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MCL coexpression mm9:143: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0003682;chromatin binding;0.00591370900014409;20670,22589,15201!GO:0000785;chromatin;0.0163874003207195;20670,22589,15201!GO:0000792;heterochromatin;0.0163874003207195;22589,15201!GO:0031508;centric heterochromatin formation;0.0261974345576382;15201!GO:0031055;chromatin remodeling at centromere;0.0261974345576382;15201!GO:0044427;chromosomal part;0.0261974345576382;20670,22589,15201!GO:0005694;chromosome;0.0365932161652959;20670,22589,15201!GO:0043403;skeletal muscle regeneration;0.0479840728769563;20670!GO:0010216;maintenance of DNA methylation;0.0479840728769563;15201!GO:0005721;centric heterochromatin;0.0497174278804884;15201!GO:0006346;methylation-dependent chromatin silencing;0.0497174278804884;15201!GO:0004386;helicase activity;0.0497174278804884;22589,15201!
|ontology_enrichment_celltype=CL:0000349!1.58e-86!3;CL:0000351!1.58e-86!3
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000358!1.58e-86!3;UBERON:0000307!1.58e-86!3;UBERON:0007010!1.58e-86!3
|tfbs_overrepresentation_for_novel_motifs=0.38048,0.68474,0.941006,0.0254173,0.0192054,0.552062,0.177723,0.361639,0.0409623,0.150527,0.463821,0.832721,0.25726,0.375208,0.20192,0,0.227122,0.0165828,0.2927,0.148776,0.224977,0.344433,0.373369,0.260848,0.0992213,0.705667,0.965289,0.106289,0.591752,0.33124,0.20346,0.103961,0.0393064,0.47836,0.117855,0.439312,0.0702243,0.0598323,0.0221791,0.362935,0.088494,0.211389,0.202267,0.120157,1.4631,0.157274,0.0392052,0.0427938,1.15015,0.281241,0.0575642,0.263961,0.390349,0.52571,0.187817,0.0785376,1.41493,0.303131,0.552724,0.198554,0.650815,0.514921,0.343766,0.0539325,0.215134,0.239144,0.276192,0.550916,0.093093,0.428427,0.265157,0.120843,0.127509,0.20828,0.0830868,0.0365513,2.0897,0.0362988,1.53063,1.61015,0.123376,0.524629,0.275405,0.0555145,0.437246,0.00171642,10.5156,1.234,0.157637,0.69383,0.326193,0.14444,0.109834,0.283086,1.04888,1.11173,1.42328,0.358333,0.153736,0.155873,0.128427,0.339003,0.167502,0.210388,0.459235,0.0982363,0.271122,0.427157,0.57068,0.128156,0.549918,0.503681,1.62006,0.0491535,0.331406,0.0862423,0.112305,0.0264969,0.0639158,0.603802,0.607665,0.403376,0.437116,0.333753,0.372346,0.0893726,0.0722004,0.106705,0.755274,0.798088,0.477695,0.482812,0.254877,3.38451,0.347557,5.46031,0.404199,0.0997983,0.836957,1.03749,0.66523,0.279478,0.245805,0.108751,0.20311,0.593595,0.156136,0.999616,0.056842,0.562359,0.121164,0.0467187,0.178444,1.97579,0.416676,0.2288,0.495435,0.230452,0.223573,0.607286,0.852528,0.141358,0.624246,0.354978,0.199955,0.400997,0.317087,0.826647,0.224212
}}

