GO:0001843neural tube closure0.0408015330915254
GO:0014020primary neural tube formation0.0408015330915254
GO:0001841neural tube formation0.0408015330915254
GO:0001839neural plate morphogenesis0.0408015330915254
GO:0001838embryonic epithelial tube formation0.0408015330915254
GO:0001840neural plate development0.0408015330915254
GO:0021915neural tube development0.0408015330915254
GO:0016331morphogenesis of embryonic epithelium0.0408015330915254
GO:0008270zinc ion binding0.0427512187222919
GO:0003677DNA binding0.0427512187222919



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
nervous system3.66e-3275
central nervous system8.75e-3273
regional part of nervous system2.00e-3054
neurectoderm4.65e-3064
neural plate4.65e-3064
presumptive neural plate4.65e-3064
ectoderm-derived structure1.52e-2995
ectoderm1.52e-2995
presumptive ectoderm1.52e-2995
neural tube2.24e-2852
neural rod2.24e-2852
future spinal cord2.24e-2852
neural keel2.24e-2852
ecto-epithelium3.67e-2573
brain3.76e-2547
future brain3.76e-2547
regional part of brain3.08e-2446
pre-chordal neural plate1.50e-2349
anterior neural tube1.22e-1940
regional part of forebrain2.57e-1939
forebrain2.57e-1939
future forebrain2.57e-1939
gray matter1.99e-1634
structure with developmental contribution from neural crest1.08e-1592
brain grey matter3.93e-1329
regional part of telencephalon3.93e-1329
telencephalon3.93e-1329
posterior neural tube2.86e-0912
chordal neural plate2.86e-0912
cerebral cortex1.37e-0721
cerebral hemisphere1.37e-0721
pallium1.37e-0721
basal ganglion1.99e-078
nuclear complex of neuraxis1.99e-078
aggregate regional part of brain1.99e-078
collection of basal ganglia1.99e-078
cerebral subcortex1.99e-078
diencephalon2.63e-0710
future diencephalon2.63e-0710


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)
MA0003.10.6678
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.10.736185
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.11.12075
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.11.68574
MA0058.10.50032
MA0059.10.513699
MA0060.10.881183
MA0061.10.364227
MA0063.10
MA0066.11.76548
MA0067.11.41352
MA0068.11.71065
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.11.13827
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.11.33193
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.453686
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.693075
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.11.30068
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.8026
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.21827
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.749235
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.20.47695
MA0065.20.929207
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.12.45609
MA0163.11.79895
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.216.6343
MA0102.21.79669
MA0258.10.91616
MA0259.11.71005
MA0442.10
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