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|ontology_enrichment_uberon=UBERON:0004119!3.82e-15!118;UBERON:0000925!3.82e-15!118;UBERON:0006595!3.82e-15!118;UBERON:0001007!1.66e-14!116;UBERON:0001555!1.66e-14!116;UBERON:0007026!1.66e-14!116;UBERON:0004921!1.83e-13!114;UBERON:0002193!1.11e-11!48;UBERON:0002405!1.11e-11!48;UBERON:0002390!4.82e-10!45;UBERON:0003061!4.82e-10!45;UBERON:0002384!2.12e-09!46;UBERON:0004923!2.75e-09!24;UBERON:0000490!8.16e-09!66;UBERON:0000160!2.22e-08!31;UBERON:0000344!2.61e-08!15;UBERON:0003929!3.28e-08!55;UBERON:0005911!1.78e-07!69;UBERON:0005409!1.81e-07!47;UBERON:0002371!3.60e-07!16;UBERON:0001242!4.14e-07!13;UBERON:0000060!4.14e-07!13;UBERON:0001262!4.14e-07!13;UBERON:0004786!4.14e-07!13;UBERON:0002204!9.52e-07!32
|ontology_enrichment_uberon=UBERON:0004119!3.82e-15!118;UBERON:0000925!3.82e-15!118;UBERON:0006595!3.82e-15!118;UBERON:0001007!1.66e-14!116;UBERON:0001555!1.66e-14!116;UBERON:0007026!1.66e-14!116;UBERON:0004921!1.83e-13!114;UBERON:0002193!1.11e-11!48;UBERON:0002405!1.11e-11!48;UBERON:0002390!4.82e-10!45;UBERON:0003061!4.82e-10!45;UBERON:0002384!2.12e-09!46;UBERON:0004923!2.75e-09!24;UBERON:0000490!8.16e-09!66;UBERON:0000160!2.22e-08!31;UBERON:0000344!2.61e-08!15;UBERON:0003929!3.28e-08!55;UBERON:0005911!1.78e-07!69;UBERON:0005409!1.81e-07!47;UBERON:0002371!3.60e-07!16;UBERON:0001242!4.14e-07!13;UBERON:0000060!4.14e-07!13;UBERON:0001262!4.14e-07!13;UBERON:0004786!4.14e-07!13;UBERON:0002204!9.52e-07!32
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.883225,0.297937,0.360062,0.580303,0.373426,0.458558,0.392928,0.411053,1.53832,0.417132,0.447169,0.124608,0.470194,1.15381,0,0.656089,0.19356,0.113609,0.205418,0.26524,0.60924,0.469335,1.094,0.822446,1.24179,0.709649,1.01819,0.67135,0.572447,0.379806,0.754912,0.560002,0.31333,0.614653,0.0351598,0.184038,1.12869,0.166348,0.143746,0.196807,0.38461,0.56316,0.617704,0.434259,1.6507,0.578773,0.407653,0.772185,0.677281,0.639101,0.522137,0.550735,0.894161,0.911367,0.47699,0.249055,0.435119,0.68053,0.47505,0.735292,0.531188,0.854737,1.52021,0.487593,1.60248,1.04613,1.3932,0.730718,1.24673,0.76885,0.404236,0.356247,0.944464,0.320434,0.0893951,0.0942164,2.38336,0.718494,0.268962,0.129727,0.673009,0.529804,0.119727,0.830765,0.538155,0.182066,0.271714,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,0.455999,0.122617,0.770215,0.57902,0.234357,0.541671,0.754637,0.87698,0.639679,0.638654,1.77029,0.696857,0.403887,0.750985,0.736223,0.845852,0.878738,0.26996,1.08155,1.12221,0.195318,0.409202,0.363536,1.58124,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.59809,0.86025,0.353344,1.01535,0.48999,1.14365,0.33206,0.877308,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.58382,0.0806411,0.305197,0.895708,0.46758,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.841258,0.629147,0.482049,0.53929,0.445669,0.19482
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.883225,0.297937,0.360062,0.580303,0.373426,0.458558,0.392928,0.411053,1.53832,0.417132,0.447169,0.124608,0.470194,1.15381,0,0.656089,0.19356,0.113609,0.205418,0.26524,0.60924,0.469335,1.094,0.822446,1.24179,0.709649,1.01819,0.67135,0.572447,0.379806,0.754912,0.560002,0.31333,0.614653,0.0351598,0.184038,1.12869,0.166348,0.143746,0.196807,0.38461,0.56316,0.617704,0.434259,1.6507,0.578773,0.407653,0.772185,0.677281,0.639101,0.522137,0.550735,0.894161,0.911367,0.47699,0.249055,0.435119,0.68053,0.47505,0.735292,0.531188,0.854737,1.52021,0.487593,1.60248,1.04613,1.3932,0.730718,1.24673,0.76885,0.404236,0.356247,0.944464,0.320434,0.0893951,0.0942164,2.38336,0.718494,0.268962,0.129727,0.673009,0.529804,0.119727,0.830765,0.538155,0.182066,0.271714,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,0.455999,0.122617,0.770215,0.57902,0.234357,0.541671,0.754637,0.87698,0.639679,0.638654,1.77029,0.696857,0.403887,0.750985,0.736223,0.845852,0.878738,0.26996,1.08155,1.12221,0.195318,0.409202,0.363536,1.58124,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.59809,0.86025,0.353344,1.01535,0.48999,1.14365,0.33206,0.877308,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.58382,0.0806411,0.305197,0.895708,0.46758,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.841258,0.629147,0.482049,0.53929,0.445669,0.19482