Latest revision as of 14:46, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:114739327..114739352,+p@chr11:114739327..114739352
+
Mm9::chr11:57645188..57645191,+p@chr11:57645188..57645191
+
Mm9::chr11:62325189..62325193,+p@chr11:62325189..62325193
+
Mm9::chr11:69469061..69469069,+p@chr11:69469061..69469069
+
Mm9::chr11:84714631..84714648,+p@chr11:84714631..84714648
+
Mm9::chr12:119478036..119478039,+p@chr12:119478036..119478039
+
Mm9::chr12:13000013..13000020,+p@chr12:13000013..13000020
+
Mm9::chr12:13000114..13000147,+p@chr12:13000114..13000147
+
Mm9::chr12:19960090..19960092,+p@chr12:19960090..19960092
+
Mm9::chr13:120217189..120217192,+p11@Paip1
Mm9::chr13:120217203..120217220,+p6@Paip1
Mm9::chr13:120217223..120217253,+p3@Paip1
Mm9::chr13:120217256..120217292,+p4@Paip1
Mm9::chr13:120218522..120218537,+p@chr13:120218522..120218537
+
Mm9::chr13:98252702..98252714,+p@chr13:98252702..98252714
+
Mm9::chr14:118623119..118623169,-p@chr14:118623119..118623169
-
Mm9::chr14:22300650..22300661,+p@chr14:22300650..22300661
+
Mm9::chr14:55557445..55557452,+p16@Cmtm5
Mm9::chr14:55557459..55557474,+p6@Cmtm5
Mm9::chr14:70591371..70591391,-p@chr14:70591371..70591391
-
Mm9::chr14:76879103..76879114,+p@chr14:76879103..76879114
+
Mm9::chr15:73098797..73098800,-p@chr15:73098797..73098800
-
Mm9::chr15:9399200..9399211,-p@chr15:9399200..9399211
-
Mm9::chr16:17253208..17253227,+p@chr16:17253208..17253227
+
Mm9::chr17:6988793..6988807,-p@chr17:6988793..6988807
-
Mm9::chr17:6989789..6989810,-p@chr17:6989789..6989810
-
Mm9::chr18:35047173..35047178,+p@chr18:35047173..35047178
+
Mm9::chr19:39005498..39005519,+p5@Hells
Mm9::chr1:163718620..163718627,-p5@Fasl
Mm9::chr1:163718631..163718637,-p4@Fasl
Mm9::chr2:10361502..10361506,+p@chr2:10361502..10361506
+
Mm9::chr2:122084320..122084337,+p@chr2:122084320..122084337
+
Mm9::chr2:165726392..165726402,-p@chr2:165726392..165726402
-
Mm9::chr2:172371713..172371724,+p@chr2:172371713..172371724
+
Mm9::chr2:172371729..172371732,+p@chr2:172371729..172371732
+
Mm9::chr3:145420223..145420231,+p@chr3:145420223..145420231
+
Mm9::chr3:41364609..41364613,+p@chr3:41364609..41364613
+
Mm9::chr3:51025111..51025122,+p@chr3:51025111..51025122
+
Mm9::chr3:51025125..51025133,+p@chr3:51025125..51025133
+
Mm9::chr3:51025153..51025167,+p@chr3:51025153..51025167
+
Mm9::chr4:104608878..104608883,+p@chr4:104608878..104608883
+
Mm9::chr4:104608897..104608911,+p@chr4:104608897..104608911
+
Mm9::chr4:149611832..149611846,+p3@LOC100045967
p3@LOC100503183
p4@Eno1
p4@Gm5506
Mm9::chr4:19225404..19225405,+p1@ENSMUST00000118921
Mm9::chr4:34328331..34328332,-p1@ENSMUST00000121657
Mm9::chr4:57302931..57302943,-p@chr4:57302931..57302943
-
Mm9::chr4:58657475..58657480,+p@chr4:58657475..58657480
+
Mm9::chr5:116474238..116474288,-p4@Prkab1
Mm9::chr5:33770454..33770461,+p@chr5:33770454..33770461
+
Mm9::chr5:34325739..34325749,+p6@Gm1673
Mm9::chr5:34326390..34326399,+p5@Gm1673
Mm9::chr5:66542427..66542436,-p12@Rbm47
Mm9::chr5:66542544..66542547,-p26@Rbm47
Mm9::chr5:66542571..66542582,-p13@Rbm47
Mm9::chr5:66542601..66542614,-p10@Rbm47
Mm9::chr5:67389856..67389879,+p@chr5:67389856..67389879
+
Mm9::chr6:124704032..124704035,-p@chr6:124704032..124704035
-
Mm9::chr6:124707257..124707284,-p@chr6:124707257..124707284
-
Mm9::chr7:3155374..3155377,-p@chr7:3155374..3155377
-
Mm9::chr7:3155548..3155553,-p@chr7:3155548..3155553
-
Mm9::chr7:89919526..89919566,+p@chr7:89919526..89919566
+
Mm9::chr8:109128151..109128162,+p5@Cdh1
Mm9::chr8:122090417..122090425,-p@chr8:122090417..122090425
-
Mm9::chr8:125978140..125978186,+p@chr8:125978140..125978186
+
Mm9::chr8:26201813..26201823,-p11@Plekha2
Mm9::chr8:26201836..26201844,-p12@Plekha2
Mm9::chr8:28582047..28582054,+p@chr8:28582047..28582054
+
Mm9::chr8:82163391..82163418,+p5@Otud4
Mm9::chr9:110751971..110751974,+p5@Prss46
Mm9::chr9:118387565..118387569,+p6@Eomes
Mm9::chr9:118387742..118387753,+p3@Eomes
Mm9::chrX:103123886..103123922,-p3@Atrx
Mm9::chrX:135868446..135868457,+p2@Trap1a
Mm9::chrX:135868692..135868701,+p@chrX:135868692..135868701
+
Mm9::chrX:135870030..135870033,+p@chrX:135870030..135870033
+
Mm9::chrX:135870382..135870395,+p@chrX:135870382..135870395
+
Mm9::chrX:135870429..135870440,+p@chrX:135870429..135870440
+
Mm9::chrX:135870446..135870470,+p@chrX:135870446..135870470
+
Mm9::chrX:34232525..34232558,-p@chrX:34232525..34232558
-
Mm9::chrX:7400016..7400027,+p@chrX:7400016..7400027
+


