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MCL coexpression mm9:395: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0.83583834026633,0.91900286371768,0.947633152250406,0.881332898446202,1.12233476542984,1.07830402174266,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0682179984609265,0,0,0.989416931249455,1.04811734733577,1.00472804621769,1.14372845255933,1.12939889978474,1.18692982536219,1.2207843293052,1.24020277838083,0,0,0,1.09878436566319,1.16031862635451,1.13540300980271,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110544086345426,0,0,0,0,0,0.152695919012311,0,0,0,0,0,0,0,0,0,0,0.488626533724438,0,0,0,0,0,0,0,0,0.0959343498639139,0,0,0,0,0,1.08577226985806,0,0,1.10113154294345,0,0,0,0,0,0,0,0,0,0,0,0.0509235292940968,0.0131273748409159,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.761925190823026,0.83365142113495,0,0.0906941294286938,0.249687382386845,0.457289708400562,0.535698895681917,0.5858423339189,0.861176759138655,0.64920611408497,0.641636311666273,0.660980815923246,0.707079898582048,0.971619458613376,0.963593926268611,0.926132107400521,0,0.00464651662414683,0,0,0,0.0313109092713487,0.0517208153718376,0,0,0.0505333231410966,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0774164737207147,0,0,0,0,0,0,0,0,0.171460468508421,0.10582914506561,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0141547202286131,0,0,0.0666134705129898,0,0,0,0.0695225542217822,0,0,0.249268054106361,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.727653729805214,0,0,0.0586431937472424,0,0,0,0,0,0,0,0,0,0.0803809427109337,0.309485414598145,0.263956212342459,0.438842929987089,0.23720893372168,0.282381427491861,0.200204786486022,1.08723547855756,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.041718751492076,0.0148469187060084,0,0,0.140631100498272,0,0,0,0.109025443285684,0.138417952808354,0.238699938618885,0.0843504501108034,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0430098214247758,0,0,0.0871588832444397,0.081359932135904,0.0516843939467948,0.0978461107777356,0.0587345645323533,0.0753914498230722,0.0787384357649569,0.0990244263857601,0.0898139621139603,0,0.0905291472420136,0.0766073954291401,0.0983625250397581,0.0651748954453978,0.0433061373618431,0.100652321300684,0.0413750428799012,0.109487193952731,0.0748964051866952,0.109378527916094,0.0729583017401753,0.0151856963046814,0.0553034373508932,0,0.0924644954689594,0.0545541045585081,0,0.0625582350728301,0.0766064454112358,0,0.0271481506682342,0.155257708002722,0.0760168881589905,0.0865703124974023,0
|gostat_on_MCL_coexpression=GO:0019673;GDP-mannose metabolic process;0.0379889027227832;218138!GO:0008446;GDP-mannose 4,6-dehydratase activity;0.0379889027227832;218138!GO:0005923;tight junction;0.0379889027227832;60363,27375!GO:0002074;extraocular skeletal muscle development;0.0379889027227832;18741!GO:0008095;inositol-1,4,5-triphosphate receptor activity;0.0379889027227832;16440!GO:0043296;apical junction complex;0.0379889027227832;60363,27375!GO:0016327;apicolateral plasma membrane;0.0379889027227832;60363,27375!GO:0005220;inositol 1,4,5-triphosphate-sensitive calcium-release channel activity;0.0467543555281221;16440!
|ontology_enrichment_celltype=CL:0002563!1.04e-10!9;CL:0002251!1.04e-10!9;CL:0000239!2.08e-07!6;CL:0000677!2.08e-07!6;CL:0000212!2.08e-07!6;CL:0000584!2.08e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!1.84e-29!31;UBERON:0005409!4.70e-29!47;UBERON:0000344!3.69e-17!15;UBERON:0001242!4.26e-15!13;UBERON:0000060!4.26e-15!13;UBERON:0001262!4.26e-15!13;UBERON:0004786!4.26e-15!13;UBERON:0004923!6.55e-11!24;UBERON:0003350!1.04e-10!9;UBERON:0004808!1.04e-10!9;UBERON:0001277!1.04e-10!9;UBERON:0001007!6.76e-09!116;UBERON:0001555!6.76e-09!116;UBERON:0007026!6.76e-09!116;UBERON:0004119!1.66e-08!118;UBERON:0000925!1.66e-08!118;UBERON:0006595!1.66e-08!118;UBERON:0000485!3.15e-08!11;UBERON:0004921!7.86e-08!114
}}

