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|ontology_enrichment_uberon=UBERON:0002193!5.79e-18!48;UBERON:0002405!5.79e-18!48;UBERON:0002390!1.13e-15!45;UBERON:0003061!1.13e-15!45;UBERON:0000077!3.12e-13!35;UBERON:0004177!4.94e-11!29;UBERON:0005057!4.94e-11!29;UBERON:0002384!3.34e-10!46;UBERON:0003081!7.09e-10!87;UBERON:0002370!1.14e-09!23;UBERON:0000974!1.14e-09!23;UBERON:0004807!1.14e-09!23;UBERON:0005058!1.14e-09!23;UBERON:0003351!1.14e-09!23;UBERON:0009113!1.14e-09!23;UBERON:0003295!1.14e-09!23;UBERON:0009722!1.14e-09!23;UBERON:0005562!1.14e-09!23;UBERON:0007690!1.14e-09!23;UBERON:0000065!1.29e-09!41;UBERON:0001004!3.28e-09!42;UBERON:0006562!4.69e-09!24;UBERON:0003408!4.69e-09!24;UBERON:0001557!4.69e-09!24;UBERON:0001042!4.69e-09!24;UBERON:0008814!4.69e-09!24;UBERON:0009145!4.69e-09!24;UBERON:0000926!1.95e-08!120;UBERON:0004120!1.95e-08!120;UBERON:0006603!1.95e-08!120;UBERON:0000072!1.68e-07!27
|ontology_enrichment_uberon=UBERON:0002193!5.79e-18!48;UBERON:0002405!5.79e-18!48;UBERON:0002390!1.13e-15!45;UBERON:0003061!1.13e-15!45;UBERON:0000077!3.12e-13!35;UBERON:0004177!4.94e-11!29;UBERON:0005057!4.94e-11!29;UBERON:0002384!3.34e-10!46;UBERON:0003081!7.09e-10!87;UBERON:0002370!1.14e-09!23;UBERON:0000974!1.14e-09!23;UBERON:0004807!1.14e-09!23;UBERON:0005058!1.14e-09!23;UBERON:0003351!1.14e-09!23;UBERON:0009113!1.14e-09!23;UBERON:0003295!1.14e-09!23;UBERON:0009722!1.14e-09!23;UBERON:0005562!1.14e-09!23;UBERON:0007690!1.14e-09!23;UBERON:0000065!1.29e-09!41;UBERON:0001004!3.28e-09!42;UBERON:0006562!4.69e-09!24;UBERON:0003408!4.69e-09!24;UBERON:0001557!4.69e-09!24;UBERON:0001042!4.69e-09!24;UBERON:0008814!4.69e-09!24;UBERON:0009145!4.69e-09!24;UBERON:0000926!1.95e-08!120;UBERON:0004120!1.95e-08!120;UBERON:0006603!1.95e-08!120;UBERON:0000072!1.68e-07!27
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.0206456,0.330161,1.02163,0.645379,0.40827,0.495658,0.146465,0.154135,1.75347,0.453212,0.484001,0.146657,0.507558,0.680035,0,0.696644,0.22065,0.134657,0.528436,0.296085,0.047629,0.50668,1.20034,0.337218,0.534339,0.128175,0.428336,1.35822,0.0963992,0.414842,0.796599,5.22362,0.364174,0.242923,0.0500417,0.210533,0.480503,0.191662,0.167387,0.224094,0.419787,0.163087,0.244285,4.0175,0.383899,0.618203,0.443479,0.573356,0.271021,0.679429,0.560572,0.30602,0.937018,0.954342,1.28038,0.279148,0.471658,0.12126,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.116281,0.107966,0.113315,0.607043,0.759798,0.81171,0.463363,0.713779,1.39458,0.858535,0.873141,0.0800961,1.88733,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.515495,0.444003,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,1.18588,0.265919,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,1.08745,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,1.35119,0.806961,1.613,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.041769,0.938577,0.178329,0.526881,1.01974,1.38016,0.705025,0.352329,0.950885,1.1483,2.02526,0.763895,0.345891,0.669337,0.519673,0.602679,0.482466,0.00844742
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.0206456,0.330161,1.02163,0.645379,0.40827,0.495658,0.146465,0.154135,1.75347,0.453212,0.484001,0.146657,0.507558,0.680035,0,0.696644,0.22065,0.134657,0.528436,0.296085,0.047629,0.50668,1.20034,0.337218,0.534339,0.128175,0.428336,1.35822,0.0963992,0.414842,0.796599,5.22362,0.364174,0.242923,0.0500417,0.210533,0.480503,0.191662,0.167387,0.224094,0.419787,0.163087,0.244285,4.0175,0.383899,0.618203,0.443479,0.573356,0.271021,0.679429,0.560572,0.30602,0.937018,0.954342,1.28038,0.279148,0.471658,0.12126,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.116281,0.107966,0.113315,0.607043,0.759798,0.81171,0.463363,0.713779,1.39458,0.858535,0.873141,0.0800961,1.88733,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.515495,0.444003,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,1.18588,0.265919,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,1.08745,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,1.35119,0.806961,1.613,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.041769,0.938577,0.178329,0.526881,1.01974,1.38016,0.705025,0.352329,0.950885,1.1483,2.02526,0.763895,0.345891,0.669337,0.519673,0.602679,0.482466,0.00844742
