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MCL coexpression mm9:272: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000988!9.73e-07!32;CL:0002032!9.73e-07!32;CL:0000037!9.73e-07!32;CL:0000566!9.73e-07!32;CL:0000837!9.73e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!1.38e-14!23;UBERON:0000974!1.38e-14!23;UBERON:0004807!1.38e-14!23;UBERON:0005058!1.38e-14!23;UBERON:0003351!1.38e-14!23;UBERON:0009113!1.38e-14!23;UBERON:0003295!1.38e-14!23;UBERON:0009722!1.38e-14!23;UBERON:0005562!1.38e-14!23;UBERON:0007690!1.38e-14!23;UBERON:0006562!6.24e-14!24;UBERON:0003408!6.24e-14!24;UBERON:0001557!6.24e-14!24;UBERON:0001042!6.24e-14!24;UBERON:0008814!6.24e-14!24;UBERON:0009145!6.24e-14!24;UBERON:0000072!2.97e-12!27;UBERON:0004177!2.50e-11!29;UBERON:0005057!2.50e-11!29;UBERON:0002390!1.54e-10!45;UBERON:0003061!1.54e-10!45;UBERON:0002193!8.89e-10!48;UBERON:0002405!8.89e-10!48;UBERON:0000077!3.50e-09!35;UBERON:0000063!3.50e-09!35;UBERON:0007811!6.79e-09!36;UBERON:0000065!1.16e-07!41;UBERON:0001004!1.88e-07!42;UBERON:0000153!2.99e-07!43
|tfbs_overrepresentation_for_novel_motifs=0.487079,0.57557,0.432388,0.579286,0.428845,0.61199,0.827479,0.204568,0.395089,0.383649,0.110217,0.127377,0.578224,0.141157,0.764025,0,0.268829,0.991124,0.513917,0.476804,0.359144,0.783037,0.140634,0.222069,0.203316,0.476423,0.983428,0.320983,0.554665,0.0942073,0.302501,0.345924,0.208387,0.402733,0.103182,0.187151,0.0752937,0.125378,0.324181,0.258033,0.418198,0.309235,0.362012,0.479427,0.238362,0.941084,0.212558,0.105003,0.169663,0.30772,0.711629,0.174075,0.661055,0.462148,0.477006,0.446098,0.324148,0.120379,0.661105,0.443095,0.330215,0.180052,0.433367,0.248044,0.15191,0.277492,0.596353,0.920398,0.326579,0.781435,0.174783,0.10137,0.315141,0.505848,0.058254,0.224639,0.243174,0.591613,0.849865,1.45066,0.608364,0.28165,0.529616,0.549604,0.408287,7.9699e-05,0.319797,0.318069,0.215887,1.07627,0.659258,0.412394,0.356069,0.234168,0.807388,0.273875,0.824044,0.358304,0.610209,0.139752,0.378383,0.345703,0.44741,0.25656,0.710864,0.30866,0.299999,0.336675,1.04104,0.649407,0.472108,0.448913,0.161871,0.112926,0.665677,0.41349,0.718913,0.0821019,0.269784,0.368798,0.510527,0.233232,0.158574,2.47308,0.715313,0.319766,0.138785,0.35069,0.594996,0.239081,0.433157,0.56298,1.3952,0.153414,0.685415,4.58523,1.30869,1.58374,0.640623,1.43657,1.04548,0.600569,0.16595,0.354213,0.25114,0.309829,0.614813,1.39749,0.510206,0.0206358,0.191837,0.0160387,0.46348,0.287349,0.907318,0.533955,1.58314,0.507254,0.481842,0.0658133,0.649247,0.407582,0.32011,0.0588925,0.248774,0.148453,0.927915,0.398249,0.0987744
|tfbs_overrepresentation_jaspar=MA0003.1;0.168577,MA0004.1;0.979684,MA0006.1;0.0992039,MA0007.1;0.074003,MA0009.1;0.366963,MA0014.1;5.14683e-05,MA0017.1;0.121681,MA0019.1;0.229805,MA0024.1;0.332319,MA0025.1;0.564682,MA0027.1;1.93116,MA0028.1;0.107755,MA0029.1;0.315482,MA0030.1;0.320542,MA0031.1;0.293406,MA0038.1;0.476304,MA0040.1;0.377038,MA0041.1;0.187429,MA0042.1;0.694688,MA0043.1;1.13476,MA0046.1;0.396073,MA0048.1;1.67578,MA0050.1;0.669135,MA0051.1;0.48978,MA0052.1;0.997688,MA0055.1;2.46272,MA0056.1;0,MA0057.1;0.0212171,MA0058.1;1.48133,MA0059.1;1.09636,MA0060.1;0.0454236,MA0061.1;0.332043,MA0063.1;0,MA0066.1;0.150832,MA0067.1;0.664516,MA0068.1;0.126795,MA0069.1;0.383839,MA0070.1;0.37599,MA0071.1;0.324912,MA0072.1;0.369163,MA0073.1;2.0391e-05,MA0074.1;0.130125,MA0076.1;0.0347575