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MCL coexpression mm9:135: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0050808;synapse organization and biogenesis;0.00137789429448995;11735,18189!GO:0043062;extracellular structure organization and biogenesis;0.0035257483889904;11735,18189!GO:0005246;calcium channel regulator activity;0.0285057235666322;18189!GO:0042734;presynaptic membrane;0.0285057235666322;18189!GO:0016043;cellular component organization and biogenesis;0.0285057235666322;11735,50997,18189!GO:0016247;channel regulator activity;0.0285057235666322;18189!GO:0015457;auxiliary transport protein activity;0.0285057235666322;18189!GO:0007416;synaptogenesis;0.0299260890401764;18189!GO:0007399;nervous system development;0.0302070969093827;11735,18189!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.55e-28!54;UBERON:0002021!8.05e-28!10;UBERON:0000411!8.05e-28!10;UBERON:0001950!8.05e-28!10;UBERON:0001049!2.62e-27!52;UBERON:0005068!2.62e-27!52;UBERON:0006241!2.62e-27!52;UBERON:0007135!2.62e-27!52;UBERON:0002346!5.11e-27!64;UBERON:0003075!5.11e-27!64;UBERON:0007284!5.11e-27!64;UBERON:0000955!1.06e-25!47;UBERON:0006238!1.06e-25!47;UBERON:0002616!6.77e-24!46;UBERON:0001017!2.67e-23!73;UBERON:0010371!6.00e-23!73;UBERON:0002020!1.25e-22!34;UBERON:0001016!1.62e-22!75;UBERON:0003056!5.83e-22!49;UBERON:0002619!5.95e-22!17;UBERON:0003528!2.62e-21!29;UBERON:0002791!2.62e-21!29;UBERON:0001893!2.62e-21!29;UBERON:0004121!6.16e-21!95;UBERON:0000924!6.16e-21!95;UBERON:0006601!6.16e-21!95;UBERON:0003080!8.14e-21!40;UBERON:0000956!2.33e-20!21;UBERON:0001869!2.33e-20!21;UBERON:0000203!2.33e-20!21;UBERON:0002780!4.01e-19!39;UBERON:0001890!4.01e-19!39;UBERON:0006240!4.01e-19!39;UBERON:0010314!5.77e-17!92;UBERON:0000025!2.05e-09!114;UBERON:0004111!1.96e-08!122;UBERON:0000064!1.64e-07!99;UBERON:0003076!5.64e-07!12;UBERON:0003057!5.64e-07!12
}}

Latest revision as of 14:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:101542314..101542317,+p@chr10:101542314..101542317
+
Mm9::chr10:69487700..69487704,+p@chr10:69487700..69487704
+
Mm9::chr11:118351432..118351434,+p@chr11:118351432..118351434
+
Mm9::chr11:87138563..87138575,-p@chr11:87138563..87138575
-
Mm9::chr12:110802874..110802886,+p@chr12:110802874..110802886
+
Mm9::chr12:62817529..62817531,+p@chr12:62817529..62817531
+
Mm9::chr12:68183103..68183110,-p@chr12:68183103..68183110
-
Mm9::chr12:71364422..71364433,-p@chr12:71364422..71364433
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Mm9::chr12:75991077..75991098,-p@chr12:75991077..75991098
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Mm9::chr12:83808041..83808052,+p@chr12:83808041..83808052
+
Mm9::chr12:90319824..90319827,+p@chr12:90319824..90319827
+
Mm9::chr13:42885960..42885977,+p@chr13:42885960..42885977
+
Mm9::chr13:83714811..83714842,-p@chr13:83714811..83714842
-
Mm9::chr14:119844844..119844853,+p@chr14:119844844..119844853
+
Mm9::chr15:65967019..65967021,-p@chr15:65967019..65967021
-
Mm9::chr16:37112654..37112669,-p@chr16:37112654..37112669
-
Mm9::chr16:49739336..49739339,+p@chr16:49739336..49739339
+
Mm9::chr16:75399982..75399991,-p@chr16:75399982..75399991
-
Mm9::chr16:81269950..81269959,+p@chr16:81269950..81269959
+
Mm9::chr17:27108920..27108923,+p@chr17:27108920..27108923
+
Mm9::chr17:27109317..27109326,+p@chr17:27109317..27109326
+
Mm9::chr17:49113379..49113392,+p@chr17:49113379..49113392
+
Mm9::chr17:90436147..90436158,-p@chr17:90436147..90436158
-
Mm9::chr17:90436235..90436241,+p@chr17:90436235..90436241
+
Mm9::chr17:90712627..90712639,-p@chr17:90712627..90712639
-
Mm9::chr18:86577926..86577934,+p@chr18:86577926..86577934
+
Mm9::chr19:8742249..8742252,+p@chr19:8742249..8742252
+
Mm9::chr1:125367228..125367232,-p@chr1:125367228..125367232
