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MCL coexpression mm9:667: Difference between revisions

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{{MCL_coexpression_mm9
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pancreas development;0.00964225058894429;20677!GO:0032392;DNA geometric change;0.0192776334780389;17220!GO:0006268;DNA unwinding during replication;0.0192776334780389;17220!GO:0032508;DNA duplex unwinding;0.0192776334780389;17220!GO:0031016;pancreas development;0.0192776334780389;20677!GO:0035272;exocrine system development;0.0192776334780389;20677!GO:0006270;DNA replication initiation;0.0192776334780389;17220!GO:0003678;DNA helicase activity;0.0214160708560177;17220!GO:0003697;single-stranded DNA binding;0.0214160708560177;17220!GO:0008483;transaminase activity;0.0260155338005554;20677!GO:0008094;DNA-dependent ATPase activity;0.0280263626984292;17220!GO:0016769;transferase activity, transferring nitrogenous groups;0.0280970367728147;20677!GO:0006261;DNA-dependent DNA replication;0.0330165802311582;17220!GO:0043566;structure-specific DNA binding;0.0330165802311582;17220!GO:0006355;regulation of transcription, DNA-dependent;0.047119967891685;20677,17220!GO:0006351;transcription, DNA-dependent;0.047119967891685;20677,17220!GO:0032774;RNA biosynthetic process;0.047119967891685;20677,17220!GO:0003677;DNA binding;0.047119967891685;20677,17220!GO:0045449;regulation of transcription;0.047119967891685;20677,17220!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.047119967891685;20677,17220!GO:0006350;transcription;0.047119967891685;20677,17220!GO:0010468;regulation of gene expression;0.0480498860111905;20677,17220!GO:0031323;regulation of cellular metabolic process;0.0480628636693369;20677,17220!GO:0004386;helicase activity;0.0480628636693369;17220!GO:0019222;regulation of metabolic process;0.0480628636693369;20677,17220!GO:0006260;DNA replication;0.0480628636693369;17220!GO:0016070;RNA metabolic 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|gostat_on_MCL_coexpression=GO:0031017;exocrine pancreas development;0.00964225058894429;20677!GO:0032392;DNA geometric change;0.0192776334780389;17220!GO:0006268;DNA unwinding during replication;0.0192776334780389;17220!GO:0032508;DNA duplex unwinding;0.0192776334780389;17220!GO:0031016;pancreas development;0.0192776334780389;20677!GO:0035272;exocrine system development;0.0192776334780389;20677!GO:0006270;DNA replication initiation;0.0192776334780389;17220!GO:0003678;DNA helicase activity;0.0214160708560177;17220!GO:0003697;single-stranded DNA binding;0.0214160708560177;17220!GO:0008483;transaminase activity;0.0260155338005554;20677!GO:0008094;DNA-dependent ATPase activity;0.0280263626984292;17220!GO:0016769;transferase activity, transferring nitrogenous groups;0.0280970367728147;20677!GO:0006261;DNA-dependent DNA replication;0.0330165802311582;17220!GO:0043566;structure-specific DNA binding;0.0330165802311582;17220!GO:0006355;regulation of transcription, DNA-dependent;0.047119967891685;20677,17220!GO:0006351;transcription, DNA-dependent;0.047119967891685;20677,17220!GO:0032774;RNA biosynthetic process;0.047119967891685;20677,17220!GO:0003677;DNA binding;0.047119967891685;20677,17220!GO:0045449;regulation of transcription;0.047119967891685;20677,17220!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.047119967891685;20677,17220!GO:0006350;transcription;0.047119967891685;20677,17220!GO:0010468;regulation of gene expression;0.0480498860111905;20677,17220!GO:0031323;regulation of cellular metabolic process;0.0480628636693369;20677,17220!GO:0004386;helicase activity;0.0480628636693369;17220!GO:0019222;regulation of metabolic process;0.0480628636693369;20677,17220!GO:0006260;DNA replication;0.0480628636693369;17220!GO:0016070;RNA metabolic process;0.0480628636693369;20677,17220!
|ontology_enrichment_celltype=CL:0000393!8.92e-09!39;CL:0000211!8.92e-09!39;CL:0000540!3.74e-08!33;CL:0000047!3.74e-08!33;CL:0000031!3.74e-08!33;CL:0000404!3.74e-08!33;CL:0000055!8.10e-08!49;CL:0000221!3.28e-07!44;CL:0000133!3.28e-07!44;CL:0002319!4.13e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.140695,0.269904,0.329881,0.176699,0.342839,0.425757,0.106126,0.362206,0.401738,0.385334,0.414631,0.345518,0.437133,0.189961,0,0.619876,0.170475,1.60971,0.171249,0.238546,0.281622,0.436294,0.175485,0.276437,0.4628,0.0908349,0.949712,0.213277,0.231659,0.349031,0.717576,0.168723,0.0786762,0.19035,1.69598,0.161521,0.411296,0.144953,0.123934,0.173534,0.353696,0.0243896,0.191571,0.0900858,0.319944,0.543674,0.376103,0.208261,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.60268,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.110167,0.0307733,0.905636,0.0810502,0.0742951,0.0786324,0.532872,0.681539,0.242107,0.357936,0.636582,0.495545,0.333618,0.792744,0.123451,0.291599,1.29984,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.805383,0.694736,0.732731,0.543917,0.437273,0.161581,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.286453,0.840348,0.243062,0.390066,1.0825,0.512539,0.337757,0.333247,1.50549,2.13447,0.910937,0.572279,0.464505,0.532013,2.56224,0.685116,5.05137,0.723425,1.00525,0.183744,0.821997,0.323373,2.23742,0.456508,1.10385,0.0275241,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.93276,0.546641,1.84176,0.302077,0.527071,0.0664621,0.0240729,0.857198,0.415832,0.455644,0.93735,0.488969,0.199652,0.290467,0.299755,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.484323,0.413167,0.0654894
}}

