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MCL coexpression mm9:404: Difference between revisions

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{{MCL_coexpression_mm9
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immune response;0.00662029788576228;81897,17079,27007!GO:0002376;immune system process;0.00982787891518943;81897,14991,14256,17079,27007!GO:0006955;immune response;0.0138557547202701;81897,14991,17079,27007!GO:0015794;glycerol-3-phosphate transport;0.0138557547202701;224674!GO:0015168;glycerol transmembrane transporter activity;0.0138557547202701;224674!GO:0015665;alcohol transmembrane transporter activity;0.0138557547202701;224674!GO:0015793;glycerol transport;0.0138557547202701;224674!GO:0015169;glycerol-3-phosphate transmembrane transporter activity;0.0138557547202701;224674!GO:0015166;polyol transmembrane transporter activity;0.0138557547202701;224674!GO:0006127;glycerophosphate shuttle;0.0138557547202701;224674!GO:0032394;MHC class Ib receptor activity;0.0138557547202701;27007!GO:0006952;defense response;0.017404129739248;81897,14991,17079,27007!GO:0002223;stimulatory C-type lectin receptor signaling pathway;0.0217661712758409;27007!GO:0015791;polyol transport;0.0217661712758409;224674!GO:0002220;innate immune response activating cell surface receptor signaling 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|gostat_on_MCL_coexpression=GO:0045087;innate immune response;0.00662029788576228;81897,17079,27007!GO:0002376;immune system process;0.00982787891518943;81897,14991,14256,17079,27007!GO:0006955;immune response;0.0138557547202701;81897,14991,17079,27007!GO:0015794;glycerol-3-phosphate transport;0.0138557547202701;224674!GO:0015168;glycerol transmembrane transporter activity;0.0138557547202701;224674!GO:0015665;alcohol transmembrane transporter activity;0.0138557547202701;224674!GO:0015793;glycerol transport;0.0138557547202701;224674!GO:0015169;glycerol-3-phosphate transmembrane transporter activity;0.0138557547202701;224674!GO:0015166;polyol transmembrane transporter activity;0.0138557547202701;224674!GO:0006127;glycerophosphate shuttle;0.0138557547202701;224674!GO:0032394;MHC class Ib receptor activity;0.0138557547202701;27007!GO:0006952;defense response;0.017404129739248;81897,14991,17079,27007!GO:0002223;stimulatory C-type lectin receptor signaling pathway;0.0217661712758409;27007!GO:0015791;polyol transport;0.0217661712758409;224674!GO:0002220;innate immune response activating cell surface receptor signaling pathway;0.0406034808888695;27007!
