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|ontology_enrichment_uberon=UBERON:0002193!9.15e-17!48;UBERON:0002405!9.15e-17!48;UBERON:0002390!2.30e-15!45;UBERON:0003061!2.30e-15!45;UBERON:0004177!3.67e-11!29;UBERON:0005057!3.67e-11!29;UBERON:0000077!2.90e-09!35;UBERON:0002370!1.50e-08!23;UBERON:0000974!1.50e-08!23;UBERON:0004807!1.50e-08!23;UBERON:0005058!1.50e-08!23;UBERON:0003351!1.50e-08!23;UBERON:0009113!1.50e-08!23;UBERON:0003295!1.50e-08!23;UBERON:0009722!1.50e-08!23;UBERON:0005562!1.50e-08!23;UBERON:0007690!1.50e-08!23;UBERON:0006562!4.55e-08!24;UBERON:0003408!4.55e-08!24;UBERON:0001557!4.55e-08!24;UBERON:0001042!4.55e-08!24;UBERON:0008814!4.55e-08!24;UBERON:0009145!4.55e-08!24;UBERON:0003081!1.22e-07!87;UBERON:0000065!4.25e-07!41;UBERON:0001004!7.84e-07!42;UBERON:0000926!9.15e-07!120;UBERON:0004120!9.15e-07!120;UBERON:0006603!9.15e-07!120
|ontology_enrichment_uberon=UBERON:0002193!9.15e-17!48;UBERON:0002405!9.15e-17!48;UBERON:0002390!2.30e-15!45;UBERON:0003061!2.30e-15!45;UBERON:0004177!3.67e-11!29;UBERON:0005057!3.67e-11!29;UBERON:0000077!2.90e-09!35;UBERON:0002370!1.50e-08!23;UBERON:0000974!1.50e-08!23;UBERON:0004807!1.50e-08!23;UBERON:0005058!1.50e-08!23;UBERON:0003351!1.50e-08!23;UBERON:0009113!1.50e-08!23;UBERON:0003295!1.50e-08!23;UBERON:0009722!1.50e-08!23;UBERON:0005562!1.50e-08!23;UBERON:0007690!1.50e-08!23;UBERON:0006562!4.55e-08!24;UBERON:0003408!4.55e-08!24;UBERON:0001557!4.55e-08!24;UBERON:0001042!4.55e-08!24;UBERON:0008814!4.55e-08!24;UBERON:0009145!4.55e-08!24;UBERON:0003081!1.22e-07!87;UBERON:0000065!4.25e-07!41;UBERON:0001004!7.84e-07!42;UBERON:0000926!9.15e-07!120;UBERON:0004120!9.15e-07!120;UBERON:0006603!9.15e-07!120
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.534222,0.367606,0.434198,0.720982,0.448401,0.538088,0.515265,0.181564,0.386846,0.494602,0.526159,0.515774,0.550255,0.275867,0,0.742571,0.703873,0.160384,1.53919,0.332107,0.485665,0.549359,0.258745,0.374936,0.577606,0.466037,0.469052,0.303071,0.757024,0.455168,0.843667,0.699026,0.839887,0.276324,0.60397,0.242032,0.522578,0.631914,0.195877,0.256422,0.460258,0.450632,1.39283,0.663502,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,1.067,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.140213,0.409836,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.501608,0.920903,0.025519,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.887702,1.00333,0.96962,0.337254,0.499714,1.21576,0.254749,0.143112,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,1.09252,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.766041,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0628627
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.534222,0.367606,0.434198,0.720982,0.448401,0.538088,0.515265,0.181564,0.386846,0.494602,0.526159,0.515774,0.550255,0.275867,0,0.742571,0.703873,0.160384,1.53919,0.332107,0.485665,0.549359,0.258745,0.374936,0.577606,0.466037,0.469052,0.303071,0.757024,0.455168,0.843667,0.699026,0.839887,0.276324,0.60397,0.242032,0.522578,0.631914,0.195877,0.256422,0.460258,0.450632,1.39283,0.663502,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,1.067,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.140213,0.409836,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.501608,0.920903,0.025519,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.887702,1.00333,0.96962,0.337254,0.499714,1.21576,0.254749,0.143112,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,1.09252,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.766041,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0628627
|tfbs_overrepresentation_jaspar=MA0003.1;0.400153,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.0611475,MA0017.1;1.46217,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.523649,MA0056.1;0,MA0057.1;0.643187,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.574356,MA0061.1;0.638933,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;1.61305,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;1.38205,MA0074.1;1.31555,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.980744,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.49616,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.823589,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;1.06639,