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MCL coexpression mm9:295: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000117!2.59e-20!23;CL:0000337!2.59e-20!23;CL:0000540!2.24e-12!33;CL:0000047!2.24e-12!33;CL:0000031!2.24e-12!33;CL:0000404!2.24e-12!33;CL:0000221!1.61e-10!44;CL:0000133!1.61e-10!44;CL:0002319!3.26e-10!43;CL:0000393!3.60e-09!39;CL:0000211!3.60e-09!39;CL:0000055!7.09e-08!49;CL:0002609!1.24e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!2.39e-36!64;UBERON:0003075!2.39e-36!64;UBERON:0007284!2.39e-36!64;UBERON:0000073!2.40e-35!54;UBERON:0001049!1.74e-33!52;UBERON:0005068!1.74e-33!52;UBERON:0006241!1.74e-33!52;UBERON:0007135!1.74e-33!52;UBERON:0003056!5.44e-32!49;UBERON:0010371!1.80e-31!73;UBERON:0001017!9.13e-31!73;UBERON:0001016!2.23e-30!75;UBERON:0004121!2.53e-30!95;UBERON:0000924!2.53e-30!95;UBERON:0006601!2.53e-30!95;UBERON:0000955!1.19e-29!47;UBERON:0006238!1.19e-29!47;UBERON:0002616!1.53e-28!46;UBERON:0002020!1.46e-27!34;UBERON:0003080!1.11e-26!40;UBERON:0002780!9.47e-26!39;UBERON:0001890!9.47e-26!39;UBERON:0006240!9.47e-26!39;UBERON:0003528!2.11e-23!29;UBERON:0002791!2.11e-23!29;UBERON:0001893!2.11e-23!29;UBERON:0010314!1.14e-20!92;UBERON:0000956!4.69e-17!21;UBERON:0001869!4.69e-17!21;UBERON:0000203!4.69e-17!21;UBERON:0002619!3.92e-13!17;UBERON:0002021!3.73e-09!10;UBERON:0000411!3.73e-09!10;UBERON:0001950!3.73e-09!10;UBERON:0002420!1.86e-07!8;UBERON:0007245!1.86e-07!8;UBERON:0010009!1.86e-07!8;UBERON:0010011!1.86e-07!8;UBERON:0000454!1.86e-07!8;UBERON:0003076!3.70e-07!12;UBERON:0003057!3.70e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.563357,0.132787,0.866811,0.321531,0.514709,0.341268,0.156184,0.127519,0.28567,3.10323,1.3158,0.455019,0.456801,0.163767,0.891169,0,0.808967,0.108166,0.0379364,0.0754182,0.051421,0.389275,0.49061,0.113773,0.243279,0.181283,0.378002,0.115815,0.158858,0.867546,0.350793,0.378722,0.48539,0.173722,0.565272,3.63689,0.742842,0.146713,0.0179607,2.43995,0.0265062,0.724863,0.672905,0.0326861,0.170118,0.63494,0.673722,1.2796,0.247617,1.02552,0.778906,1.09454,0.120687,0.498054,0.513233,0.168251,0.688152,0.141285,0.0893413,4.58209,0.951303,0.205372,0.531917,0.759634,0.175326,0.307787,0.634702,0.961967,0.358731,0.821947,1.71111,0.135285,0.280414,0.542659,0.181217,0.979638,0.173584,0.2317,0.348727,0.0529873,0.0497067,0.312115,0.204396,0.119369,0.442898,0.514602,4.26434,2.25099,0.243285,1.11866,0.698467,0.447112,0.389188,1.65982,0.641,0.342741,0.124357,0.391493,0.674146,0.193508,0.243122,0.378494,0.482983,0.285951,0.285156,1.19035,0.331187,0.387316,0.20165,0.193419,7.93879,3.12183,2.75685,0.133166,0.704965,0.110009,0.735404,0.0992033,0.299754,1.46585,0.547427,0.261521,0.182466,0.23106,0.755173,0.35168,0.485689,0.38364,0.633325,0.123216,0.468394,0.311725,0.606596,0.176939,0.72494,51.6886,0.277116,0.111771,0.679593,1.47999,1.08773,0.638981,0.19035,0.387274,0.280284,0.358643,0.242008,1.44084,0.082151,0.519832,0.0183802,0.665527,0.499416,0.069779,0.176344,0.571287,0.199688,0.142068,0.263291,0.581933,0.688329,0.442174,0.352036,3.15159,0.277809,0.171615,0.738351,0.147927,0.0640266
}}

Latest revision as of 15:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80924310..80924312,+p1@ENSMUST00000156926
Mm9::chr13:20564559..20564605,+p11@Elmo1
Mm9::chr17:25570208..25570252,-p3@Cacna1h
Mm9::chr17:27078365..27078409,+p@chr17:27078365..27078409
+
Mm9::chr18:16967125..16967186,-p5@Cdh2
Mm9::chr18:23009239..23009260,-p6@Nol4
Mm9::chr18:23009281..23009296,-p5@Nol4
Mm9::chr1:75476081..75476092,+p2@Tmem198
Mm9::chr1:91476722..91476755,+p@chr1:91476722..91476755
+
Mm9::chr2:151907338..151907360,+p2@Scrt2
Mm9::chr2:6805522..6805544,-p@chr2:6805522..6805544
-
Mm9::chr2:6805564..6805576,-p@chr2:6805564..6805576
-
Mm9::chr2:6805920..6805945,-p@chr2:6805920..6805945
-
Mm9::chr2:6805947..6805952,-p@chr2:6805947..6805952
-
Mm9::chr2:6805954..6805965,-p@chr2:6805954..6805965
-
Mm9::chr2:6805967..6805984,-p@chr2:6805967..6805984
-
Mm9::chr2:6805986..6806003,-p@chr2:6805986..6806003
-
Mm9::chr2:6806004..6806015,-p16@Celf2
Mm9::chr2:6806021..6806037,-p11@Celf2
Mm9::chr3:7366589..7366594,+p4@Pkia
Mm9::chr4:102432769..102432789,+p3@Sgip1
Mm9::chr4:116550032..116550058,+p1@Zswim5
Mm9::chr5:108298312..108298329,-p11@Evi5
Mm9::chr5:65522238..65522249,+p9@Klhl5
Mm9::chr6:138373114..138373132,-p7@Lmo3
Mm9::chr6:47194358..47194416,+p1@Cntnap2
Mm9::chr6:90732504..90732523,-p13@Iqsec1
Mm9::chr8:48373638..48373649,-p@chr8:48373638..48373649
-


