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MCL coexpression mm9:480: Difference between revisions

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{{MCL_coexpression_mm9
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conjugating enzyme activity;0.00945807736893712;20610!GO:0016925;protein sumoylation;0.00945807736893712;20610!GO:0005832;chaperonin-containing T-complex;0.00945807736893712;12468!GO:0032446;protein modification by small protein conjugation;0.0455539663794155;20610!GO:0051082;unfolded protein 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|coexpression_dpi_cluster_scores_median=0,0.249840410757572,0.326606131490152,0.34436414095139,0.398406570656378,0.256121063793369,0.259499216289486,0.447135479910527,0.466989182237863,0.505105319667054,0.180026585552633,0.072138508895553,0.544087092376384,0.478526372636431,0,0.0543299948305892,0,0.0821614131578185,0.109045386809429,0.153628809860867,0,0.153753351269646,0.175871565828897,0,0,0.284903471905092,0.0810131410105771,0.0847446845832032,0.0283309137558158,0,0.0156941782456069,0.792016380170843,0.680699206340439,1.17841721701916,0.388147062841962,0.221398217279998,0.551617975135764,0.264124112013994,0.286454507893675,0.17709207744165,0.441647142913664,0.154814611573824,0.124651088335849,0.0221069954750942,0,0.0645169782406436,0,0,0,0,0,0,0.400349590316914,0.516671631171344,0.351010317532,-0.0179416751269198,0,-0.00565804803990499,-0.0472245945615809,0,0,0,-0.0472245945615809,0,0,0,0,0.00396903029424805,0,0,0.00834773522226749,0,0,0,0,0,-0.0065465064543101,0,0,0,0,0,0,-0.0472245945615809,0,-0.0481354699899057,0,0,0.0134820223840935,0,0.750712988840431,0,0,-0.0472245945615809,0,0,0.0329571869723213,0.027599496046413,0.0248710354945629,0,0.0572260417947564,-0.0712812415377886,-0.0481354699899057,-0.0712812415377886,0.0851089148667383,0.0508511892428002,0,0,0.0287230608855789,0.041619983881749,0,0,0,0,0,0,0,0,0,0,0,0,-0.0472245945615809,0,0,-0.0481354699899057,0.13336176105449,0.204093579732844,0.178482233814886,0,0,-0.0472245945615809,0,-0.0188280634837044,0,0,0,0,0,0,0.0531247310291112,-0.0472245945615809,0,-0.0362155163133562,0,0,0.0388988969149198,0,0.0134980146318363,0.000666344855433126,0.0231646770535338,0,0,0,0,0,0.159732709202384,0.177193191421967,0.185745685173696,0,0,0,0,0,0,-0.0434175236516529,0,-0.0274638162012458,0,0,0,0,0,0,0,-0.00468664160343879,0,0,0,0,0,0,0,0.00107504168457764,0,0,0,0,0,-0.0472245945615809,0,0,0.0875008669285915,0,-0.0481354699899057,0,0.066933988485352,0.0294389011296462,1.52263396769048e-05,0,0,0,0,0,0,0.0126614573706485,0.00893388535222721,0.0225525335239055,0.0482520695628364,0.0352591380872643,0,0,0,0,0,0,-0.011205748253996,0,0.0736278867910527,0,0,0,0.0126752872451779,0,0.0214547122431862,0,0,0.0123266619096519,0,0.0616919113883327,0,0,0,0,0,0,0,0,-0.051223230