-
Mm9::chr1:126433179..126433191,-p@chr1:126433179..126433191
-
Mm9::chr1:126584616..126584620,-p@chr1:126584616..126584620
-
Mm9::chr1:130094249..130094253,+p@chr1:130094249..130094253
+
Mm9::chr2:21572063..21572066,+p@chr2:21572063..21572066
+
Mm9::chr2:26967521..26967534,-p@chr2:26967521..26967534
-
Mm9::chr2:62163994..62163996,+p@chr2:62163994..62163996
+
Mm9::chr3:156397709..156397711,+p@chr3:156397709..156397711
+
Mm9::chr3:25768754..25768768,-p@chr3:25768754..25768768
-
Mm9::chr3:80492057..80492068,-p@chr3:80492057..80492068
-
Mm9::chr3:80495059..80495068,-p@chr3:80495059..80495068
-
Mm9::chr4:103349411..103349416,+p@chr4:103349411..103349416
+
Mm9::chr4:103358365..103358370,+p@chr4:103358365..103358370
+
Mm9::chr4:103847759..103847793,+p@chr4:103847759..103847793
+
Mm9::chr4:126885535..126885547,+p@chr4:126885535..126885547
+
Mm9::chr4:138013520..138013534,+p@chr4:138013520..138013534
+
Mm9::chr4:46800475..46800496,+p@chr4:46800475..46800496
+
Mm9::chr4:75748748..75748753,-p@chr4:75748748..75748753
-
Mm9::chr4:76783734..76783735,-p@chr4:76783734..76783735
-
Mm9::chr4:77410279..77410283,-p@chr4:77410279..77410283
-
Mm9::chr4:77502680..77502686,-p@chr4:77502680..77502686
-
Mm9::chr4:77649487..77649490,-p@chr4:77649487..77649490
-
Mm9::chr4:77694800..77694811,-p@chr4:77694800..77694811
-
Mm9::chr4:85034168..85034189,+p@chr4:85034168..85034189
+
Mm9::chr5:19591405..19591419,+p@chr5:19591405..19591419
+
Mm9::chr6:110613417..110613421,+p@chr6:110613417..110613421
+
Mm9::chr6:37157664..37157672,-p@chr6:37157664..37157672
-
Mm9::chr6:39829616..39829621,+p@chr6:39829616..39829621
+
Mm9::chr6:77195239..77195243,+p@chr6:77195239..77195243
+
Mm9::chr6:77428004..77428010,-p@chr6:77428004..77428010
-
Mm9::chr6:80124074..80124083,+p@chr6:80124074..80124083
+
Mm9::chr7:129771954..129771962,+p@chr7:129771954..129771962
+
Mm9::chr7:129772412..129772419,+p@chr7:129772412..129772419
+
Mm9::chr7:151610022..151610026,+p@chr7:151610022..151610026
+
Mm9::chr7:3390811..3390821,+p@chr7:3390811..3390821
+
Mm9::chr7:51615106..51615133,+p@chr7:51615106..51615133
+
Mm9::chr7:6846959..6846962,+p@chr7:6846959..6846962
+
Mm9::chr7:71898163..71898179,+p@chr7:71898163..71898179
+
Mm9::chr7:98375028..98375032,+p@chr7:98375028..98375032
+
Mm9::chr7:98415879..98415883,+p@chr7:98415879..98415883
+
Mm9::chr7:98612377..98612404,+p@chr7:98612377..98612404
+
Mm9::chr7:99596117..99596118,+p@chr7:99596117..99596118
+
Mm9::chr7:99596122..99596143,+p@chr7:99596122..99596143
+
Mm9::chr8:14849922..14849935,+p@chr8:14849922..14849935
+
Mm9::chr8:17270601..17270603,-p@chr8:17270601..17270603
-
Mm9::chr8:30261015..30261059,-p@chr8:30261015..30261059
-
Mm9::chr8:4214085..4214096,-p@chr8:4214085..4214096
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Mm9::chr9:27993024..27993049,+p@chr9:27993024..27993049
+
Mm9::chr9:28728585..28728593,+p@chr9:28728585..28728593
+
Mm9::chr9:28728673..28728680,+p@chr9:28728673..28728680
+
Mm9::chr9:32072245..32072249,+p@chr9:32072245..32072249
+
Mm9::chr9:37352538..37352543,+p@chr9:37352538..37352543
+
Mm9::chr9:37352646..37352651,+p@chr9:37352646..37352651
+
Mm9::chrX:20439299..20439311,-p@chrX:20439299..20439311
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Mm9::chrX:58381175..58381184,+p@chrX:58381175..58381184
+
Mm9::chrX:67597813..67597823,-p@chrX:67597813..67597823
-
Mm9::chrX:7229928..7229937,-p@chrX:7229928..7229937
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Mm9::chrX:84418227..84418237,-p@chrX:84418227..84418237
-


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:0050808synapse organization and biogenesis0.00137789429448995
GO:0043062extracellular structure organization and biogenesis0.0035257483889904