|tfbs_overrepresentation_jaspar=MA0003.1;0.00972621,MA0004.1;1.02263,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;1.28203,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.0824771,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0198867,MA0056.1;0,MA0057.1;0.549903,MA0058.1;1.49242,MA0059.1;0.849123,MA0060.1;0.169058,MA0061.1;0.194456,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.266547,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.662187,MA0074.1;0.488775,MA0076.1;1.40007,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;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;1.30984,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.35523,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.980871,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;2.51361,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;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.568165,MA0145.1;0.0543321,MA0146.1;0.0111657,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;1.7688,MA0035.2;0.482026,MA0039.2;0.0156581,MA0138.2;1.52535,MA0002.2;0.447007,MA0137.2;0.783415,MA0104.2;0.476119,MA0047.2;0.533516,MA0112.2;0.0543294,MA0065.2;0.200864,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.0809407,MA0155.1;0.0631765,MA0156.1;1.39718,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;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.0340753,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.196451,MA0442.1;0
}}
}}

Revision as of 12:16, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:57909488..57909491,+p3@Ranbp2
Mm9::chr10:61957572..61957584,-p@chr10:61957572..61957584
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Mm9::chr10:61957587..61957611,-p@chr10:61957587..61957611
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Mm9::chr10:61957621..61957632,-p@chr10:61957621..61957632
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Mm9::chr10:61957717..61957729,-p@chr10:61957717..61957729
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Mm9::chr10:61960605..61960621,-p@chr10:61960605..61960621
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Mm9::chr10:61970485..61970512,-p1@Srgn
Mm9::chr17:57244824..57244844,+p1@Tnfsf9
Mm9::chr2:167877446..167877452,-p@chr2:167877446..167877452
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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:0033371T cell secretory granule organization and biogenesis0.00143811976113516
GO:0033366protein localization in secretory granule0.00143811976113516
GO:0033377maintenance of protein localization in T cell secretory granule0.00143811976113516
GO:0033374protein localization in T cell secretory granule0.00143811976113516
GO:0033365protein localization in organelle0.00143811976113516
GO:0033370maintenance of protein localization in mast cell secretory granule0.00143811976113516
GO:0033382maintenance of granzyme B localization in T cell secretory granule0.00143811976113516
GO:0033375protease localization in T cell secretory granule0.00143811976113516
GO:0033373maintenance of protease localization in mast cell secretory granule0.00143811976113516
GO:0033367protein localization in mast cell secretory granule0.00143811976113516
GO:0033364mast cell secretory granule organization and biogenesis0.00143811976113516
GO:0042629mast cell granule0.00143811976113516
GO:0033368protease localization in mast cell secretory granule0.00143811976113516
GO:0033363secretory granule organization and biogenesis0.00143811976113516
GO:0033380granzyme B localization in T cell secretory granule0.00143811976113516
GO:0033379maintenance of protease localization in T cell secretory granule0.00143811976113516
GO:0050709negative regulation of protein secretion0.00383456581097931
GO:0050710negative regulation of cytokine secretion0.00383456581097931
GO:0050707regulation of cytokine secretion0.00605391414152312
GO:0050663cytokine secretion0.00690108397284551
GO:0045185maintenance of protein localization0.00940902219581238
GO:0051605protein maturation via proteolysis0.00940902219581238
GO:0051604protein maturation0.00999937901019018
GO:0016050vesicle organization and biogenesis0.0110381045952215
GO:0051048negative regulation of secretion0.0110381045952215
GO:0050708regulation of protein secretion0.0123811320450737
GO:0051235maintenance of localization0.0127734838112938
GO:0005164tumor necrosis factor receptor binding0.014268718486589
GO:0032813tumor necrosis factor receptor superfamily binding0.014268718486589
GO:0045184establishment of protein localization0.0176249390066471
GO:0008104protein localization0.0192594749502943