793987,0,0,0.0795322036726475,0.0843118936574509,0.0176346254726557,0.0396146804420831,0.0154079908707505,0,0.0228226804923993,0.0983718676042211,-0.0334505424420822,-0.00293669044170514,0,0.0183129057945705,-0.00496645402514762,0,0.0613438799974024,0,0.00375634043794562,0,0,0,0,0,0,0,0,0.0273201415535887,0.0719044921483595,0,0.0843392403965415,0.0308056497862896,0,0,0.0169287034652231,0,0.0591905589309771,0,0.106668522189672,-0.00627532875862334,0,0,0,0,-0.0472245945615809,0.0563876958257866,0,0.032034908270233,0,0,0.0890710978636876,0.127090816446242,0.193070533481811,0.191115493074292,-0.0481354699899057,0,0,0,0,0,0,-0.00484091926985354,-0.0153705182404476,0.00570584585197563,0,0,0,0.066128646308054,0.0451189204361731,0.0527554171614426,0,0.000967452294728235,0.0531569878936061,0.0826843900821455,0.0939761495634833,0.150348155779907,0.115217636055919,0.0723897890807209,0.0330036126006997,0,0.0616356028590838,0,0.0583003653347582,0.151935912108864,0.0798802230592418,0.0616083799021044,0.0797788474440915,0.0675364139287958,0.0992911790909638,0.125306333141759,-0.0358130509711399,0,0.0562854747876698,0,0,0,0,0,0,-0.00377089283214047,-0.045557047432656,0,0.0207377337637635,-0.0472245945615809,-0.0472245945615809,-0.0472245945615809,0,-0.0472245945615809,0,0,0,0,0,0,0,0,0.00680567722839992,0.0171140495099303,0,0,0,0,0,-0.0240566469762076,-0.00520599038142291,-0.0481354699899057,0,0,0,0,-0.00447375146551086,0,0,0,0,-0.0015959531673288,0,-0.0060376287940784,0,0,-0.000457892984367492,-0.0472245945615809,0,0,0,0,0,0,0,-0.00891609752943745
|gostat_on_MCL_coexpression=GO:0019949;SUMO conjugating enzyme activity;0.00945807736893712;20610!GO:0016925;protein sumoylation;0.00945807736893712;20610!GO:0005832;chaperonin-containing T-complex;0.00945807736893712;12468!GO:0032446;protein modification by small protein conjugation;0.0455539663794155;20610!GO:0051082;unfolded protein binding;0.0469544530664094;12468!
|ontology_enrichment_celltype=CL:0000988!1.86e-13!32;CL:0002032!1.86e-13!32;CL:0000037!1.86e-13!32;CL:0000566!1.86e-13!32;CL:0000837!1.86e-13!32;CL:0002242!2.95e-11!16;CL:0002031!2.00e-10!25;CL:0000838!1.11e-09!12;CL:0000084!6.14e-09!11;CL:0000827!6.14e-09!11;CL:0002320!6.75e-09!46;CL:0000134!6.75e-09!46;CL:0000542!8.27e-09!13;CL:0000051!8.27e-09!13;CL:0002371!3.56e-08!118;CL:0000791!8.38e-08!9;CL:0000789!8.38e-08!9;CL:0002420!8.38e-08!9;CL:0002419!8.38e-08!9;CL:0000790!8.38e-08!9;CL:0002563!8.53e-08!9;CL:0002251!8.53e-08!9;CL:0000034!2.02e-07!97;CL:0000219!2.52e-07!54;CL:0000624!4.34e-07!8;CL:0000548!5.48e-07!115;CL:0000255!5.48e-07!115;CL:0000738!6.09e-07!17;CL:0002087!6.09e-07!17
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!6.75e-09!46;UBERON:0003350!8.53e-08!9;UBERON:0004808!8.53e-08!9;UBERON:0001277!8.53e-08!9;UBERON:0000485!3.24e-07!11;UBERON:0000490!5.19e-07!66
}}

