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|ontology_enrichment_uberon=UBERON:0000160!2.04e-37!31;UBERON:0000344!5.17e-37!15;UBERON:0001242!6.08e-31!13;UBERON:0000060!6.08e-31!13;UBERON:0001262!6.08e-31!13;UBERON:0004786!6.08e-31!13;UBERON:0005409!1.84e-23!47;UBERON:0004923!3.24e-22!24;UBERON:0003350!6.35e-18!9;UBERON:0004808!6.35e-18!9;UBERON:0001277!6.35e-18!9;UBERON:0002108!9.58e-15!4;UBERON:0000485!1.63e-14!11;UBERON:0000331!1.06e-11!3;UBERON:0002116!1.06e-11!3;UBERON:0001204!1.06e-11!3;UBERON:0001168!1.06e-11!3;UBERON:0001007!1.99e-09!116;UBERON:0001555!1.99e-09!116;UBERON:0007026!1.99e-09!116;UBERON:0004119!3.37e-09!118;UBERON:0000925!3.37e-09!118;UBERON:0006595!3.37e-09!118;UBERON:0001962!1.31e-07!2;UBERON:0001961!1.31e-07!2;UBERON:0001744!1.31e-07!2;UBERON:0004921!1.66e-07!114
|ontology_enrichment_uberon=UBERON:0000160!2.04e-37!31;UBERON:0000344!5.17e-37!15;UBERON:0001242!6.08e-31!13;UBERON:0000060!6.08e-31!13;UBERON:0001262!6.08e-31!13;UBERON:0004786!6.08e-31!13;UBERON:0005409!1.84e-23!47;UBERON:0004923!3.24e-22!24;UBERON:0003350!6.35e-18!9;UBERON:0004808!6.35e-18!9;UBERON:0001277!6.35e-18!9;UBERON:0002108!9.58e-15!4;UBERON:0000485!1.63e-14!11;UBERON:0000331!1.06e-11!3;UBERON:0002116!1.06e-11!3;UBERON:0001204!1.06e-11!3;UBERON:0001168!1.06e-11!3;UBERON:0001007!1.99e-09!116;UBERON:0001555!1.99e-09!116;UBERON:0007026!1.99e-09!116;UBERON:0004119!3.37e-09!118;UBERON:0000925!3.37e-09!118;UBERON:0006595!3.37e-09!118;UBERON:0001962!1.31e-07!2;UBERON:0001961!1.31e-07!2;UBERON:0001744!1.31e-07!2;UBERON:0004921!1.66e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,0.394491,0.227651,0.40827,0.495658,0.880357,0.154135,0.314043,0.453212,0.484001,0.449446,0.507558,0.24249,0,0.696644,0.62892,0.419123,0.902262,0.296085,0.713323,0.50668,0.226287,0.337218,0.534339,0.801525,0.428336,0.268347,0.319094,0.414842,0.796599,0.218674,0.113369,0.242923,0.281474,1.1396,0.480503,0.191662,0.167387,0.637027,0.419787,0.371854,0.684206,0.158271,0.998423,0.618203,0.443479,0.314152,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.764433,0.471658,0.770972,0.512521,0.776777,0.569793,0.952934,0.668331,0.525334,1.68713,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.745723,0.987652,0.371787,0.107966,0.364033,0.607043,0.759798,0.299972,0.463363,0.713779,0.568383,0.858535,0.873141,0.0800961,0.439624,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,0.188213,0.515495,0.444003,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.265919,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,1.30862,1.18781,0.177062,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,1.07771,1.50578,1.92834,0.364791,0.649035,0.098204,0.369078,0.938577,0.178329,1.3067,1.01974,1.38016,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,1.21195,0.00844742
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,0.394491,0.227651,0.40827,0.495658,0.880357,0.154135,0.314043,0.453212,0.484001,0.449446,0.507558,0.24249,0,0.696644,0.62892,0.419123,0.902262,0.296085,0.713323,0.50668,0.226287,0.337218,0.534339,0.801525,0.428336,0.268347,0.319094,0.414842,0.796599,0.218674,0.113369,0.242923,0.281474,1.1396,0.480503,0.191662,0.167387,0.637027,0.419787,0.371854,0.684206,0.158271,0.998423,0.618203,0.443479,0.314152,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.764433,0.471658,0.770972,0.512521,0.776777,0.569793,0.952934,0.668331,0.525334,1.68713,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.745723,0.987652,0.371787,0.107966,0.364033,0.607043,0.759798,0.299972,0.463363,0.713779,0.568383,0.858535,0.873141,0.0800961,0.439624,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,0.188213,0.515495,0.444003,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.265919,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,1.30862,1.18781,0.177062,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,1.07771,1.50578,1.92834,0.364791,0.649035,0.098204,0.369078,0.938577,0.178329,1.3067,1.01974,1.38016,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,1.21195,0.00844742