Latest revision as of 15:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:29041020..29041041,-p@chr13:29041020..29041041
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Mm9::chr13:29041931..29041947,-p@chr13:29041931..29041947
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Mm9::chr13:29042107..29042118,-p@chr13:29042107..29042118
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Mm9::chr13:29042426..29042441,-p@chr13:29042426..29042441
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Mm9::chr13:29042631..29042655,-p@chr13:29042631..29042655
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Mm9::chr13:29043308..29043321,-p1@ENSMUST00000099654
Mm9::chr13:29043389..29043410,+p@chr13:29043389..29043410
+
Mm9::chr13:29043435..29043446,+p@chr13:29043435..29043446
+
Mm9::chr13:29043513..29043517,+p@chr13:29043513..29043517
+
Mm9::chr13:29045559..29045574,-p1@Sox4
Mm9::chr5:138612220..138612261,-p2@Mcm7


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:0031017exocrine pancreas development0.00964225058894429
GO:0032392DNA geometric change0.0192776334780389
GO:0006268DNA unwinding during replication0.0192776334780389
GO:0032508DNA duplex unwinding0.0192776334780389
GO:0031016pancreas development0.0192776334780389
GO:0035272exocrine system development0.0192776334780389
GO:0006270DNA replication initiation0.0192776334780389
GO:0003678DNA helicase activity0.0214160708560177
GO:0003697single-stranded DNA binding0.0214160708560177
GO:0008483transaminase activity0.0260155338005554
GO:0008094DNA-dependent ATPase activity0.0280263626984292
GO:0016769transferase activity, transferring nitrogenous groups0.0280970367728147
GO:0006261DNA-dependent DNA replication0.0330165802311582
GO:0043566structure-specific DNA binding0.0330165802311582
GO:0006355regulation of transcription, DNA-dependent0.047119967891685
GO:0006351transcription, DNA-dependent0.047119967891685
GO:0032774RNA biosynthetic process0.047119967891685
GO:0003677DNA binding0.047119967891685
GO:0045449regulation of transcription0.047119967891685
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.047119967891685
GO:0006350transcription0.047119967891685
GO:0010468regulation of gene expression0.0480498860111905
GO:0031323regulation of cellular metabolic process0.0480628636693369
GO:0004386helicase activity0.0480628636693369
GO:0019222regulation of metabolic process0.0480628636693369
GO:0006260DNA replication0.0480628636693369
GO:0016070RNA metabolic process0.0480628636693369



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><br><br>

Cell Type
Ontology termp-valuen
electrically responsive cell8.92e-0939
electrically active cell8.92e-0939
neuron3.74e-0833
neuronal stem cell3.74e-0833
neuroblast3.74e-0833
electrically signaling cell3.74e-0833
non-terminally differentiated cell8.10e-0849
ectodermal cell3.28e-0744
neurectodermal cell3.28e-0744
neural cell4.13e-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)
MA0003.10.00322434
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.10.00333639
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.11.62787
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.111.4662
MA0042.16.66152
MA0043.10.837621
MA0046.10.778239
MA0048.10.054097
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.0098576
MA0056.10
MA0057.10.406124
MA0058.10.246908
MA0059.10.257372
MA0060.10.789184
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.735122
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.31412
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.0293443
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.216742
MA0105.10.0759118
MA0106.10.509454
MA0107.10.211681
MA0108.21.4389
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.145642
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.103495
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.11.24578
MA0144.10.147954
MA0145.10.0329586
MA0146.10.183077
MA0147.10.475899
MA0148.10.912216
MA0149.10.269772
MA0062.20.573094
MA0035.20.412747
MA0039.20.0387728
MA0138.20.555696
MA0002.20.699393
MA0137.20.230686
MA0104.20.11535
MA0047.21.16804
MA0112.20.133279
MA0065.21.30208
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.0529077
MA0155.10.154271
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.495113
MA0160.10.347545
MA0161.10
MA0162.10.388731
MA0163.10.0916052
MA0164.10.437937
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.20.0743239
MA0102.21.45844
MA0258.10.135621
MA0259.10.891672
MA0442.10
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