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:0003682chromatin binding0.00591370900014409
GO:0000785chromatin0.0163874003207195
GO:0000792heterochromatin0.0163874003207195
GO:0031508centric heterochromatin formation0.0261974345576382
GO:0031055chromatin remodeling at centromere0.0261974345576382
GO:0044427chromosomal part0.0261974345576382
GO:0005694chromosome0.0365932161652959
GO:0043403skeletal muscle regeneration0.0479840728769563
GO:0010216maintenance of DNA methylation0.0479840728769563
GO:0005721centric heterochromatin0.0497174278804884
GO:0006346methylation-dependent chromatin silencing0.0497174278804884
GO:0004386helicase activity0.0497174278804884



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>

Cell Type
Ontology termp-valuen
extraembryonic cell1.58e-863
trophoblast cell1.58e-863

Uber Anatomy
Ontology termp-valuen
blastocyst1.58e-863
blastula1.58e-863
cleaving embryo1.58e-863


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)
MA0003.10.763154
MA0004.10.0781036
MA0006.10.00787643
MA0007.10.460784
MA0009.11.78879
MA0014.10.000816268
MA0017.10.0810899
MA0019.10.699631
MA0024.10.656366
MA0025.10.251839
MA0027.11.52347
MA0028.10.672747
MA0029.11.52323
MA0030.10.625379
MA0031.10.261647
MA0038.10.0907584
MA0040.10.122333
MA0041.11.18026
MA0042.10.830091
MA0043.10.166932
MA0046.10.13408
MA0048.10.160232
MA0050.10.914059
MA0051.10.733506
MA0052.10.793365
MA0055.10.0246321
MA0056.10
MA0057.12.24342
MA0058.10.139619
MA0059.10.00124758
MA0060.10.17137
MA0061.10.376474
MA0063.10
MA0066.10.212817
MA0067.10.88019
MA0068.10.133413
MA0069.10.126488
MA0070.10.121697
MA0071.10.632624
MA0072.11.23501
MA0073.10.602873
MA0074.10.851697
MA0076.10.875793
MA0077.10.348426
MA0078.10.119211
MA0081.10.332912
MA0083.10.166483
MA0084.10.597622
MA0087.10.142877
MA0088.10.694563
MA0089.10
MA0090.11.46849
MA0091.10.0294623
MA0092.10.856785
MA0093.10.032249
MA0095.10
MA0098.10
MA0100.10.0583684
MA0101.10.296921
MA0103.10.431044
MA0105.10.169007
MA0106.10.297103
MA0107.10.0860541
MA0108.20.196117
MA0109.10
MA0111.10.445472
MA0113.10.104821
MA0114.10.366633
MA0115.10.168523
MA0116.10.110333
MA0117.10.150597
MA0119.10.173229
MA0122.10.161516
MA0124.10.291845
MA0125.10.241033
MA0130.10
MA0131.10.171164
MA0132.10
MA0133.10
MA0135.10.551436
MA0136.12.15735
MA0139.10.241791
MA0140.10.0583129
MA0141.10.340964
MA0142.10.900014
MA0143.10.518329
MA0144.13.33593
MA0145.10.354745
MA0146.10.610072
MA0147.10.011821
MA0148.10.0905375
MA0149.116.9847
MA0062.22.10584
MA0035.20.32326
MA0039.20.00559598
MA0138.20.164242
MA0002.20.169779
MA0137.22.56154
MA0104.20.000742439
MA0047.20.090279
MA0112.20.0697442
MA0065.20.275907
MA0150.10.951144
MA0151.10
MA0152.10.703367
MA0153.10.19819
MA0154.10.498388
MA0155.10.109694
MA0156.13.26665
MA0157.10.467299
MA0158.10
MA0159.10.136518
MA0160.10.200965
MA0161.10
MA0162.10.0045559
MA0163.10.241889
MA0164.10.0749616
MA0080.23.95885
MA0018.20.205319
MA0099.21.01282
MA0079.20.227994
MA0102.20.643812
MA0258.10.312187
MA0259.10.00940868
MA0442.10
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