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;1.36991,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;1.35732,MA0139.1;0.506952,MA0140.1;0.519484,MA0141.1;1.56635,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.246409,MA0146.1;0.0169049,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.84271,MA0035.2;0.524137,MA0039.2;0.589101,MA0138.2;0.675599,MA0002.2;0.513194,MA0137.2;0.32312,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.90045,MA0065.2;0.528619,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.0804339,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0925951,MA0163.1;0.991519,MA0164.1;0.551114,MA0080.2;2.26,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.837555,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:30, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:62272200..62272221,-p11@Ncor1
Mm9::chr16:4679660..4679699,-p2@Coro7
Mm9::chr2:155805181..155805202,-p@chr2:155805181..155805202
-
Mm9::chr7:134281321..134281341,-p1@Spn
Mm9::chr7:150191554..150191578,+p2@Tspan32
Mm9::chr7:82731110..82731121,+p@chr7:82731110..82731121
+
Mm9::chr7:82731147..82731158,+p@chr7:82731147..82731158
+
Mm9::chr8:114060166..114060201,+p2@Znrf1


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:0001808negative regulation of type IV hypersensitivity0.0112754494454306
GO:0002710negative regulation of T cell mediated immunity0.0112754494454306
GO:0001807regulation of type IV hypersensitivity0.0112754494454306
GO:0001806type IV hypersensitivity0.0112754494454306
GO:0008367bacterial binding0.0112754494454306
GO:0002704negative regulation of leukocyte mediated immunity0.0112754494454306
GO:0002865negative regulation of acute inflammatory response to antigenic stimulus0.0112754494454306
GO:0050688regulation of defense response to virus0.0112754494454306
GO:0002862negative regulation of inflammatory response to antigenic stimulus0.0112754494454306
GO:0002884negative regulation of hypersensitivity0.0112754494454306
GO:0002674negative regulation of acute inflammatory response0.0112754494454306
GO:0002707negative regulation of lymphocyte mediated immunity0.0112754494454306
GO:0002698negative regulation of immune effector process0.014495417890902
GO:0001562response to protozoan0.014495417890902
GO:0002709regulation of T cell mediated immunity0.0169057622049432
GO:0042535positive regulation of tumor necrosis factor biosynthetic process0.0169057622049432
GO:0031254trailing edge0.0169057622049432
GO:0002820negative regulation of adaptive immune response0.0169057622049432
GO:0001931uropod0.0169057622049432
GO:0002823negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0169057622049432
GO:0042534regulation of tumor necrosis factor biosynthetic process0.0169057622049432
GO:0050777negative regulation of immune response0.0169057622049432
GO:0002683negative regulation of immune system process0.0169057622049432
GO:0042533tumor necrosis factor biosynthetic process0.0169057622049432
GO:0031294lymphocyte costimulation0.0186505461425434
GO:0045060negative thymic T cell selection0.0186505461425434
GO:0002456T cell mediated immunity0.0186505461425434
GO:0043383negative T cell selection0.0186505461425434
GO:0031295T cell costimulation0.0186505461425434
GO:0051607defense response to virus0.0202802464374892
GO:0031348negative regulation of defense response0.0213406109698887
GO:0050728negative regulation of inflammatory response0.0213406109698887
GO:0002883regulation of hypersensitivity0.0213406109698887
GO:0002673regulation of acute inflammatory response0.0213406109698887
GO:0002438acute inflammatory response to antigenic stimulus0.0213406109698887
GO:0002864regulation of acute inflammatory response to antigenic stimulus0.0213406109698887
GO:0002524hypersensitivity0.0213406109698887
GO:0000299integral to membrane of membrane fraction0.0213406109698887
GO:0007162negative regulation of cell adhesion0.0219975137052059
GO:0042130negative regulation of T cell proliferation0.0219975137052059
GO:0002861regulation of inflammatory response to antigenic stimulus0.0219975137052059
GO:0002437inflammatory response to antigenic stimulus0.0219975137052059
GO:0045061thymic T cell selection0.0219975137052059
GO:0032640tumor necrosis factor production0.0230305870421663
GO:0045058T cell selection0.024429934716648