|tfbs_overrepresentation_jaspar=MA0003.1;1.53513,MA0004.1;0.360508,MA0006.1;0.604851,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;2.6738,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;2.57895,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.236433,MA0050.1;2.71608,MA0051.1;4.34423,MA0052.1;0.801048,MA0055.1;2.04176,MA0056.1;0,MA0057.1;0.471918,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.8754,MA0061.1;2.95057,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.484739,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;1.02422,MA0072.1;0.783532,MA0073.1;1.78317,MA0074.1;0.451832,MA0076.1;3.65654,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.0379749,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;2.21397,MA0103.1;0.67982,MA0105.1;2.13991,MA0106.1;0.543967,MA0107.1;4.46719,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.90605,MA0113.1;0.516916,MA0114.1;0.167085,MA0115.1;0.878749,MA0116.1;0.604438,MA0117.1;0.846964,MA0119.1;0.293392,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;1.45836,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;1.18666,MA0139.1;0.121562,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;0.163161,MA0146.1;0.412111,MA0147.1;0.530496,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;3.53266,MA0035.2;0.44524,MA0039.2;1.66029,MA0138.2;0.590987,MA0002.2;0.781868,MA0137.2;0.257017,MA0104.2;0.418613,MA0047.2;0.495607,MA0112.2;0.163154,MA0065.2;0.163769,MA0150.1;0.916186,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.501928,MA0155.1;0.732931,MA0156.1;1.28579,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;1.7893,MA0163.1;4.74746,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;2.09889,MA0102.2;1.49914,MA0258.1;0.473611,MA0259.1;0.170828,MA0442.1;0
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Revision as of 12:12, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98219716..98219771,+p1@Stard3
Mm9::chr13:24893063..24893082,+p1@BC005537
Mm9::chr15:76181104..76181175,-p2@Sharpin
Mm9::chr17:34056590..34056621,+p1@Tapbp
Mm9::chr17:34056624..34056635,+p2@Tapbp
Mm9::chr17:35400032..35400045,+p1@H2-D1
Mm9::chr5:34868446..34868518,+p1@Sh3bp2
Mm9::chr7:20408047..20408125,-p1@Bcl3
Mm9::chr7:51809271..51809325,-p1@Nr1h2
Mm9::chr7:86993077..86993110,-p2@Anpep


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:0002474antigen processing and presentation of peptide antigen via MHC class I0.00724505164829319
GO:0048002antigen processing and presentation of peptide antigen0.00924049014773828
GO:0019882antigen processing and presentation0.00924049014773828
GO:0050823peptide antigen stabilization0.00924049014773828
GO:0045082positive regulation of interleukin-10 biosynthetic process0.00924049014773828
GO:0002312B cell activation during immune response0.00924049014773828
GO:0045074regulation of interleukin-10 biosynthetic process0.00924049014773828
GO:0002315marginal zone B cell differentiation0.00924049014773828
GO:0042536negative regulation of tumor necrosis factor biosynthetic process0.00924049014773828
GO:0002313mature B cell differentiation during immune response0.00924049014773828
GO:0042091interleukin-10 biosynthetic process0.00924049014773828
GO:0050822peptide stabilization0.00924049014773828
GO:0002266follicular dendritic cell activation0.0138580772896944
GO:0002268follicular dendritic cell differentiation0.0138580772896944
GO:0042832defense response to protozoan0.0138580772896944
GO:0002335mature B cell differentiation0.0138580772896944
GO:0001562response to protozoan0.0195605928569083
GO:0045064T-helper 2 cell differentiation0.0211089724546047
GO:0019883antigen processing and presentation of endogenous antigen0.0211089724546047
GO:0002483antigen processing and presentation of endogenous peptide antigen0.0211089724546047
GO:0019885antigen processing and presentation of endogenous peptide antigen via MHC class I0.0211089724546047
GO:0032613interleukin-10 production0.0221431809126398
GO:0019730antimicrobial humoral response0.0221431809126398
GO:0042534regulation of tumor necrosis factor biosynthetic process0.0221431809126398
GO:0042092T-helper 2 type immune response0.0221431809126398
GO:0042533tumor necrosis factor biosynthetic process0.0221431809126398
GO:0002376immune system process0.0221431809126398
GO:0002467germinal center formation0.0221431809126398
GO:0017127cholesterol transporter activity0.0221431809126398
GO:0032729positive regulation of interferon-gamma production0.0221431809126398
GO:0015248sterol transporter activity0.0221431809126398
GO:0048536spleen development0.0221431809126398
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.0221431809126398
GO:0002292T cell differentiation during immune response0.0221431809126398
GO:0042093T-helper cell differentiation0.0221431809126398
