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|ontology_enrichment_uberon=UBERON:0004119!1.29e-10!118;UBERON:0000925!1.29e-10!118;UBERON:0006595!1.29e-10!118;UBERON:0000475!6.60e-10!150;UBERON:0001007!6.94e-10!116;UBERON:0001555!6.94e-10!116;UBERON:0007026!6.94e-10!116;UBERON:0004921!1.02e-09!114;UBERON:0009569!3.42e-08!66;UBERON:0005177!5.32e-08!79;UBERON:0005172!6.05e-08!49;UBERON:0005173!6.05e-08!49;UBERON:0002417!6.05e-08!49;UBERON:0000916!6.05e-08!49;UBERON:0001041!7.38e-08!80;UBERON:0002100!8.32e-08!90;UBERON:0001048!4.25e-07!134;UBERON:0000468!4.43e-07!333
|ontology_enrichment_uberon=UBERON:0004119!1.29e-10!118;UBERON:0000925!1.29e-10!118;UBERON:0006595!1.29e-10!118;UBERON:0000475!6.60e-10!150;UBERON:0001007!6.94e-10!116;UBERON:0001555!6.94e-10!116;UBERON:0007026!6.94e-10!116;UBERON:0004921!1.02e-09!114;UBERON:0009569!3.42e-08!66;UBERON:0005177!5.32e-08!79;UBERON:0005172!6.05e-08!49;UBERON:0005173!6.05e-08!49;UBERON:0002417!6.05e-08!49;UBERON:0000916!6.05e-08!49;UBERON:0001041!7.38e-08!80;UBERON:0002100!8.32e-08!90;UBERON:0001048!4.25e-07!134;UBERON:0000468!4.43e-07!333
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.750994,0.269904,0.329881,0.176699,0.907763,0.425757,0.345089,0.732132,0.208174,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.170475,0.318616,1.06389,0.670854,0.521547,0.436294,0.520732,0.276437,0.4628,0.304017,0.361771,0.611503,0.500344,0.349031,0.717576,0.168723,0.270473,0.19035,0.308746,0.161521,0.411296,0.873942,0.391645,0.173534,0.353696,0.478787,0.191571,0.557517,0.319944,0.543674,0.376103,0.208261,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,1.83442,1.01274,0.441884,0.698157,0.496904,0.383763,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.355763,0.126035,0.905636,0.582533,0.54852,0.570456,0.532872,0.681539,0.242107,0.357936,0.636582,0.495545,0.101814,0.792744,0.256335,0.0525502,0.500771,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.694736,0.732731,0.543917,0.0534645,0.161581,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.286453,0.840348,0.243062,0.390066,1.0825,0.172131,0.170188,0.333247,0.621127,0.931584,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,1.10612,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,0.0275241,0.811774,0.934673,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,1.34861,1.84176,0.816464,1.60254,0.0664621,0.103135,0.857198,0.824171,0.455644,0.93735,0.488969,0.199652,0.290467,0.299755,1.06466,3.09795,0.685546,0.776587,0.593295,0.448733,0.160658,0.413167,0.276798
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.750994,0.269904,0.329881,0.176699,0.907763,0.425757,0.345089,0.732132,0.208174,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.170475,0.318616,1.06389,0.670854,0.521547,0.436294,0.520732,0.276437,0.4628,0.304017,0.361771,0.611503,0.500344,0.349031,0.717576,0.168723,0.270473,0.19035,0.308746,0.161521,0.411296,0.873942,0.391645,0.173534,0.353696,0.478787,0.191571,0.557517,0.319944,0.543674,0.376103,0.208261,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,1.83442,1.01274,0.441884,0.698157,0.496904,0.383763,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.355763,0.126035,0.905636,0.582533,0.54852,0.570456,0.532872,0.681539,0.242107,0.357936,0.636582,0.495545,0.101814,0.792744,0.256335,0.0525502,0.500771,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.694736,0.732731,0.543917,0.0534645,0.161581,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.286453,0.840348,0.243062,0.390066,1.0825,0.172131,0.170188,0.333247,0.621127,0.931584,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,1.10612,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,0.0275241,0.811774,0.934673,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,1.34861,1.84176,0.816464,1.60254,0.0664621,0.103135,0.857198,0.824171,0.455644,0.93735,0.488969,0.199652,0.290467,0.299755,1.06466,3.09795,0.685546,0.776587,0.593295,0.448733,0.160658,0.413167,0.276798
|tfbs_overrepresentation_jaspar=MA0003.1;0.570495,MA0004.1;0.330313,MA0006.1;0.186435,MA0007.1;0.850001,MA0009.1;0.743257,MA0014.1;1.22114,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.440822,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.479469,MA0056.1;0,MA0057.1;0.406124,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.12537,MA0061.1;1.42191,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.0500842,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;2.58254e-05,MA0074.1;0.419185,MA0076.1;0.223625,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.849797,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.906056,MA0092.1;1.47462,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.619698,MA0105.1;1.41301,MA0106.1;0.509454,MA0107.1;0.607721,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.145642,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;0.265536,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.103495,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.452699,MA0145.1;0.57264,MA0146.1;0.0833862,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.0791588,MA0035.2;0.412747,MA0039.2;0.00487869,MA0138.2;0.555696,MA0002.2;0.343346,MA0137.2;0.230686,MA0104.2;0.11535,MA0047.2;0.46201,MA0112.2;0.313687,MA0065.2;0.314773,MA0150.1;0.316876,MA0151.1;0,MA0152.1;1.16826,MA0153.1;0.889592,MA0154.1;1.6326,MA0155.1;0.354827,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;1.52694,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.103104,MA0163.1;0.563751,MA0164.1;0.437937,MA0080.2;0.609443,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;0.0102382,MA0102.2;1.45844,MA0258.1;0.421574,MA0259.1;0.14914,MA0442.1;0
}}
}}