,MA0077.1;0.351866,MA0078.1;0.540438,MA0081.1;1.19525,MA0083.1;0.445897,MA0084.1;0.971934,MA0087.1;0.409958,MA0088.1;0.108715,MA0089.1;0,MA0090.1;0.505079,MA0091.1;1.02362,MA0092.1;0.234618,MA0093.1;1.19047,MA0095.1;0,MA0098.1;0,MA0100.1;0.123725,MA0101.1;0.420824,MA0103.1;0.131431,MA0105.1;0.582906,MA0106.1;0.188607,MA0107.1;0.549081,MA0108.2;0.687911,MA0109.1;0,MA0111.1;0.913323,MA0113.1;0.170658,MA0114.1;0.0614218,MA0115.1;0.448923,MA0116.1;0.746023,MA0117.1;0.42191,MA0119.1;0.422018,MA0122.1;0.438479,MA0124.1;0.616327,MA0125.1;0.55037,MA0130.1;0,MA0131.1;0.64304,MA0132.1;0,MA0133.1;0,MA0135.1;0.477472,MA0136.1;0.859001,MA0139.1;0.0305298,MA0140.1;0.123662,MA0141.1;0.150112,MA0142.1;0.282551,MA0143.1;0.180984,MA0144.1;0.846083,MA0145.1;0.00980741,MA0146.1;0.0914666,MA0147.1;0.906014,MA0148.1;0.296488,MA0149.1;0.432073,MA0062.2;0.24544,MA0035.2;0.126246,MA0039.2;2.38626e-06,MA0138.2;0.221177,MA0002.2;4.32262,MA0137.2;0.616043,MA0104.2;0.915095,MA0047.2;0.156958,MA0112.2;0.0288521,MA0065.2;0.496457,MA0150.1;0.257198,MA0151.1;0,MA0152.1;0.475315,MA0153.1;0.491737,MA0154.1;0.243616,MA0155.1;0.272931,MA0156.1;0.588508,MA0157.1;0.259017,MA0158.1;0,MA0159.1;0.201016,MA0160.1;0.089496,MA0161.1;0,MA0162.1;0.00115095,MA0163.1;0.45771,MA0164.1;0.141659,MA0080.2;1.70465,MA0018.2;0.147322,MA0099.2;0.619984,MA0079.2;3.46361e-09,MA0102.2;1.0223,MA0258.1;0.145079,MA0259.1;0.337688,MA0442.1;0
}}

Latest revision as of 15:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:79457764..79457771,+p@chr12:79457764..79457771
+
Mm9::chr13:28931259..28931267,+p@chr13:28931259..28931267
+
Mm9::chr14:77090431..77090436,+p@chr14:77090431..77090436
+
Mm9::chr14:77094832..77094840,-p@chr14:77094832..77094840
-
Mm9::chr15:97651417..97651453,-p@chr15:97651417..97651453
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Mm9::chr16:49792628..49792641,-p@chr16:49792628..49792641
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Mm9::chr16:49854460..49854472,+p@chr16:49854460..49854472
+
Mm9::chr16:91793806..91793817,+p@chr16:91793806..91793817
+
Mm9::chr17:32246056..32246059,+p@chr17:32246056..32246059
+
Mm9::chr18:15366299..15366306,-p@chr18:15366299..15366306
-
Mm9::chr18:35988452..35988469,+p@chr18:35988452..35988469
+
Mm9::chr1:137607949..137607972,+p@chr1:137607949..137607972
+
Mm9::chr1:138143330..138143333,-p@chr1:138143330..138143333
-
Mm9::chr1:38834429..38834436,-p@chr1:38834429..38834436
-
Mm9::chr1:92946103..92946113,+p@chr1:92946103..92946113
+
Mm9::chr3:135271365..135271376,-p20@Nfkb1
Mm9::chr3:58934672..58934686,-p12@P2ry14
Mm9::chr3:68497952..68497969,+p@chr3:68497952..68497969
+
Mm9::chr3:68498017..68498026,+p@chr3:68498017..68498026
+
Mm9::chr5:137041384..137041400,-p@chr5:137041384..137041400
-
Mm9::chr5:148211876..148211908,-p1@Flt3
Mm9::chr5:148211928..148211953,-p2@Flt3
Mm9::chr5:148212024..148212049,+p@chr5:148212024..148212049
+
Mm9::chr5:39267947..39267996,-p1@Clnk
Mm9::chr6:48539449..48539467,+p4@Gm5111
Mm9::chr6:48539483..48539498,+p2@Gm5111
Mm9::chr6:48539505..48539527,+p5@Gm5111
Mm9::chr6:52184225..52184236,-p@chr6:52184225..52184236
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Mm9::chr7:149628870..149628902,+p6@Tnni2
Mm9::chr9:57282766..57282792,-p@chr9:57282766..57282792
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Mm9::chr9:71010895..71010907,-p6@Aqp9