GO:0002703regulation of leukocyte mediated immunity0.024429934716648
GO:0002706regulation of lymphocyte mediated immunity0.024429934716648
GO:0050868negative regulation of T cell activation0.0246732476426524
GO:0008624induction of apoptosis by extracellular signals0.0246732476426524
GO:0002697regulation of immune effector process0.0246732476426524
GO:0050672negative regulation of lymphocyte proliferation0.0246732476426524
GO:0032945negative regulation of mononuclear cell proliferation0.0246732476426524
GO:0002819regulation of adaptive immune response0.027501868906009
GO:0002822regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.0.027501868906009
GO:0033077T cell differentiation in the thymus0.0301260709408571
GO:0051250negative regulation of lymphocyte activation0.0301260709408571
GO:0042102positive regulation of T cell proliferation0.0319583419061254
GO:0031347regulation of defense response0.0326021990965578
GO:0051241negative regulation of multicellular organismal process0.0326021990965578
GO:0050727regulation of inflammatory response0.0326021990965578
GO:0042108positive regulation of cytokine biosynthetic process0.0353734580124094
GO:0032946positive regulation of mononuclear cell proliferation0.0385149164805372
GO:0050671positive regulation of lymphocyte proliferation0.0385149164805372
GO:0045727positive regulation of translation0.0421072289428701
GO:0042129regulation of T cell proliferation0.0432242556945791
GO:0050870positive regulation of T cell activation0.0432242556945791
GO:0031328positive regulation of cellular biosynthetic process0.0432242556945791
GO:0048583regulation of response to stimulus0.0435742622990178
GO:0030155regulation of cell adhesion0.0439139104015371
GO:0009615response to virus0.0471136079639364
GO:0042035regulation of cytokine biosynthetic process0.0473928022269503
GO:0050670regulation of lymphocyte proliferation0.0481839177904082
GO:0032944regulation of mononuclear cell proliferation0.0481839177904082
GO:0009891positive regulation of biosynthetic process0.0481839177904082
GO:0042098T cell proliferation0.0486756628513152
GO:0005625soluble fraction0.0486756628513152



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
hemolymphoid system9.15e-1748
immune system9.15e-1748
hematopoietic system2.30e-1545
blood island2.30e-1545
hemopoietic organ3.67e-1129
immune organ3.67e-1129
mixed endoderm/mesoderm-derived structure2.90e-0935
thymus1.50e-0823
neck1.50e-0823
respiratory system epithelium1.50e-0823
hemolymphoid system gland1.50e-0823
pharyngeal epithelium1.50e-0823
thymic region1.50e-0823
pharyngeal gland1.50e-0823
entire pharyngeal arch endoderm1.50e-0823
thymus primordium1.50e-0823
early pharyngeal endoderm1.50e-0823
pharynx4.55e-0824
gland of gut4.55e-0824
upper respiratory tract4.55e-0824
chordate pharynx4.55e-0824
pharyngeal arch system4.55e-0824
pharyngeal region of foregut4.55e-0824
lateral plate mesoderm1.22e-0787
respiratory tract4.25e-0741
respiratory system7.84e-0742
mesoderm9.15e-07120
mesoderm-derived structure9.15e-07120
presumptive mesoderm9.15e-07120


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)
MA0003.10.400153
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.0611475
MA0017.11.46217
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.523649
MA0056.10
MA0057.10.643187
MA0058.10.341628
MA0059.10.353484
MA0060.10.574356
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.11.61305
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.11.38205
MA0074.11.31555
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.823589
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.11.36991
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.11.35732
MA0139.10.506952
MA0140.10.519484
MA0141.11.56635
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.246409
MA0146.10.0169049
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.84271
MA0035.20.524137
MA0039.20.589101
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.90045
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.0804339
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0925951
MA0163.10.991519
MA0164.10.551114
MA0080.22.26
MA0018.20.560731
MA0099.20.669311
MA0079.20.837555
MA0102.21.59466
MA0258.10.60477
MA0259.10.227035
MA0442.10
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