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MCL coexpression mm9:549: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002113!2.73e-35!14;UBERON:0003918!2.73e-35!14;UBERON:0011143!2.73e-35!14;UBERON:0005095!2.73e-35!14;UBERON:0007687!2.73e-35!14;UBERON:0006554!3.69e-27!18;UBERON:0001008!1.16e-25!19;UBERON:0000489!4.34e-23!21;UBERON:0003103!1.49e-10!43;UBERON:0005172!4.42e-09!49;UBERON:0005173!4.42e-09!49;UBERON:0002417!4.42e-09!49;UBERON:0000916!4.42e-09!49;UBERON:0003104!5.29e-07!61;UBERON:0009142!5.29e-07!61
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|tfbs_overrepresentation_jaspar=MA0003.1;0.0804299,MA0004.1;0.279808,MA0006.1;0.451962,MA0007.1;0.267314,MA0009.1;0.678286,MA0014.1;0.0332236,MA0017.1;0.499735,MA0019.1;1.26393,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;0.155127,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.602366,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.0835619,MA0056.1;0,MA0057.1;0.127633,MA0058.1;0.202403,MA0059.1;0.212009,MA0060.1;0.0941959,MA0061.1;0.113212,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;0.571204,MA0069.1;0.698271,MA0070.1;0.688999,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;0.0356907,MA0074.1;0.363923,MA0076.1;0.181159,MA0077.1;0.660245,MA0078.1;0.443468,MA0081.1;0.651709,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.204026,MA0089.1;0,MA0090.1;1.2955,MA0091.1;0.290854,MA0092.1;0.251716,MA0093.1;0.161141,MA0095.1;0,MA0098.1;0,MA0100.1;0.353762,MA0101.1;0.219061,MA0103.1;0.519343,MA0105.1;0.196316,MA0106.1;0.450539,MA0107.1;0.508149,MA0108.2;0.527977,MA0109.1;0,MA0111.1;1.33881,MA0113.1;0.424958,MA0114.1;0.359761,MA0115.1;0.773793,MA0116.1;0.451594,MA0117.1;0.742722,MA0119.1;0.626271,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.0756871,MA0140.1;0.353662,MA0141.1;0.555407,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.737036,MA0145.1;1.02938,MA0146.1;0.0462894,MA0147.1;0.121834,MA0148.1;0.796977,MA0149.1;0.223436,MA0062.2;0.0556611,MA0035.2;0.357786,MA0039.2;0.0150018,MA0138.2;0.495254,MA0002.2;1.42746,MA0137.2;0.55008,MA0104.2;0.0856657,MA0047.2;1.84133,MA0112.2;0.0201854,MA0065.2;0.0897174,MA0150.1;0.737147,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.139881,MA0155.1;0.105935,MA0156.1;0.180505,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.803691,MA0160.1;0.296006,MA0161.1;0,MA0162.1;0.0597766,MA0163.1;0.232458,MA0164.1;0.993886,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;1.22689,MA0079.2;0.746449,MA0102.2;1.38728,MA0258.1;0.103004,MA0259.1;0.367748,MA0442.1;0
}}

Latest revision as of 15:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:3291643..3291648,+p@chr10:3291643..3291648
+
Mm9::chr10:75036195..75036209,+p15@Ggt1
Mm9::chr12:31949130..31949155,+p@chr12:31949130..31949155
+
Mm9::chr12:70892312..70892325,-p@chr12:70892312..70892325
-
Mm9::chr16:26463232..26463247,+p3@Cldn16
Mm9::chr16:55523894..55523897,-p@chr16:55523894..55523897
-
Mm9::chr17:43640962..43640970,-p@chr17:43640962..43640970
-
Mm9::chr1:129203283..129203329,+p6@Mgat5
Mm9::chr1:13650826..13650836,-p3@Lactb2
Mm9::chr2:62249752..62249763,-p@chr2:62249752..62249763
-
Mm9::chr2:74543143..74543158,+p9@Hoxd8
Mm9::chr7:31244710..31244719,+p4@Nphs1
Mm9::chr7:31244771..31244782,+p2@Nphs1


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:0030144alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity0.0374681592963941
GO:0004662CAAX-protein geranylgeranyltransferase activity0.0374681592963941



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
kidney2.73e-3514
kidney mesenchyme2.73e-3514
upper urinary tract2.73e-3514
kidney rudiment2.73e-3514
kidney field2.73e-3514
urinary system structure3.69e-2718
renal system1.16e-2519
cavitated compound organ4.34e-2321
compound organ1.49e-1043
abdomen element4.42e-0949
abdominal segment element4.42e-0949
abdominal segment of trunk4.42e-0949
abdomen4.42e-0949
mesenchyme5.29e-0761
entire embryonic mesenchyme5.29e-0761


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)
MA0003.10.0804299
MA0004.10.279808
MA0006.10.451962
MA0007.10.267314
MA0009.10.678286
MA0014.10.0332236
MA0017.10.499735
MA0019.11.26393
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.602366
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.0835619
MA0056.10
MA0057.10.127633
MA0058.10.202403
MA0059.10.212009
MA0060.10.0941959
MA0061.10.113212
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.10.571204
MA0069.10.698271
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.10.0356907
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.651709
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.204026
MA0089.10
MA0090.11.2955
MA0091.10.290854
MA0092.10.251716
MA0093.10.161141
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.10.219061
MA0103.10.519343
MA0105.10.196316
MA0106.10.450539
MA0107.10.508149
MA0108.20.527977
MA0109.10
MA0111.11.33881
MA0113.10.424958
MA0114.10.359761
MA0115.10.773793
MA0116.10.451594
MA0117.10.742722
MA0119.10.626271
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.0756871
MA0140.10.353662
MA0141.10.555407
MA0142.10.575041
MA0143.10.439766
MA0144.10.737036
MA0145.11.02938
MA0146.10.0462894
MA0147.10.121834
MA0148.10.796977
MA0149.10.223436
MA0062.20.0556611
MA0035.20.357786
MA0039.20.0150018
MA0138.20.495254
MA0002.21.42746
MA0137.20.55008
MA0104.20.0856657
MA0047.21.84133
MA0112.20.0201854
MA0065.20.0897174
MA0150.10.737147
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.139881
MA0155.10.105935
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.803691
MA0160.10.296006
MA0161.10
MA0162.10.0597766
MA0163.10.232458
MA0164.10.993886
MA0080.20.170995
MA0018.20.390455
MA0099.21.22689
MA0079.20.746449
MA0102.21.38728
MA0258.10.103004
MA0259.10.367748
MA0442.10
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