Revision as of 12:05, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:100750866..100750891,-p@chr11:100750866..100750891
-
Mm9::chr12:60289431..60289446,+p@chr12:60289431..60289446
+
Mm9::chr13:34274534..34274552,-p@chr13:34274534..34274552
-
Mm9::chr15:12251371..12251380,+p5@Golph3
Mm9::chr15:96518755..96518774,-p@chr15:96518755..96518774
-
Mm9::chr19:46589812..46589830,+p@chr19:46589812..46589830
+
Mm9::chr2:133378740..133378753,+p2@Bmp2
Mm9::chr4:59489147..59489161,-p@chr4:59489147..59489161
-
Mm9::chr5:65213356..65213412,+p6@Klf3
Mm9::chr5:65213459..65213485,+p12@Klf3
Mm9::chr5:65214223..65214249,+p@chr5:65214223..65214249
+


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:0048711positive regulation of astrocyte differentiation0.0274145700786072
GO:0048710regulation of astrocyte differentiation0.0274145700786072
GO:0014015positive regulation of gliogenesis0.0274145700786072
GO:0045687positive regulation of glial cell differentiation0.0274145700786072
GO:0045778positive regulation of ossification0.0274145700786072
GO:0046852positive regulation of bone remodeling0.0274145700786072
GO:0045669positive regulation of osteoblast differentiation0.0274145700786072
GO:0048708astrocyte differentiation0.0274145700786072
GO:0001837epithelial to mesenchymal transition0.0274145700786072
GO:0014013regulation of gliogenesis0.0274145700786072
GO:0045685regulation of glial cell differentiation0.0274145700786072
GO:0045667regulation of osteoblast differentiation0.0334984357436158
GO:0035051cardiac cell differentiation0.0386425113870819
GO:0001658ureteric bud branching0.0430481817489659
GO:0030282bone mineralization0.0495686167483751
GO:0030278regulation of ossification0.0495686167483751
GO:0001649osteoblast differentiation0.0495686167483751
GO:0030509BMP signaling pathway0.0495686167483751
GO:0046850regulation of bone remodeling0.0495686167483751
GO:0001657ureteric bud development0.0495686167483751
GO:0015171amino acid transmembrane transporter activity0.0495686167483751
GO:0042475odontogenesis of dentine-containing teeth0.0495686167483751
GO:0042476odontogenesis0.0495686167483751
GO:0010001glial cell differentiation0.0495686167483751
GO:0048762mesenchymal cell differentiation0.0495686167483751
GO:0014031mesenchymal cell development0.0495686167483751
GO:0042063gliogenesis0.0495686167483751
GO:0006865amino acid transport0.0495686167483751
GO:0001656metanephros development0.0495686167483751
GO:0045597positive regulation of cell differentiation0.0495686167483751
GO:0007179transforming growth factor beta receptor signaling pathway0.0495686167483751



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
endoderm-derived structure1.29e-10118
endoderm1.29e-10118
presumptive endoderm1.29e-10118
organism subdivision6.60e-10150
digestive system6.94e-10116
digestive tract6.94e-10116
primitive gut6.94e-10116
subdivision of digestive tract1.02e-09114
subdivision of trunk3.42e-0866
trunk region element5.32e-0879
abdomen element6.05e-0849
abdominal segment element6.05e-0849
abdominal segment of trunk6.05e-0849
abdomen6.05e-0849
foregut7.38e-0880
trunk8.32e-0890
primordium4.25e-07134
multi-cellular organism4.43e-07333


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)
MA0003.10.570495
MA0004.10.330313
MA0006.10.186435
MA0007.10.850001
MA0009.10.743257
MA0014.11.22114
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.440822
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.479469
MA0056.10
MA0057.10.406124
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.11.42191
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.0500842
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.12.58254e-05
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.849797
MA0089.10
MA0090.10.299987
MA0091.10.906056
MA0092.11.47462
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.619698
MA0105.11.41301
MA0106.10.509454
MA0107.10.607721
MA0108.20.589413
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
MA0143.10.49828
MA0144.10.452699
MA0145.10.57264
MA0146.10.0833862
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.20.0791588
MA0035.20.412747
MA0039.20.00487869
MA0138.20.555696
MA0002.20.343346
MA0137.20.230686
MA0104.20.11535
MA0047.20.46201
MA0112.20.313687
MA0065.20.314773
MA0150.10.316876
MA0151.10
MA0152.11.16826
MA0153.10.889592
MA0154.11.6326
MA0155.10.354827
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.11.52694
MA0160.10.347545
MA0161.10
MA0162.10.103104
MA0163.10.563751
MA0164.10.437937
MA0080.20.609443
MA0018.20.446948
MA0099.20.549696
MA0079.20.0102382
MA0102.21.45844
MA0258.10.421574
MA0259.10.14914
MA0442.10
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