|ontology_enrichment_celltype=CL:0000988!2.78e-10!32;CL:0002032!2.78e-10!32;CL:0000037!2.78e-10!32;CL:0000566!2.78e-10!32;CL:0000837!2.78e-10!32;CL:0000049!1.78e-09!19;CL:0002320!7.47e-08!46;CL:0000134!7.47e-08!46;CL:0000763!1.41e-07!16;CL:0002031!1.46e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!8.50e-20!48;UBERON:0002405!8.50e-20!48;UBERON:0002390!1.10e-17!45;UBERON:0003061!1.10e-17!45;UBERON:0002371!2.78e-12!16;UBERON:0001474!2.16e-11!22;UBERON:0004765!2.16e-11!22;UBERON:0001434!2.16e-11!22;UBERON:0003081!4.61e-11!87;UBERON:0000926!7.22e-10!120;UBERON:0004120!7.22e-10!120;UBERON:0006603!7.22e-10!120;UBERON:0002204!7.58e-09!32;UBERON:0002384!7.47e-08!46;UBERON:0000077!1.49e-07!35;UBERON:0004177!1.53e-07!29;UBERON:0005057!1.53e-07!29;UBERON:0001041!5.40e-07!80
|tfbs_overrepresentation_for_novel_motifs=0.457576,0.0521604,0.133309,0.178048,0.24857,1.05122,0.254787,0.130554,0.32877,0.190064,0.221763,0.687282,0.30879,0.264234,0.0791346,0,0.42315,0.0671461,0.514215,0.11724,0.358501,0.153134,0.263535,1.3538,0.138033,0.285776,0.106674,0.202945,0.646362,0.353285,0.192916,0.512187,0.23475,0.424507,0.574198,0.0928537,0.0618293,0.242872,0.052341,0.652383,0.243076,0.196576,0.249206,0.0801495,0.635508,0.170437,0.355451,0.614044,0.714807,0.317394,0.408111,0.307229,0.063174,0.641205,0.657376,0.269785,0.100694,0.23598,0.740917,0.268198,0.494318,0.314847,0.154301,0.398468,0.278491,0.433342,0.785371,1.12243,0.490165,0.979213,0.12178,1.32008,0.00424418,0.6886,0.0918517,0.018158,0.692891,0.346003,0.479091,1.76623,0.323638,0.438213,0.31368,1.68368,0.582029,0.0422746,0.20676,0.35371,0.359539,1.2816,0.851763,0.586575,0.523661,0.545909,0.0506699,0.380698,0.303029,0.526183,0.355664,0.0526066,0.061865,0.511936,0.625103,0.408622,0.407717,0.196264,0.459578,0.211422,0.116526,0.112248,0.875636,0.626748,1.21373,0.640523,0.858505,0.240644,0.14458,0.180644,0.424276,0.217483,0.693645,0.380657,0.287218,0.345253,0.910454,0.482363,0.261058,0.517583,0.783932,0.939532,0.609469,0.173056,0.75595,0.280468,0.879201,0.0658603,0.15539,0.197578,0.832159,1.64606,1.25025,0.789841,0.804509,0.521565,0.402166,0.572489,0.941495,1.60668,0.475114,0.0717633,0.600737,0.0028093,0.642658,0.174823,0.765783,0.718834,0.30804,0.603495,0.453591,0.155206,0.841238,0.581248,0.482758,0.442531,0.39934,0.273933,2.92304,0.684489,0.0768587
|tfbs_overrepresentation_jaspar=MA0003.1;0.263084,MA0004.1;0.178381,MA0006.1;0.0769247,MA0007.1;0.168178,MA0009.1;0.535932,MA0014.1;0.0353374,MA0017.1;0.30345,MA0019.1;0.376509,MA0024.1;0.496718,MA0025.1;1.77711,MA0027.1;2.14278,MA0028.1;0.0821841,MA0029.1;0.477444,MA0030.1;1.21364,MA0031.1;1.14633,MA0038.1;0.285714,MA0040.1;0.547233,MA0041.1;1.30829,MA0042.1;0.384176,MA0043.1;0.624178,MA0046.1;0.568473,MA0048.1;0.0534545,MA0050.1;2.48288,MA0051.1;1.44763,MA0052.1;0.554531,MA0055.1;0.00468145,MA0056.1;0,MA0057.1;0.262449,MA0058.1;0.117003,MA0059.1;1.27869,MA0060.1;0.0417645,MA0061.1;0.438647,MA0063.1;0,MA0066.1;0.277072,MA0067.1;0.857286,MA0068.1;2.68906,MA0069.1;0.554839,MA0070.1;0.54606,MA0071.1;0.20507,MA0072.1;0.538403,MA0073.1;5.11713,MA0074.1;0.249359,MA0076.1;0.101055,MA0077.1;0.518913,MA0078.1;0.855296,MA0081.1;0.429201,MA0083.1;0.623446,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;0.0711238,MA0089.1;0,MA0090.1;0.15538,MA0091.1;1.04884,MA0092.1;0.471747,MA0093.1;0.0864726,MA0095.1;0,MA0098.1;0,MA0100.1;0.675637,MA0101.1;0.40675,MA0103.1;0.319254,MA0105.1;0.213264,MA0106.1;0.325663,MA0107.1;0.310214,MA0108.2;0.395878,MA0109.1;0,MA0111.1;0.494436,MA0113.1;0.818211,MA0114.1;0.195359,MA0115.1;0.626759,MA0116.1;0.265278,MA0117.1;0.597086,MA0119.1;0.130171,MA0122.1;0.615314,MA0124.1;0.80652,MA0125.1;0.736412,MA0130.1;0,MA0131.1;0.372683,MA0132.1;0,MA0133.1;0,MA0135.1;0.657882,MA0136.1;0.731186,MA0139.1;0.550862,MA0140.1;0.240513,MA0141.1;0.708661,MA0142.1;0.439269,MA0143.1;0.847878,MA0144.1;0.0540242,MA0145.1;0.179881,MA0146.1;0.0222468,MA0147.1;0.215066,MA0148.1;1.66813,MA0149.1;0.133214,MA0062.2;0.22343,MA0035.2;0.68369,MA0039.2;0.57107,MA0138.2;0.366012,MA0002.2;0.306205,MA0137.2;0.3443,MA0104.2;0.337396,MA0047.2;1.41968,MA0112.2;0.766028,MA0065.2;0.327992,MA0150.1;0.502665,MA0151.1;0,MA0152.1;0.778204,MA0153.1;0.67335,MA0154.1;0.494059,MA0155.1;0.215697,MA0156.1;0.330301,MA0157.1;1.05883,MA0158.1;0,MA0159.1;0.494347,MA0160.1;0.191754,MA0161.1;0,MA0162.1;0.23251,MA0163.1;0.0605054,MA0164.1;0.264905,MA0080.2;1.58522,MA0018.2;0.272436,MA0099.2;1.68893,MA0079.2;1.02407,MA0102.2;1.22663,MA0258.1;0.709555,MA0259.1;0.201267,MA0442.1;0
}}

Latest revision as of 15:14, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:103483602..103483666,+p1@Cd180
Mm9::chr15:74787548..74787574,+p@chr15:74787548..74787574
+
Mm9::chr15:74787580..74787590,+p@chr15:74787580..74787590
+
Mm9::chr17:37407159..37407194,+p1@H2-M3
Mm9::chr17:47906140..47906150,+p6@Tfeb
Mm9::chr19:12873064..12873079,+p1@Lpxn
Mm9::chr2:156955718..156955728,-p6@Samhd1
Mm9::chr2:163471573..163471583,-p@chr2:163471573..163471583
-
Mm9::chr2:61425777..61425781,+p@chr2:61425777..61425781
+
Mm9::chr3:145812822..145812832,+p3@Mcoln2
Mm9::chr4:43467472..43467507,-p1@Cd72
p1@LOC100504743
Mm9::chr6:129573858..129573884,-p2@Klrk1
Mm9::chr6:29476741..29476752,+p4@Irf5
Mm9::chr7:52391761..52391821,-p2@Flt3l
p2@Rpl13a
Mm9::chr9:106124929..106124960,+p1@Tlr9
Mm9::chr9:106124969..106124997,+p2@Tlr9
Mm9::chr9:37063208..37063220,-p7@Slc37a2
Mm9::chr9:37063231..37063250,-p6@Slc37a2
Mm9::chr9:45077218..45077239,-p1@Il10ra


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:0045087innate immune response0.00662029788576228
GO:0002376immune system process0.00982787891518943
GO:0006955immune response0.0138557547202701
GO:0015794glycerol-3-phosphate transport0.0138557547202701
GO:0015168glycerol transmembrane transporter activity0.0138557547202701
GO:0015665alcohol transmembrane transporter activity0.0138557547202701
GO:0015793glycerol transport0.0138557547202701
GO:0015169glycerol-3-phosphate transmembrane transporter activity0.0138557547202701
GO:0015166polyol transmembrane transporter activity0.0138557547202701
GO:0006127glycerophosphate shuttle0.0138557547202701
GO:0032394MHC class Ib receptor activity0.0138557547202701
GO:0006952defense response0.017404129739248