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
neurectoderm2.39e-3664
neural plate2.39e-3664
presumptive neural plate2.39e-3664
regional part of nervous system2.40e-3554
neural tube1.74e-3352
neural rod1.74e-3352
future spinal cord1.74e-3352
neural keel1.74e-3352
pre-chordal neural plate5.44e-3249
ecto-epithelium1.80e-3173
central nervous system9.13e-3173
nervous system2.23e-3075
ectoderm-derived structure2.53e-3095
ectoderm2.53e-3095
presumptive ectoderm2.53e-3095
brain1.19e-2947
future brain1.19e-2947
regional part of brain1.53e-2846
gray matter1.46e-2734
anterior neural tube1.11e-2640
regional part of forebrain9.47e-2639
forebrain9.47e-2639
future forebrain9.47e-2639
brain grey matter2.11e-2329
regional part of telencephalon2.11e-2329
telencephalon2.11e-2329
structure with developmental contribution from neural crest1.14e-2092
cerebral cortex4.69e-1721
cerebral hemisphere4.69e-1721
pallium4.69e-1721
regional part of cerebral cortex3.92e-1317
occipital lobe3.73e-0910
visual cortex3.73e-0910
neocortex3.73e-0910
basal ganglion1.86e-078
nuclear complex of neuraxis1.86e-078
aggregate regional part of brain1.86e-078
collection of basal ganglia1.86e-078
cerebral subcortex1.86e-078
posterior neural tube3.70e-0712
chordal neural plate3.70e-0712


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)
MA0003.10.379891
MA0004.10.0975472
MA0006.10.550726
MA0007.10.302154
MA0009.10.400415
MA0014.10.730011
MA0017.10.0387728
MA0019.10.715766
MA0024.10.364667
MA0025.10.602538
MA0027.11.97512
MA0028.10.136208
MA0029.10.917544
MA0030.10.352483
MA0031.10.32434
MA0038.10.181232
MA0040.10.410788
MA0041.10.0630027
MA0042.10.0577521
MA0043.10.482118
MA0046.10.430358
MA0048.10.333455
MA0050.10.117881
MA0051.10.187057
MA0052.10.417501
MA0055.10.425878
MA0056.10
MA0057.10.167885
MA0058.10.0551302
MA0059.10.216766
MA0060.10.0623149
MA0061.10.0186287
MA0063.10
MA0066.10.517519
MA0067.10.70379
MA0068.10.0361631
MA0069.10.417784
MA0070.10.409709
MA0071.10.117424
MA0072.10.402681
MA0073.11.7822
MA0074.10.462458
MA0076.10.0450749
MA0077.10.384853
MA0078.10.60168
MA0081.10.0694651
MA0083.10.481435
MA0084.11.01381
MA0087.11.13054
MA0088.10.0384374
MA0089.10
MA0090.10.277096
MA0091.10.104243
MA0092.10.583262
MA0093.10.0363286
MA0095.10
MA0098.10
MA0100.10.144919
MA0101.10.227319
MA0103.10.163216
MA0105.10.72164
MA0106.10.214456
MA0107.10.156862
MA0108.20.274781
MA0109.10
MA0111.10.615225
MA0113.10.195372
MA0114.10.0181479
MA0115.10.484531
MA0116.10.126154
MA0117.10.45687
MA0119.10.0637713
MA0122.10.473843
MA0124.10.654966
MA0125.10.587987
MA0130.10
MA0131.10.254613
MA0132.10
MA0133.10
MA0135.10.513709
MA0136.10.164081
MA0139.10.254691
MA0140.10.44491
MA0141.10.184267
MA0142.10.841192
MA0143.10.206363
MA0144.10.213127
MA0145.10.0169355
MA0146.10.326202
MA0147.10.0938338
MA0148.10.105845
MA0149.10.0658075
MA0062.20.00456066
MA0035.20.45195
MA0039.20.154123
MA0138.20.248854
MA0002.20.0451583
MA0137.20.406246
MA0104.20.145422
MA0047.20.180736
MA0112.20.0169336
MA0065.20.101098
MA0150.12.12683
MA0151.10
MA0152.10.180805
MA0153.10.528268
MA0154.10.190869
MA0155.10.128748
MA0156.10.044778
MA0157.10.288518
MA0158.10
MA0159.10.25085
MA0160.10.107415
MA0161.10
MA0162.10.559426
MA0163.10.174212
MA0164.10.164307
MA0080.20.0405418
MA0018.20.508301
MA0099.20.244313
MA0079.21.23786
MA0102.21.06444
MA0258.10.186786
MA0259.10.414234
MA0442.10
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