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MCL coexpression mm9:1331: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0005923;tight junction;0.00170156244089007;58220,56217!GO:0043296;apical junction complex;0.00170156244089007;58220,56217!GO:0016327;apicolateral plasma membrane;0.00170156244089007;58220,56217!GO:0005911;intercellular junction;0.00355302463365568;58220,56217!GO:0004385;guanylate kinase activity;0.00933391733597315;56217!GO:0030054;cell junction;0.0153730212532083;58220,56217!GO:0019201;nucleotide kinase activity;0.0249864984349492;56217!GO:0016776;phosphotransferase activity, phosphate group as acceptor;0.0407822118572064;56217!GO:0019205;nucleobase, nucleoside, nucleotide kinase activity;0.0426733997204883;56217!GO:0016301;kinase activity;0.0426733997204883;240505,56217!GO:0019992;diacylglycerol binding;0.0426733997204883;240505!GO:0005938;cell cortex;0.0426733997204883;58220!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0426733997204883;240505,56217!GO:0007242;intracellular signaling cascade;0.0426733997204883;240505,58220!
|ontology_enrichment_celltype=CL:0000066!2.06e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!2.41e-14!31;UBERON:0005409!3.96e-12!47;UBERON:0000344!3.51e-09!15;UBERON:0000464!4.86e-09!57;UBERON:0004119!5.68e-09!118;UBERON:0000925!5.68e-09!118;UBERON:0006595!5.68e-09!118;UBERON:0005178!6.69e-09!17;UBERON:0005181!6.69e-09!17;UBERON:0002224!6.69e-09!17;UBERON:0000915!6.69e-09!17;UBERON:0008947!6.69e-09!17;UBERON:0003258!6.69e-09!17;UBERON:0000466!9.10e-09!79;UBERON:0001007!1.29e-08!116;UBERON:0001555!1.29e-08!116;UBERON:0007026!1.29e-08!116;UBERON:0001242!2.69e-08!13;UBERON:0000060!2.69e-08!13;UBERON:0001262!2.69e-08!13;UBERON:0004786!2.69e-08!13;UBERON:0005177!5.42e-08!79;UBERON:0004921!6.01e-08!114;UBERON:0005153!3.95e-07!17;UBERON:0002048!4.16e-07!14;UBERON:0000117!4.16e-07!14;UBERON:0000171!4.16e-07!14;UBERON:0000170!4.16e-07!14;UBERON:0005597!4.16e-07!14;UBERON:0000118!4.16e-07!14
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,3.34076,0.599767,0.632897,1.28144,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.86893,0.426133,1.17476,0.657163,0.345236,0.472505,0.686615,0.63639,1.40396,0.394364,0.534301,0.558142,0.960397,0.892985,0.589948,0.956447,0.607065,2.38064,1.52228,0.303703,0.752287,0.342638,0.56353,0.0995018,0.959963,1.02402,0.524258,0.77511,0.589246,0.0835644,1.02809,0.839084,0.714419,0.995874,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,4.64017,1.156,1.7706,1.08629,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,5.55221,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,1.42973,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,2.74322,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,1.64681,2.32256,8.75335,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,1.73883
|tfbs_overrepresentation_jaspar=MA0003.1;4.33829,MA0004.1;1.3269,MA0006.1;0.945134,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;3.35198,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;2.15574,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;1.22706,MA0056.1;0,MA0057.1;0.457693,MA0058.1;0.436487,MA0059.1;1.14076,MA0060.1;4.84383,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.169297,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.725434,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.988233,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;2.72692,MA0105.1;0.57901,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;2.39942,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;1.2655,MA0140.1;1.51549,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;1.814,MA0146.1;4.28855,MA0147.1;3.24836,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;4.68324,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;3.75187,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;10.2792,MA0163.1;0.664494,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;6.27804,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;1.5079,MA0442.1;0
}}

Latest revision as of 16:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:79849983..79850006,+p2@Mpp5
Mm9::chr19:6306626..6306638,+p4@Cdc42bpg
Mm9::chr2:167906524..167906535,+p4@Pard6b
Mm9::chr2:167906603..167906622,+p1@Pard6b
Mm9::chr2:167906639..167906655,+p2@Pard6b
Mm9::chr2:4638871..4638939,+p1@Bend7


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:0005923tight junction0.00170156244089007
GO:0043296apical junction complex0.00170156244089007
GO:0016327apicolateral plasma membrane0.00170156244089007
GO:0005911intercellular junction0.00355302463365568
GO:0004385guanylate kinase activity0.00933391733597315
GO:0030054cell junction0.0153730212532083
GO:0019201nucleotide kinase activity0.0249864984349492
GO:0016776phosphotransferase activity, phosphate group as acceptor0.0407822118572064
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0426733997204883
GO:0016301kinase activity0.0426733997204883
GO:0019992diacylglycerol binding0.0426733997204883
GO:0005938cell cortex0.0426733997204883
GO:0016772transferase activity, transferring phosphorus-containing groups0.0426733997204883
GO:0007242intracellular signaling cascade0.0426733997204883



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
epithelial cell2.06e-0725

Uber Anatomy
Ontology termp-valuen
intestine2.41e-1431
gastrointestinal system3.96e-1247
mucosa3.51e-0915
anatomical space4.86e-0957
endoderm-derived structure5.68e-09118
endoderm5.68e-09118
presumptive endoderm5.68e-09118
thoracic cavity element6.69e-0917
thoracic segment organ6.69e-0917
thoracic cavity6.69e-0917
thoracic segment of trunk6.69e-0917
respiratory primordium6.69e-0917
endoderm of foregut6.69e-0917
immaterial anatomical entity9.10e-0979
digestive system1.29e-08116
digestive tract1.29e-08116
primitive gut1.29e-08116
intestinal mucosa2.69e-0813
anatomical wall2.69e-0813
wall of intestine2.69e-0813
gastrointestinal system mucosa2.69e-0813
trunk region element5.42e-0879
subdivision of digestive tract6.01e-08114
epithelial bud3.95e-0717
lung4.16e-0714
respiratory tube4.16e-0714
respiration organ4.16e-0714
pair of lungs4.16e-0714
lung primordium4.16e-0714
lung bud4.16e-0714


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)
MA0003.14.33829
MA0004.11.3269
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.13.35198
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.12.15574
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.11.22706
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.11.14076
MA0060.14.84383
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.169297
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.12.72692
MA0105.10.57901
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.12.39942
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.11.2655
MA0140.11.51549
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.11.814
MA0146.14.28855
MA0147.13.24836
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.24.68324
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.23.75187
MA0047.20.685741
MA0112.20.37938
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.110.2792
MA0163.10.664494
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.26.27804
MA0102.21.7182
MA0258.10.290587
MA0259.11.5079
MA0442.10
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