GO:0002223stimulatory C-type lectin receptor signaling pathway0.0217661712758409
GO:0015791polyol transport0.0217661712758409
GO:0002220innate immune response activating cell surface receptor signaling pathway0.0406034808888695



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
hemolymphoid system8.50e-2048
immune system8.50e-2048
hematopoietic system1.10e-1745
blood island1.10e-1745
bone marrow2.78e-1216
bone element2.16e-1122
skeletal element2.16e-1122
skeletal system2.16e-1122
lateral plate mesoderm4.61e-1187
mesoderm7.22e-10120
mesoderm-derived structure7.22e-10120
presumptive mesoderm7.22e-10120
musculoskeletal system7.58e-0932
connective tissue7.47e-0846
mixed endoderm/mesoderm-derived structure1.49e-0735
hemopoietic organ1.53e-0729
immune organ1.53e-0729
foregut5.40e-0780


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)
MA0003.10.263084
MA0004.10.178381
MA0006.10.0769247
MA0007.10.168178
MA0009.10.535932
MA0014.10.0353374
MA0017.10.30345
MA0019.10.376509
MA0024.10.496718
MA0025.11.77711
MA0027.12.14278
MA0028.10.0821841
MA0029.10.477444
MA0030.11.21364
MA0031.11.14633
MA0038.10.285714
MA0040.10.547233
MA0041.11.30829
MA0042.10.384176
MA0043.10.624178
MA0046.10.568473
MA0048.10.0534545
MA0050.12.48288
MA0051.11.44763
MA0052.10.554531
MA0055.10.00468145
MA0056.10
MA0057.10.262449
MA0058.10.117003
MA0059.11.27869
MA0060.10.0417645
MA0061.10.438647
MA0063.10
MA0066.10.277072
MA0067.10.857286
MA0068.12.68906
MA0069.10.554839
MA0070.10.54606
MA0071.10.20507
MA0072.10.538403
MA0073.15.11713
MA0074.10.249359
MA0076.10.101055
MA0077.10.518913
MA0078.10.855296
MA0081.10.429201
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.10.0711238
MA0089.10
MA0090.10.15538
MA0091.11.04884
MA0092.10.471747
MA0093.10.0864726
MA0095.10
MA0098.10
MA0100.10.675637
MA0101.10.40675
MA0103.10.319254
MA0105.10.213264
MA0106.10.325663
MA0107.10.310214
MA0108.20.395878
MA0109.10
MA0111.10.494436
MA0113.10.818211
MA0114.10.195359
MA0115.10.626759
MA0116.10.265278
MA0117.10.597086
MA0119.10.130171
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.10.372683
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.731186
MA0139.10.550862
MA0140.10.240513
MA0141.10.708661
MA0142.10.439269
MA0143.10.847878
MA0144.10.0540242
MA0145.10.179881
MA0146.10.0222468
MA0147.10.215066
MA0148.11.66813
MA0149.10.133214
MA0062.20.22343
MA0035.20.68369
MA0039.20.57107
MA0138.20.366012
MA0002.20.306205
MA0137.20.3443
MA0104.20.337396
MA0047.21.41968
MA0112.20.766028
MA0065.20.327992
MA0150.10.502665
MA0151.10
MA0152.10.778204
MA0153.10.67335
MA0154.10.494059
MA0155.10.215697
MA0156.10.330301
MA0157.11.05883
MA0158.10
MA0159.10.494347
MA0160.10.191754
MA0161.10
MA0162.10.23251
MA0163.10.0605054
MA0164.10.264905
MA0080.21.58522
MA0018.20.272436
MA0099.21.68893
MA0079.21.02407
MA0102.21.22663
MA0258.10.709555
MA0259.10.201267
MA0442.10
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