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MCL coexpression mm9:920: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!2.91e-15!48;UBERON:0002405!2.91e-15!48;UBERON:0002390!2.69e-14!45;UBERON:0003061!2.69e-14!45;UBERON:0001007!1.34e-09!116;UBERON:0001555!1.34e-09!116;UBERON:0007026!1.34e-09!116;UBERON:0004119!1.96e-09!118;UBERON:0000925!1.96e-09!118;UBERON:0006595!1.96e-09!118;UBERON:0004921!3.60e-09!114;UBERON:0004177!7.49e-09!29;UBERON:0005057!7.49e-09!29;UBERON:0001041!1.28e-08!80;UBERON:0000077!1.65e-08!35;UBERON:0001004!9.57e-08!42;UBERON:0003408!2.20e-07!24;UBERON:0000065!2.67e-07!41;UBERON:0006562!5.49e-07!24;UBERON:0001557!5.49e-07!24;UBERON:0001042!5.49e-07!24;UBERON:0008814!5.49e-07!24;UBERON:0009145!5.49e-07!24;UBERON:0002370!6.93e-07!23;UBERON:0000974!6.93e-07!23;UBERON:0004807!6.93e-07!23;UBERON:0005058!6.93e-07!23;UBERON:0003351!6.93e-07!23;UBERON:0009113!6.93e-07!23;UBERON:0003295!6.93e-07!23;UBERON:0009722!6.93e-07!23;UBERON:0005562!6.93e-07!23;UBERON:0007690!6.93e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.720982,0.448401,0.538088,0.173246,1.02512,0.687027,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.703873,1.4996,0.29826,0.332107,0.485665,0.549359,0.717658,0.374936,0.577606,0.466037,0.469052,0.818708,0.376624,0.455168,0.843667,0.699026,0.425071,0.276324,0.185086,0.242032,0.522578,0.631914,0.195877,0.256422,0.460258,0.450632,0.27776,0.0824666,0.423266,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.140213,0.131016,0.136938,0.651651,0.806481,0.336166,0.530481,0.759925,0.612313,0.968721,0.920903,1.15003,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,0.663249,0.681235,0.679141,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.331912
}}

Latest revision as of 16:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:87562456..87562471,+p@chr11:87562456..87562471
+
Mm9::chr14:45608251..45608286,+p1@Ptger2
Mm9::chr17:69766781..69766805,+p2@ENSMUST00000097289
Mm9::chr2:167602975..167603013,+p1@ENSMUST00000139927
Mm9::chr3:106563434..106563448,-p@chr3:106563434..106563448
-
Mm9::chr3:106592965..106592990,-p1@Cd53
Mm9::chr3:108714724..108714742,+p@chr3:108714724..108714742
+
Mm9::chr9:121584220..121584230,-p@chr9:121584220..121584230
-


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:0004960thromboxane receptor activity0.00730293432441445
GO:0004953icosanoid receptor activity0.00730293432441445
GO:0004954prostanoid receptor activity0.00730293432441445



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 system2.91e-1548
immune system2.91e-1548
hematopoietic system2.69e-1445
blood island2.69e-1445
digestive system1.34e-09116
digestive tract1.34e-09116
primitive gut1.34e-09116
endoderm-derived structure1.96e-09118
endoderm1.96e-09118
presumptive endoderm1.96e-09118
subdivision of digestive tract3.60e-09114
hemopoietic organ7.49e-0929
immune organ7.49e-0929
foregut1.28e-0880
mixed endoderm/mesoderm-derived structure1.65e-0835
respiratory system9.57e-0842
gland of gut2.20e-0724
respiratory tract2.67e-0741
pharynx5.49e-0724
upper respiratory tract5.49e-0724
chordate pharynx5.49e-0724
pharyngeal arch system5.49e-0724
pharyngeal region of foregut5.49e-0724
thymus6.93e-0723
neck6.93e-0723
respiratory system epithelium6.93e-0723
hemolymphoid system gland6.93e-0723
pharyngeal epithelium6.93e-0723
thymic region6.93e-0723
pharyngeal gland6.93e-0723
entire pharyngeal arch endoderm6.93e-0723
thymus primordium6.93e-0723
early pharyngeal endoderm6.93e-0723


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)
MA0003.10.602903
MA0004.10.434673
MA0006.10.271714
MA0007.11.07722
MA0009.10.870101
MA0014.10.325341
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.523649
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.12.0636
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.000755986
MA0074.10.531046
MA0076.11.52758
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.11.29122
MA0101.10.950493
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.10.814533
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.633896
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.11.69575
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.11.63575
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.12.32782
MA0139.10.506952
MA0140.11.29098
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.11.19766
MA0145.11.35361
MA0146.10.636109
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.23.38762
MA0035.20.524137
MA0039.20.0706842
MA0138.20.675599
MA0002.20.988033
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.527225
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.11.65123
MA0155.10.275377
MA0156.11.52462
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0211019
MA0163.10.0836563
MA0164.10.551114
MA0080.22.26
MA0018.21.37842
MA0099.20.669311
MA0079.20.0137335
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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