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MCL coexpression mm9:310: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.055070113547423,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0118216574128583,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.035202928666058,1.16634720980688,1.01924236818323,1.09864867715926,0.656335006687276,1.10560791765994,0,0,0,0,0,0.00450846790957537,0.229126297154297,0.18440492317299,0.187851281963206,0.30460546191316,0.194137048382478,0,0,0,0.531070089863674,0.685041203424323,0.0767151235804777,0.103807782330171,0.0888728720123763,0.109123086691028,0.158886068781892,0.125410958215438,0.129850362348878,0.0119519548953858,0,0.0754810338909,0.0892020436121397,0.201976684819149,0.167173527440445,0.131492242390828,0.106932678779961,0.0939251254928708,0.0752915237218914,0.0764722564738793,0.152287014265237,0.172361582440384,0,0.0158196551188907,0,0,0,0,0,0,0,0,0,0,0.0998184172516369,0,0,0,0,0,0,0,0,0,0.0163347936360048,0,0,0,0.0482820047261801,0,0,0,0,0,0,0,0,0.111524892460631,0.0797455792814942,0,0,0,0,0.0606187686764715,0.0765552211653049,0.114126735408367,0.0696031033168343,0.0433433224925046,0.143151907118368,0.0652962901395099,0.0438871819959951,0,0,0,0.0697780171824802,0.0898705446131073,0.0719048733411253,0.114588096764985,0.0944906627908513,0.0638386338766093,0.0643339036485596,0.0346875105146374,0,0,0,0.0081911752528061,0,0,0,0.0788315948399074,0,0,0,0,0,0,0.015070339025847,0,0.00233150193700966,0,0,0,0,0,0,0,0,0,0.102593174710261,0.150373517227954,0,0,0,0.00687906287434665,0,0,0,0,0,0,0,0,0,0,0,0,0.0496607367237308,0.0234910315133595,0,0,0,0.0222312594113811,0,0,0,0.0103747336588277,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0345906816709774,0.0293361777120366,0,0,0,0,0.0763464167751715,0.0914641362800683,0,0,0,0,0,0,0,0,0,0,0,0.0992575684980309,0.0288216590713588,0.0355847379748454,0.042591468988957,0.0110656948797366,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0719044921483595,0.150885517879741,0.0807835351053761,0.101369427228017,0.141050998109045,0.120910660233855,0.286896103856254,0.0540288213421369,0,0,0,0,0.0121406059579025,0,0.00418111471036131,0,0.0738741926906438,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0691464475647109,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00696268039035666,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00769854306636345,0,0,0,0,0,0.0688732037536692,0,0,0,0.0788803310556245,0,0,0.0428854115575944,0.145825435924841,0.0684580848992459,0.0773465043408035,0.0709509021908485,0,0,0.081359932135904,0.010027113822846,0,0,0.0196455196028344,0.0388749848471105,0.0287224103779109,0.0472245945615809,0.00758303103297175,0.0476191773904887,0.0140925469837791,0,0.0764702160109658,0.0565777012070054,0.056376699265577,0.00137562735405759,0.0386701282459582,0.0438474322863328,0.0358789786559309,0.107406965401072,0,0.0553034373508932,0.0440909896023284,0.107885315233444,0.0315606893466336,0.0506284326429643,0.0625582350728301,0.0520315924683041,0.136412877324794,0.0142677941185571,0.0845301845292944,0.0593592565930236,0,0