GO:0005246calcium channel regulator activity0.0285057235666322
GO:0042734presynaptic membrane0.0285057235666322
GO:0016043cellular component organization and biogenesis0.0285057235666322
GO:0016247channel regulator activity0.0285057235666322
GO:0015457auxiliary transport protein activity0.0285057235666322
GO:0007416synaptogenesis0.0299260890401764
GO:0007399nervous system development0.0302070969093827



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.55e-2854
occipital lobe8.05e-2810
visual cortex8.05e-2810
neocortex8.05e-2810
neural tube2.62e-2752
neural rod2.62e-2752
future spinal cord2.62e-2752
neural keel2.62e-2752
neurectoderm5.11e-2764
neural plate5.11e-2764
presumptive neural plate5.11e-2764
brain1.06e-2547
future brain1.06e-2547
regional part of brain6.77e-2446
central nervous system2.67e-2373
ecto-epithelium6.00e-2373
gray matter1.25e-2234
nervous system1.62e-2275
pre-chordal neural plate5.83e-2249
regional part of cerebral cortex5.95e-2217
brain grey matter2.62e-2129
regional part of telencephalon2.62e-2129
telencephalon2.62e-2129
ectoderm-derived structure6.16e-2195
ectoderm6.16e-2195
presumptive ectoderm6.16e-2195
anterior neural tube8.14e-2140
cerebral cortex2.33e-2021
cerebral hemisphere2.33e-2021
pallium2.33e-2021
regional part of forebrain4.01e-1939
forebrain4.01e-1939
future forebrain4.01e-1939
structure with developmental contribution from neural crest5.77e-1792
tube2.05e-09114
anatomical conduit1.96e-08122
organ part1.64e-0799
posterior neural tube5.64e-0712
chordal neural plate5.64e-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)
MA0003.13.32693e-15
MA0004.10.0200493
MA0006.10.00541326
MA0007.10.0167071
MA0009.10.341778
MA0014.12.43471e-09
MA0017.10.0626594
MA0019.10.356172
MA0024.10.0860428
MA0025.10.235098
MA0027.11.49755
MA0028.10.00669078
MA0029.12.57405
MA0030.10.974938
MA0031.10.873247
MA0038.10.0772628
MA0040.11.18924
MA0041.15.20506
MA0042.14.96018
MA0043.10.15313
MA0046.10.773222
MA0048.14.8482e-07
MA0050.11.12141
MA0051.10.983091
MA0052.11.21417
MA0055.18.67778e-08
MA0056.10
MA0057.10.0526847
MA0058.10.000682547
MA0059.10.0618002
MA0060.19.89659e-06
MA0061.10.0164702
MA0063.10
MA0066.10.0153203
MA0067.10.31176
MA0068.11.16988
MA0069.10.367282
MA0070.10.720281
MA0071.10.560171
MA0072.10.702408
MA0073.15.89902
MA0074.10.053414
MA0076.10.00308822
MA0077.10.319351
MA0078.10.024079
MA0081.10.44105
MA0083.10.464559
MA0084.10.575047
MA0087.11.31536
MA0088.10.270758
MA0089.10
MA0090.10.105852
MA0091.10.0723265
MA0092.10.206324
MA0093.10.00786004
MA0095.10
MA0098.10
MA0100.10.00958774
MA0101.10.0266768
MA0103.10.0726056
MA0105.10.00218688
MA0106.10.025591
MA0107.10.00231602
MA0108.20.174556
MA0109.10
MA0111.10.121221
MA0113.10.0900143
MA0114.10.0156612
MA0115.10.469429
MA0116.10.152834
MA0117.10.137503
MA0119.10.0692174
MA0122.10.452669
MA0124.10.752756
MA0125.10.638238
MA0130.10
MA0131.10.0384813
MA0132.10
MA0133.10
MA0135.11.57617
MA0136.10.332003
MA0139.10.00100814
MA0140.10.472231
MA0141.10.285295
MA0142.11.26203
MA0143.10.752849
MA0144.10.0380205
MA0145.11.15594e-06
MA0146.12.52257e-11
MA0147.10.00229867
MA0148.10.491401
MA0149.146.2475
MA0062.24.65789e-05
MA0035.20.484664
MA0039.23.8549e-13
MA0138.20.144763
MA0002.20.19554
MA0137.20.040913
MA0104.20.000427616
MA0047.20.944313
MA0112.22.64638e-05
MA0065.20.198228
MA0150.10.84678
MA0151.10
MA0152.11.30963
MA0153.11.0316
MA0154.10.000355547
MA0155.10.00852376
MA0156.10.0125523
MA0157.10.425108
MA0158.10
MA0159.10.398777
MA0160.10.0766123
MA0161.10
MA0162.11.93781e-10
MA0163.16.94021e-06
MA0164.10.332695
MA0080.20.34512
MA0018.20.0144998
MA0099.20.0349302
MA0079.21.86115e-14
MA0102.20.620824
MA0258.10.000186078
MA0259.10.000326929
MA0442.10
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