|tfbs_overrepresentation_jaspar=MA0003.1;0.00972621,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.0421798,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;1.32237,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.589612,MA0050.1;2.88159,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0198867,MA0056.1;0,MA0057.1;0.549903,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;0.194456,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.077274,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;1.10147,MA0072.1;0.825495,MA0073.1;0.00108891,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.0492918,MA0089.1;0,MA0090.1;0.951436,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;1.37229,MA0105.1;0.35523,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.868953,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.441109,MA0140.1;0.477483,MA0141.1;0.789442,MA0142.1;0.714976,MA0143.1;1.40057,MA0144.1;0.195095,MA0145.1;0.0543321,MA0146.1;0.0548413,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.043355,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.287486,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.0543294,MA0065.2;0.44341,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.276788,MA0155.1;0.0631765,MA0156.1;0.763978,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0672805,MA0163.1;0.160428,MA0164.1;1.26737,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.000746166,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.571417,MA0442.1;0
}}
}}

Revision as of 12:18, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:21501144..21501147,+p@chr11:21501144..21501147
+
Mm9::chr11:48715513..48715546,-p@chr11:48715513..48715546
-
Mm9::chr11:6129264..6129275,-p@chr11:6129264..6129275
-
Mm9::chr11:9019226..9019233,+p@chr11:9019226..9019233
+
Mm9::chr11:9019282..9019299,+p@chr11:9019282..9019299
+
Mm9::chr15:77490274..77490279,-p@chr15:77490274..77490279
-
Mm9::chr18:73975357..73975368,-p3@Me2
Mm9::chr19:53102858..53102869,-p@chr19:53102858..53102869
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Mm9::chr9:31720903..31720918,-p2@Barx2


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:0000122negative regulation of transcription from RNA polymerase II promoter0.00365576547784741
GO:0045892negative regulation of transcription, DNA-dependent0.00365576547784741
GO:0016481negative regulation of transcription0.00365576547784741
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00365576547784741
GO:0042637catagen0.00365576547784741
GO:0031324negative regulation of cellular metabolic process0.00365576547784741
GO:0009892negative regulation of metabolic process0.00400373694120981
GO:0006357regulation of transcription from RNA polymerase II promoter0.00456441499641985
GO:0005667transcription factor complex0.00456441499641985
GO:0006366transcription from RNA polymerase II promoter0.00456441499641985
GO:0044451nucleoplasm part0.00635773056744951
GO:0005654nucleoplasm0.00640120353318183
GO:0031981nuclear lumen0.00835083855626479
GO:0048820hair follicle maturation0.00863300937840844
GO:0031974membrane-enclosed lumen0.00863300937840844
GO:0043233organelle lumen0.00863300937840844
GO:0048523negative regulation of cellular process0.0101479934017225
GO:0048519negative regulation of biological process0.011067884623619
GO:0044428nuclear part0.0128492932728319
GO:0045445myoblast differentiation0.0161890987055238
GO:0022404molting cycle process0.0161890987055238
GO:0001942hair follicle development0.0161890987055238
GO:0022405hair cycle process0.0161890987055238
GO:0042633hair cycle0.0161890987055238
GO:0042303molting cycle0.0161890987055238
GO:0003714transcription corepressor activity0.0202653465137349
GO:0042692muscle cell differentiation0.0207599354898422
GO:0048741skeletal muscle fiber development0.0207599354898422