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000117!9.33e-16!23;CL:0000337!9.33e-16!23;CL:0000221!1.25e-15!44;CL:0000133!1.25e-15!44;CL:0002319!5.64e-15!43;CL:0000055!2.57e-12!49;CL:0000540!2.44e-09!33;CL:0000047!2.44e-09!33;CL:0000031!2.44e-09!33;CL:0000404!2.44e-09!33;CL:0002453!2.09e-08!8;CL:0000333!2.88e-07!10;CL:0000095!2.88e-07!10;CL:0000243!2.88e-07!10;CL:0000123!2.88e-07!10;CL:0000125!2.88e-07!10;CL:0000030!2.88e-07!10;CL:0000339!2.88e-07!10;CL:0000393!3.02e-07!39;CL:0000211!3.02e-07!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!2.05e-25!95;UBERON:0000924!2.05e-25!95;UBERON:0006601!2.05e-25!95;UBERON:0001017!8.33e-25!73;UBERON:0002346!1.48e-24!64;UBERON:0003075!1.48e-24!64;UBERON:0007284!1.48e-24!64;UBERON:0001016!1.75e-24!75;UBERON:0010371!5.47e-23!73;UBERON:0001049!8.91e-23!52;UBERON:0005068!8.91e-23!52;UBERON:0006241!8.91e-23!52;UBERON:0007135!8.91e-23!52;UBERON:0000073!1.02e-22!54;UBERON:0000955!5.44e-19!47;UBERON:0006238!5.44e-19!47;UBERON:0002616!2.63e-18!46;UBERON:0003056!3.35e-18!49;UBERON:0010314!3.55e-16!92;UBERON:0003080!1.44e-14!40;UBERON:0002780!3.97e-14!39;UBERON:0001890!3.97e-14!39;UBERON:0006240!3.97e-14!39;UBERON:0002020!2.26e-12!34;UBERON:0003076!2.66e-09!12;UBERON:0003057!2.66e-09!12;UBERON:0003528!5.60e-09!29;UBERON:0002791!5.60e-09!29;UBERON:0001893!5.60e-09!29;UBERON:0002420!4.47e-07!8;UBERON:0007245!4.47e-07!8;UBERON:0010009!4.47e-07!8;UBERON:0010011!4.47e-07!8;UBERON:0000454!4.47e-07!8
|tfbs_overrepresentation_for_novel_motifs=0.621914,1.17119,0.950477,0.110767,0.0338634,0.378043,0.515388,0.528496,0.564338,1.08404,0.145866,0.165604,1.50543,0.534797,0.633867,0,0.321317,0.30426,1.03294,0.328824,0.825721,1.15977,0.533361,0.134743,0.578246,0.199623,0.255738,0.130569,0.725665,0.720335,0.776612,0.403236,0.550846,0.377102,0.353617,0.673368,0.117656,0.163319,0.458864,0.378664,0.132316,1.28568,0.274829,0.0397417,0.788056,0.341631,0.260475,0.432194,0.0596407,0.418159,0.307679,0.622986,0.281475,0.524674,0.540069,0.546195,0.764448,0.927074,1.62294,0.184626,0.386651,0.224758,0.187517,0.298968,0.193388,0.330595,0.662968,0.992392,0.382806,0.851665,0.88603,0.0128424,0.348591,0.569888,0.611922,1.84383,0.859115,0.252107,0.372571,0.0625114,0.555365,0.33504,0.223742,0.145927,0.468641,3.17549,0.00317853,1.67541,0.264106,1.14963,0.72731,0.472928,0.41392,0.331179,0.235792,0.0178769,0.519307,0.416272,0.260664,0.126056,0.117729,0.403003,0.509378,0.308141,0.307322,0.394918,0.933867,0.426161,0.0645424,0.481537,0.605231,0.510939,0.489443,1.43163,1.74022,0.891587,2.3114,2.38566,0.322341,0.511817,0.574718,0.282956,0.20086,0.251444,0.784453,0.375593,0.178582,1.05168,0.661578,0.337079,0.494561,0.106861,0.634573,0.195077,0.753996,0.10416,1.58192,0.397628,0.708276,1.51166,1.11861,0.667289,0.209097,0.411967,1.48198,0.125712,0.262785,1.47245,0.313761,1.7854,0.4991,0.58793,0.526055,0.0191336,1.07655,0.598868,0.218838,0.165822,0.29593,0.310177,0.717087,0.467905,0.375957,0.599911,0.299755,0.1895,1.20145,0.1646,1.14034
}}

Latest revision as of 15:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:83903404..83903420,-p1@Nuak1
Mm9::chr11:8368453..8368462,-p9@Tns3
Mm9::chr12:112910294..112910300,-p@chr12:112910294..112910300
-
Mm9::chr15:30576269..30576327,+p@chr15:30576269..30576327
+
Mm9::chr15:30576422..30576441,+p@chr15:30576422..30576441
+
Mm9::chr15:89011111..89011131,-p2@Plxnb2
Mm9::chr16:18392647..18392715,+p1@Arvcf
Mm9::chr16:18392724..18392736,+p3@Arvcf
Mm9::chr19:8788690..8788697,-p17@Slc3a2
Mm9::chr19:8788816..8788826,-p14@Slc3a2
Mm9::chr1:88563264..88563269,-p@chr1:88563264..88563269
-
Mm9::chr1:88567140..88567154,-p1@Nppc
Mm9::chr2:37631749..37631778,+p1@Crb2
Mm9::chr2:37631779..37631794,+p3@Crb2
Mm9::chr2:37631801..37631817,+p2@Crb2
Mm9::chr3:89028994..89029006,+p5@Thbs3
Mm9::chr3:89030096..89030118,+p4@Thbs3
Mm9::chr5:143722156..143722172,+p2@Fscn1
Mm9::chr7:150253440..150253446,+p@chr7:150253440..150253446
+
Mm9::chr7:52147728..52147799,-p1@Med25