GO:0051649establishment of cellular localization0.0192594749502943
GO:0051641cellular localization0.0192594749502943
GO:0033036macromolecule localization0.0192594749502943
GO:0009306protein secretion0.0196914644386767
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0216923192976312
GO:0016859cis-trans isomerase activity0.0217256151948936
GO:0051028mRNA transport0.0271176221182818
GO:0050658RNA transport0.0271176221182818
GO:0051236establishment of RNA localization0.0271176221182818
GO:0050657nucleic acid transport0.0271176221182818
GO:0006403RNA localization0.0271176221182818
GO:0005643nuclear pore0.0271176221182818
GO:0051046regulation of secretion0.0271176221182818
GO:0065002intracellular protein transport across a membrane0.027333537098526
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.027333537098526
GO:0046930pore complex0.027333537098526
GO:0044453nuclear membrane part0.0291457452728465
GO:0031965nuclear membrane0.0294837957638816
GO:0001503ossification0.0421947015982399
GO:0031214biomineral formation0.0421947015982399
GO:0001816cytokine production0.0435725434786286
GO:0046849bone remodeling0.0444679453359891
GO:0005515protein binding0.0449187407769357
GO:0005635nuclear envelope0.0449187407769357
GO:0048771tissue remodeling0.0493916889321265



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
hematopoietic cell1.19e-1632
hematopoietic oligopotent progenitor cell1.19e-1632
hematopoietic stem cell1.19e-1632
angioblastic mesenchymal cell1.19e-1632
hematopoietic multipotent progenitor cell1.19e-1632
hematopoietic lineage restricted progenitor cell2.12e-1125
lymphoid lineage restricted progenitor cell6.08e-1112
connective tissue cell3.34e-1046
mesenchymal cell3.34e-1046
leukocyte5.72e-1017
nongranular leukocyte5.72e-1017
T cell5.72e-1011
pro-T cell5.72e-1011
lymphocyte7.90e-1013
common lymphoid progenitor7.90e-1013
common myeloid progenitor2.98e-0819
motile cell3.62e-0854
mature alpha-beta T cell5.71e-089
alpha-beta T cell5.71e-089
immature T cell5.71e-089
mature T cell5.71e-089
immature alpha-beta T cell5.71e-089
nucleate cell2.37e-0716
CD4-positive, alpha-beta T cell4.65e-078

Uber Anatomy
Ontology termp-valuen
hemolymphoid system5.79e-1848
immune system5.79e-1848
hematopoietic system1.13e-1545
blood island1.13e-1545
mixed endoderm/mesoderm-derived structure3.12e-1335
hemopoietic organ4.94e-1129
immune organ4.94e-1129
connective tissue3.34e-1046
lateral plate mesoderm7.09e-1087
thymus1.14e-0923
neck1.14e-0923
respiratory system epithelium1.14e-0923
hemolymphoid system gland1.14e-0923
pharyngeal epithelium1.14e-0923
thymic region1.14e-0923
pharyngeal gland1.14e-0923
entire pharyngeal arch endoderm1.14e-0923
thymus primordium1.14e-0923
early pharyngeal endoderm1.14e-0923
respiratory tract1.29e-0941
respiratory system3.28e-0942
pharynx4.69e-0924
gland of gut4.69e-0924
upper respiratory tract4.69e-0924
chordate pharynx4.69e-0924
pharyngeal arch system4.69e-0924
pharyngeal region of foregut4.69e-0924
mesoderm1.95e-08120
mesoderm-derived structure1.95e-08120
presumptive mesoderm1.95e-08120
segment of respiratory tract1.68e-0727


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
MA0004.11.02263
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
MA0028.11.28203
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.0824771
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0198867
MA0056.10
MA0057.10.549903
MA0058.11.49242
MA0059.10.849123
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.662187
MA0074.10.488775
MA0076.11.40007
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.0492918
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.11.30984
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.35523
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.980871
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.12.51361
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.568165
MA0145.10.0543321
MA0146.10.0111657
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.21.7688
MA0035.20.482026
MA0039.20.0156581
MA0138.21.52535
MA0002.20.447007
MA0137.20.783415
MA0104.20.476119
MA0047.20.533516
MA0112.20.0543294
MA0065.20.200864
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.0631765
MA0156.11.39718
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.10.160428
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.0340753
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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