Latest revision as of 15:13, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80754245..80754271,-p4@Tjp3
Mm9::chr11:113613628..113613663,-p8@Cdc42ep4
Mm9::chr11:72249013..72249031,+p2@Ggt6
Mm9::chr13:32430369..32430411,-p2@Gmds
Mm9::chr13:32430423..32430433,-p4@Gmds
Mm9::chr13:32430434..32430529,-p1@Gmds
Mm9::chr17:27194370..27194381,+p3@Itpr3
Mm9::chr17:73748609..73748621,-p2@Capn13
Mm9::chr18:61195865..61195880,-p1@Cdx1
Mm9::chr18:64820477..64820569,-p1@Atp8b1
Mm9::chr3:128918394..128918413,+p5@Pitx2
Mm9::chr3:128918433..128918448,+p8@Pitx2
Mm9::chr4:47104785..47104841,+p1@Galnt12
Mm9::chr5:114593442..114593450,+p@chr5:114593442..114593450
+
Mm9::chr5:137443766..137443777,+p6@Cldn15
Mm9::chr5:137443779..137443794,+p4@Cldn15
Mm9::chr5:137443800..137443811,+p3@Cldn15
Mm9::chr7:19851891..19851932,-p@chr7:19851891..19851932
-
Mm9::chr9:98936066..98936095,-p2@Gm1123


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:0019673GDP-mannose metabolic process0.0379889027227832
GO:0008446GDP-mannose 4,6-dehydratase activity0.0379889027227832
GO:0005923tight junction0.0379889027227832
GO:0002074extraocular skeletal muscle development0.0379889027227832
GO:0008095inositol-1,4,5-triphosphate receptor activity0.0379889027227832
GO:0043296apical junction complex0.0379889027227832
GO:0016327apicolateral plasma membrane0.0379889027227832
GO:0005220inositol 1,4,5-triphosphate-sensitive calcium-release channel activity0.0467543555281221



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>


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)
MA0003.13.13236
MA0004.10.527785
MA0006.10.265566
MA0007.10.502851
MA0009.10.535932
MA0014.10.332195
MA0017.10.6294
MA0019.10.376509
MA0024.11.24244
MA0025.10.751694
MA0027.12.14278
MA0028.10.0821841
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.285714
MA0040.10.547233
MA0041.10.129017
MA0042.10.121046
MA0043.10.624178
MA0046.10.568473
MA0048.11.86028
MA0050.10.205672
MA0051.10.2928
MA0052.10.554531
MA0055.10.19426
MA0056.10
MA0057.10.262449
MA0058.10.373672
MA0059.10.124358
MA0060.10.0417645
MA0061.10.198315
MA0063.10
MA0066.10.277072
MA0067.10.857286
MA0068.11.38061
MA0069.10.554839
MA0070.10.54606
MA0071.10.20507
MA0072.10.538403
MA0073.11.45208
MA0074.10.249359
MA0076.10.101055
MA0077.10.518913
MA0078.10.319336
MA0081.11.97569
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.10.978382
MA0089.10
MA0090.10.917865
MA0091.10.187483
MA0092.10.155586
MA0093.10.609251
MA0095.10
MA0098.10
MA0100.10.675637
MA0101.10.40675
MA0103.10.657254
MA0105.11.80186
MA0106.10.869465
MA0107.10.641343
MA0108.21.02466
MA0109.10
MA0111.10.494436
MA0113.10.302851
MA0114.11.16017
MA0115.10.626759
MA0116.10.951399
MA0117.11.45503
MA0119.10.407675
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.10.372683
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.731186
MA0139.12.1984
MA0140.10.675435
MA0141.10.10748
MA0142.10.439269
MA0143.10.847878
MA0144.11.64935
MA0145.13.58135
MA0146.17.2468
MA0147.10.469804
MA0148.10.189643
MA0149.10.133214
MA0062.20.0890335
MA0035.20.244063
MA0039.24.8056
MA0138.21.7073
MA0002.20.129512
MA0137.20.105829
MA0104.20.337396
MA0047.20.285109
MA0112.22.60446
MA0065.20.327992
MA0150.11.54487
MA0151.10
MA0152.10.285194
MA0153.10.67335
MA0154.12.28265
MA0155.12.37442
MA0156.10.330301
MA0157.10.411541
MA0158.10
MA0159.11.28673
MA0160.10.191754
MA0161.10
MA0162.11.18735
MA0163.10.853384
MA0164.10.264905
MA0080.21.07311
MA0018.20.272436
MA0099.20.947425
MA0079.21.56471
MA0102.21.22663
MA0258.10.709555
MA0259.10.444163
MA0442.10
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