GO:0048747muscle fiber development0.0207599354898422
GO:0043234protein complex0.020873176648202
GO:0006355regulation of transcription, DNA-dependent0.0230245297652552
GO:0006351transcription, DNA-dependent0.0230245297652552
GO:0021700developmental maturation0.0230245297652552
GO:0032774RNA biosynthetic process0.0230245297652552
GO:0003677DNA binding0.0230245297652552
GO:0007519skeletal muscle development0.0230245297652552
GO:0008544epidermis development0.0230245297652552
GO:0045449regulation of transcription0.0230245297652552
GO:0003682chromatin binding0.0230245297652552
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0230245297652552
GO:0007398ectoderm development0.0230245297652552
GO:0006350transcription0.0230245297652552
GO:0032991macromolecular complex0.0231208919643697
GO:0010468regulation of gene expression0.0234789215736499
GO:0031323regulation of cellular metabolic process0.0248777568436999
GO:0014706striated muscle development0.0249088824294402
GO:0007275multicellular organismal development0.0249298079320954
GO:0019222regulation of metabolic process0.0250795011298027
GO:0016070RNA metabolic process0.0255360665361971
GO:0003712transcription cofactor activity0.0255360665361971
GO:0044446intracellular organelle part0.0261352402748791
GO:0044422organelle part0.0261352402748791
GO:0016564transcription repressor activity0.027089289112185
GO:0007517muscle development0.0288363997579811
GO:0008134transcription factor binding0.031875321855894
GO:0010467gene expression0.0324322052668077
GO:0003676nucleic acid binding0.0334193720851622
GO:0032502developmental process0.0349805674959158
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.037496913465151
GO:0050794regulation of cellular process0.0424056232662334
GO:0009888tissue development0.0430751330345371



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
intestine2.04e-3731
mucosa5.17e-3715
intestinal mucosa6.08e-3113
anatomical wall6.08e-3113
wall of intestine6.08e-3113
gastrointestinal system mucosa6.08e-3113
gastrointestinal system1.84e-2347
organ component layer3.24e-2224
epithelium of mucosa6.35e-189
gastrointestinal system epithelium6.35e-189
intestinal epithelium6.35e-189
small intestine9.58e-154
simple columnar epithelium1.63e-1411
ileal mucosa1.06e-113
ileum1.06e-113
mucosa of small intestine1.06e-113
wall of small intestine1.06e-113
digestive system1.99e-09116
digestive tract1.99e-09116
primitive gut1.99e-09116
endoderm-derived structure3.37e-09118
endoderm3.37e-09118
presumptive endoderm3.37e-09118
gut-associated lymphoid tissue1.31e-072
mucosa-associated lymphoid tissue1.31e-072
lymphoid tissue1.31e-072
subdivision of digestive tract1.66e-07114


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)
MA0003.10.00972621
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.0421798
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.11.32237
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.12.88159
MA0051.10.542972
MA0052.10.84317
MA0055.10.0198867
MA0056.10
MA0057.10.549903
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.11.10147
MA0072.10.825495
MA0073.10.00108891
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.0492918
MA0089.10
MA0090.10.951436
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.11.37229
MA0105.10.35523
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.868953
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.789442
MA0142.10.714976
MA0143.11.40057
MA0144.10.195095
MA0145.10.0543321
MA0146.10.0548413
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.20.043355
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.0543294
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.10.0631765
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.10.160428
MA0164.11.26737
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.000746166
MA0102.21.5442
MA0258.10.180934
MA0259.10.571417
MA0442.10
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