Latest revision as of 15:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:41238883..41238909,-p@chr10:41238883..41238909
-
Mm9::chr10:77069406..77069425,+p8@Sumo3
Mm9::chr10:79623652..79623666,-p@chr10:79623652..79623666
-
Mm9::chr11:117515863..117515866,-p@chr11:117515863..117515866
-
Mm9::chr12:111829796..111829818,-p@chr12:111829796..111829818
-
Mm9::chr13:93380879..93380905,-p@chr13:93380879..93380905
-
Mm9::chr15:96116436..96116455,+p@chr15:96116436..96116455
+
Mm9::chr18:31794423..31794465,-p@chr18:31794423..31794465
-
Mm9::chr19:53674495..53674503,-p@chr19:53674495..53674503
-
Mm9::chr19:7292351..7292358,+p@chr19:7292351..7292358
+
Mm9::chr3:146184120..146184147,+p@chr3:146184120..146184147
+
Mm9::chr5:112705376..112705388,-p@chr5:112705376..112705388
-
Mm9::chr5:139853670..139853699,+p1@D830046C22Rik
p3@Gpr146
Mm9::chr6:85401482..85401496,+p4@Cct7
Mm9::chr8:32260438..32260442,-p1@ENSMUST00000157627


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:0019949SUMO conjugating enzyme activity0.00945807736893712
GO:0016925protein sumoylation0.00945807736893712
GO:0005832chaperonin-containing T-complex0.00945807736893712
GO:0032446protein modification by small protein conjugation0.0455539663794155
GO:0051082unfolded protein binding0.0469544530664094



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
hematopoietic cell1.86e-1332
hematopoietic oligopotent progenitor cell1.86e-1332
hematopoietic stem cell1.86e-1332
angioblastic mesenchymal cell1.86e-1332
hematopoietic multipotent progenitor cell1.86e-1332
nucleate cell2.95e-1116
hematopoietic lineage restricted progenitor cell2.00e-1025
lymphoid lineage restricted progenitor cell1.11e-0912
T cell6.14e-0911
pro-T cell6.14e-0911
connective tissue cell6.75e-0946
mesenchymal cell6.75e-0946
lymphocyte8.27e-0913
common lymphoid progenitor8.27e-0913
somatic cell3.56e-08118
mature alpha-beta T cell8.38e-089
alpha-beta T cell8.38e-089
immature T cell8.38e-089
mature T cell8.38e-089
immature alpha-beta T cell8.38e-089
intestinal epithelial cell8.53e-089
epithelial cell of alimentary canal8.53e-089
stem cell2.02e-0797
motile cell2.52e-0754
CD4-positive, alpha-beta T cell4.34e-078
animal cell5.48e-07115
eukaryotic cell5.48e-07115
leukocyte6.09e-0717
nongranular leukocyte6.09e-0717

Uber Anatomy
Ontology termp-valuen
connective tissue6.75e-0946
epithelium of mucosa8.53e-089
gastrointestinal system epithelium8.53e-089
intestinal epithelium8.53e-089
simple columnar epithelium3.24e-0711
unilaminar epithelium5.19e-0766


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)
MA0003.13.05249
MA0004.11.93809
MA0006.11.8042
MA0007.10.227553
MA0009.10.623671
MA0014.10.646122
MA0017.10.135289
MA0019.10.456268
MA0024.12.43225
MA0025.10.845702
MA0027.12.24512
MA0028.11.281
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.11.68155
MA0040.10.635404
MA0041.10.18185
MA0042.10.172351
MA0043.10.71494
MA0046.10.657417
MA0048.10.25207
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.381798
MA0056.10
MA0057.10.226212
MA0058.13.73512
MA0059.11.00391
MA0060.16.12487
MA0061.10.295622
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.446117
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.10.57708
MA0074.10.318792
MA0076.10.887528
MA0077.10.605975
MA0078.10.395048
MA0081.10.56362
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.0527415
MA0089.10
MA0090.10.212772
MA0091.10.24961
MA0092.10.213012
MA0093.13.29528
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.182791
MA0103.10.14251
MA0105.10.341877
MA0106.10.401864
MA0107.10.138378
MA0108.20.476838
MA0109.10
MA0111.10.223614
MA0113.10.377232
MA0114.10.0864402
MA0115.10.717599
MA0116.10.37608
MA0117.11.64298
MA0119.11.03177
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.10.452196
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.335579
MA0139.10.45049
MA0140.10.832119
MA0141.10.920442
MA0142.11.29772
MA0143.10.391481
MA0144.10.296781
MA0145.10.160233
MA0146.10.780669
MA0147.10.651622
MA0148.10.252062
MA0149.10.18682
MA0062.20.993862
MA0035.20.312946
MA0039.25.56745
MA0138.20.445088
MA0002.20.208749
MA0137.20.153989
MA0104.21.28985
MA0047.20.357963
MA0112.20.54155
MA0065.20.321967
MA0150.10.644946
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.752303
MA0155.11.27441
MA0156.10.45173
MA0157.10.493416
MA0158.10
MA0159.10.332142
MA0160.11.30669
MA0161.10
MA0162.12.62387
MA0163.11.09661
MA0164.10.892289
MA0080.20.430071
MA0018.20.344133
MA0099.20.439458
MA0079.26.59864
MA0102.21.32652
MA0258.11.4436
MA0259.10.299239
MA0442.10
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