Mm9::chr8:11006242..11006246,-p@chr8:11006242..11006246
-
Mm9::chr9:20550677..20550695,-p@chr9:20550677..20550695
-
Mm9::chr9:20550706..20550724,-p@chr9:20550706..20550724
-
Mm9::chr9:50564531..50564547,+p@chr9:50564531..50564547
+
Mm9::chr9:91266261..91266282,+p5@Zic4
Mm9::chrX:97925319..97925333,+p2@Gdpd2


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>

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.05e-2595
ectoderm2.05e-2595
presumptive ectoderm2.05e-2595
central nervous system8.33e-2573
neurectoderm1.48e-2464
neural plate1.48e-2464
presumptive neural plate1.48e-2464
nervous system1.75e-2475
ecto-epithelium5.47e-2373
neural tube8.91e-2352
neural rod8.91e-2352
future spinal cord8.91e-2352
neural keel8.91e-2352
regional part of nervous system1.02e-2254
brain5.44e-1947
future brain5.44e-1947
regional part of brain2.63e-1846
pre-chordal neural plate3.35e-1849
structure with developmental contribution from neural crest3.55e-1692
anterior neural tube1.44e-1440
regional part of forebrain3.97e-1439
forebrain3.97e-1439
future forebrain3.97e-1439
gray matter2.26e-1234
posterior neural tube2.66e-0912
chordal neural plate2.66e-0912
brain grey matter5.60e-0929
regional part of telencephalon5.60e-0929
telencephalon5.60e-0929
basal ganglion4.47e-078
nuclear complex of neuraxis4.47e-078
aggregate regional part of brain4.47e-078
collection of basal ganglia4.47e-078
cerebral subcortex4.47e-078


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)
MA0003.13.64505
MA0004.10.111027
MA0006.10.148601
MA0007.10.336966
MA0009.11.0889
MA0014.11.83794
MA0017.10.176804
MA0019.10.279241
MA0024.10.388875
MA0025.10.630472
MA0027.12.00714
MA0028.10.364782
MA0029.10.371051
MA0030.10.376415
MA0031.10.347586
MA0038.10.199569
MA0040.10.435948
MA0041.10.0735541
MA0042.10.0677776
MA0043.10.5085
MA0046.10.45588
MA0048.10.605593
MA0050.10.132769
MA0051.10.205659
MA0052.10.442788
MA0055.10.711074
MA0056.10
MA0057.10.540273
MA0058.10.0648829
MA0059.10.0701674
MA0060.10.6347
MA0061.10.1011
MA0063.10
MA0066.10.192176
MA0067.10.732677
MA0068.10.221384
MA0069.10.443076
MA0070.10.434849
MA0071.10.132283
MA0072.10.427684
MA0073.11.80107
MA0074.10.16874
MA0076.10.198312
MA0077.10.409496
MA0078.10.228674
MA0081.10.275922
MA0083.10.507806
MA0084.11.04444
MA0087.10.470385
MA0088.10.693904
MA0089.10
MA0090.10.310535
MA0091.11.23907
MA0092.10.642661
MA0093.10.168245
MA0095.10
MA0098.10
MA0100.10.161426
MA0101.10.257705
MA0103.10.188828
MA0105.10.202372
MA0106.11.23051
MA0107.10.0483046
MA0108.20.804161
MA0109.10
MA0111.10.675922
MA0113.11.80466
MA0114.10.0991
MA0115.10.51095
MA0116.10.96881
MA0117.10.48285
MA0119.10.549042
MA0122.10.500096
MA0124.10.683426
MA0125.10.615761
MA0130.10
MA0131.10.27582
MA0132.10
MA0133.10
MA0135.10.540552
MA0136.10.181597
MA0139.11.47263
MA0140.10.161354
MA0141.10.463338
MA0142.10.336004
MA0143.10.641011
MA0144.10.0236754
MA0145.10.763719
MA0146.16.07914
MA0147.10.272153
MA0148.10.119923
MA0149.11.96047
MA0062.20.0342153
MA0035.20.164312
MA0039.21.9986
MA0138.20.269868
MA0002.20.153717
MA0137.20.0570096
MA0104.20.175212
MA0047.20.199051
MA0112.20.373458
MA0065.20.23538
MA0150.10.336809
MA0151.10
MA0152.10.199123
MA0153.10.55531
MA0154.11.79665
MA0155.12.58343
MA0156.10.197316
MA0157.10.310784
MA0158.10
MA0159.10.121887
MA0160.10.385618
MA0161.10
MA0162.10.533446
MA0163.11.22186
MA0164.10.536173
MA0080.20.182919
MA0018.20.551637
MA0099.20.26517
MA0079.23.07565
MA0102.21.09525
MA0258.10.221064
MA0259.10.103104
MA0442.10
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