GO:0002285lymphocyte activation during immune response0.0221431809126398
GO:0015485cholesterol binding0.0221431809126398
GO:0042088T-helper 1 type immune response0.0221431809126398
GO:0002293alpha-beta T cell differentiation during immune response0.0221431809126398
GO:0002286T cell activation during immune response0.0221431809126398
GO:0006518peptide metabolic process0.0221431809126398
GO:0002366leukocyte activation during immune response0.0221431809126398
GO:0042771DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis0.0221431809126398
GO:0032649regulation of interferon-gamma production0.0221431809126398
GO:0002263cell activation during immune response0.0221431809126398
GO:0042036negative regulation of cytokine biosynthetic process0.0240640605136774
GO:0004179membrane alanyl aminopeptidase activity0.0248450617340259
GO:0043367CD4-positive, alpha beta T cell differentiation0.0248450617340259
GO:0016284alanine aminopeptidase activity0.0248450617340259
GO:0030330DNA damage response, signal transduction by p53 class mediator0.028764067195156
GO:0032934sterol binding0.0297795669440622
GO:0006700C21-steroid hormone biosynthetic process0.0297795669440622
GO:0032640tumor necrosis factor production0.0312986652257444
GO:0032609interferon-gamma production0.0321650672965152
GO:0042612MHC class I protein complex0.0321650672965152
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.0329699268078963
GO:0008207C21-steroid hormone metabolic process0.0329699268078963
GO:0001819positive regulation of cytokine production0.0380974731358029
GO:0046632alpha-beta T cell differentiation0.0393168040238089
GO:0017148negative regulation of translation0.0459903513050557
GO:0031327negative regulation of cellular biosynthetic process0.0470368520117554
GO:0042611MHC protein complex0.0472862331522246
GO:0005770late endosome0.0472862331522246



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
motile cell1.44e-0954
connective tissue cell2.12e-0946
mesenchymal cell2.12e-0946

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.82e-15118
endoderm3.82e-15118
presumptive endoderm3.82e-15118
digestive system1.66e-14116
digestive tract1.66e-14116
primitive gut1.66e-14116
subdivision of digestive tract1.83e-13114
hemolymphoid system1.11e-1148
immune system1.11e-1148
hematopoietic system4.82e-1045
blood island4.82e-1045
connective tissue2.12e-0946
organ component layer2.75e-0924
unilaminar epithelium8.16e-0966
intestine2.22e-0831
mucosa2.61e-0815
gut epithelium3.28e-0855
endo-epithelium1.78e-0769
gastrointestinal system1.81e-0747
bone marrow3.60e-0716
intestinal mucosa4.14e-0713
anatomical wall4.14e-0713
wall of intestine4.14e-0713
gastrointestinal system mucosa4.14e-0713
musculoskeletal system9.52e-0732


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)
MA0003.11.53513
MA0004.10.360508
MA0006.10.604851
MA0007.10.346734
MA0009.10.780842
MA0014.12.6738
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.12.57895
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.236433
MA0050.12.71608
MA0051.14.34423
MA0052.10.801048
MA0055.12.04176
MA0056.10
MA0057.10.471918
MA0058.10.273976
MA0059.10.28489
MA0060.10.8754
MA0061.12.95057
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.484739
MA0069.10.801381
MA0070.10.791856
MA0071.11.02422
MA0072.10.783532
MA0073.11.78317
MA0074.10.451832
MA0076.13.65654
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.0379749
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.12.21397
MA0103.10.67982
MA0105.12.13991
MA0106.10.543967
MA0107.14.46719
MA0108.20.625209
MA0109.10
MA0111.10.90605
MA0113.10.516916
MA0114.10.167085
MA0115.10.878749
MA0116.10.604438
MA0117.10.846964
MA0119.10.293392
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.11.45836
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.11.18666
MA0139.10.121562
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.163161
MA0146.10.412111
MA0147.10.530496
MA0148.10.375491
MA0149.10.2978
MA0062.23.53266
MA0035.20.44524
MA0039.21.66029
MA0138.20.590987
MA0002.20.781868
MA0137.20.257017
MA0104.20.418613
MA0047.20.495607
MA0112.20.163154
MA0065.20.163769
MA0150.10.916186
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.501928
MA0155.10.732931
MA0156.11.28579
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.11.7893
MA0163.14.74746
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.22.09889
MA0102.21.49914
MA0258.10.473611
MA0259.10.170828
MA0442.10
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