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:0042163interleukin-12 beta subunit binding0.03681586588506
GO:0045083negative regulation of interleukin-12 biosynthetic process0.03681586588506
GO:0005143interleukin-12 receptor binding0.03681586588506
GO:0019972interleukin-12 binding0.0441705672980616
GO:0043514interleukin-12 complex0.0441705672980616



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
thymus1.38e-1423
neck1.38e-1423
respiratory system epithelium1.38e-1423
hemolymphoid system gland1.38e-1423
pharyngeal epithelium1.38e-1423
thymic region1.38e-1423
pharyngeal gland1.38e-1423
entire pharyngeal arch endoderm1.38e-1423
thymus primordium1.38e-1423
early pharyngeal endoderm1.38e-1423
pharynx6.24e-1424
gland of gut6.24e-1424
upper respiratory tract6.24e-1424
chordate pharynx6.24e-1424
pharyngeal arch system6.24e-1424
pharyngeal region of foregut6.24e-1424
segment of respiratory tract2.97e-1227
hemopoietic organ2.50e-1129
immune organ2.50e-1129
hematopoietic system1.54e-1045
blood island1.54e-1045
hemolymphoid system8.89e-1048
immune system8.89e-1048
mixed endoderm/mesoderm-derived structure3.50e-0935
organ segment3.50e-0935
craniocervical region6.79e-0936
respiratory tract1.16e-0741
respiratory system1.88e-0742
anterior region of body2.99e-0743


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)
MA0003.10.168577
MA0004.10.979684
MA0006.10.0992039
MA0007.10.074003
MA0009.10.366963
MA0014.15.14683e-05
MA0017.10.121681
MA0019.10.229805
MA0024.10.332319
MA0025.10.564682
MA0027.11.93116
MA0028.10.107755
MA0029.10.315482
MA0030.10.320542
MA0031.10.293406
MA0038.10.476304
MA0040.10.377038
MA0041.10.187429
MA0042.10.694688
MA0043.11.13476
MA0046.10.396073
MA0048.11.67578
MA0050.10.669135
MA0051.10.48978
MA0052.10.997688
MA0055.12.46272
MA0056.10
MA0057.10.0212171
MA0058.11.48133
MA0059.11.09636
MA0060.10.0454236
MA0061.10.332043
MA0063.10
MA0066.10.150832
MA0067.10.664516
MA0068.10.126795
MA0069.10.383839
MA0070.10.37599
MA0071.10.324912
MA0072.10.369163
MA0073.12.0391e-05
MA0074.10.130125
MA0076.10.0347575
MA0077.10.351866
MA0078.10.540438
MA0081.11.19525
MA0083.10.445897
MA0084.10.971934
MA0087.10.409958
MA0088.10.108715
MA0089.10
MA0090.10.505079
MA0091.11.02362
MA0092.10.234618
MA0093.11.19047
MA0095.10
MA0098.10
MA0100.10.123725
MA0101.10.420824
MA0103.10.131431
MA0105.10.582906
MA0106.10.188607
MA0107.10.549081
MA0108.20.687911
MA0109.10
MA0111.10.913323
MA0113.10.170658
MA0114.10.0614218
MA0115.10.448923
MA0116.10.746023
MA0117.10.42191
MA0119.10.422018
MA0122.10.438479
MA0124.10.616327
MA0125.10.55037
MA0130.10
MA0131.10.64304
MA0132.10
MA0133.10
MA0135.10.477472
MA0136.10.859001
MA0139.10.0305298
MA0140.10.123662
MA0141.10.150112
MA0142.10.282551
MA0143.10.180984
MA0144.10.846083
MA0145.10.00980741
MA0146.10.0914666
MA0147.10.906014
MA0148.10.296488
MA0149.10.432073
MA0062.20.24544
MA0035.20.126246
MA0039.22.38626e-06
MA0138.20.221177
MA0002.24.32262
MA0137.20.616043
MA0104.20.915095
MA0047.20.156958
MA0112.20.0288521
MA0065.20.496457
MA0150.10.257198
MA0151.10
MA0152.10.475315
MA0153.10.491737
MA0154.10.243616
MA0155.10.272931
MA0156.10.588508
MA0157.10.259017
MA0158.10
MA0159.10.201016
MA0160.10.089496
MA0161.10
MA0162.10.00115095
MA0163.10.45771
MA0164.10.141659
MA0080.21.70465
MA0018.20.147322
MA0099.20.619984
MA0079.23.46361e-09
MA0102.21.0223
MA0258.10.145079
MA0259.10.337688
MA0442.10
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