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|ontology_enrichment_uberon=UBERON:0000007!3.38e-56!8;UBERON:0003296!3.38e-56!8;UBERON:0010133!3.38e-56!8;UBERON:0001894!4.52e-45!10;UBERON:0006222!4.52e-45!10;UBERON:0002780!8.16e-12!39;UBERON:0001890!8.16e-12!39;UBERON:0006240!8.16e-12!39;UBERON:0003080!1.59e-11!40;UBERON:0002616!4.79e-10!46;UBERON:0000955!7.77e-10!47;UBERON:0006238!7.77e-10!47;UBERON:0003056!1.93e-09!49;UBERON:0001049!6.63e-09!52;UBERON:0005068!6.63e-09!52;UBERON:0006241!6.63e-09!52;UBERON:0007135!6.63e-09!52;UBERON:0000073!1.40e-08!54;UBERON:0002368!9.83e-08!60;UBERON:0002346!2.95e-07!64;UBERON:0003075!2.95e-07!64;UBERON:0007284!2.95e-07!64;UBERON:0002530!3.81e-07!65
|ontology_enrichment_uberon=UBERON:0000007!3.38e-56!8;UBERON:0003296!3.38e-56!8;UBERON:0010133!3.38e-56!8;UBERON:0001894!4.52e-45!10;UBERON:0006222!4.52e-45!10;UBERON:0002780!8.16e-12!39;UBERON:0001890!8.16e-12!39;UBERON:0006240!8.16e-12!39;UBERON:0003080!1.59e-11!40;UBERON:0002616!4.79e-10!46;UBERON:0000955!7.77e-10!47;UBERON:0006238!7.77e-10!47;UBERON:0003056!1.93e-09!49;UBERON:0001049!6.63e-09!52;UBERON:0005068!6.63e-09!52;UBERON:0006241!6.63e-09!52;UBERON:0007135!6.63e-09!52;UBERON:0000073!1.40e-08!54;UBERON:0002368!9.83e-08!60;UBERON:0002346!2.95e-07!64;UBERON:0003075!2.95e-07!64;UBERON:0007284!2.95e-07!64;UBERON:0002530!3.81e-07!65
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.0513547,0.269904,0.329881,0.52369,0.342839,0.425757,0.106126,0.362206,0.208174,0.385334,1.06556,0.703175,0.437133,0.189961,0,0.619876,0.508485,0.096222,0.171249,0.670854,0.0281659,0.436294,0.175485,0.276437,0.4628,0.0908349,0.361771,0.213277,0.500344,0.349031,0.717576,0.168723,0.570676,0.19035,0.497128,0.161521,0.411296,0.144953,0.391645,0.992655,0.353696,0.104243,1.67896,0.0302553,0.319944,0.543674,0.376103,0.401883,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.60268,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.355763,0.0307733,0.905636,0.277092,0.54852,0.0786324,0.532872,0.681539,0.242107,0.357936,0.636582,1.23994,0.101814,0.792744,0.00855221,0.0106044,0.860726,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.694736,0.732731,1.34284,0.0534645,0.486605,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.781068,0.840348,0.243062,0.390066,1.0825,0.512539,0.0643992,0.333247,0.621127,0.479408,0.910937,1.4028,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,1.19208,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,1.34861,1.84176,0.302077,0.178088,0.0664621,0.103135,0.857198,0.133365,0.455644,0.93735,2.1244,0.199652,0.290467,0.299755,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,0.484323,0.413167,0.0207556
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.0513547,0.269904,0.329881,0.52369,0.342839,0.425757,0.106126,0.362206,0.208174,0.385334,1.06556,0.703175,0.437133,0.189961,0,0.619876,0.508485,0.096222,0.171249,0.670854,0.0281659,0.436294,0.175485,0.276437,0.4628,0.0908349,0.361771,0.213277,0.500344,0.349031,0.717576,0.168723,0.570676,0.19035,0.497128,0.161521,0.411296,0.144953,0.391645,0.992655,0.353696,0.104243,1.67896,0.0302553,0.319944,0.543674,0.376103,0.401883,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.60268,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.355763,0.0307733,0.905636,0.277092,0.54852,0.0786324,0.532872,0.681539,0.242107,0.357936,0.636582,1.23994,0.101814,0.792744,0.00855221,0.0106044,0.860726,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.694736,0.732731,1.34284,0.0534645,0.486605,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.781068,0.840348,0.243062,0.390066,1.0825,0.512539,0.0643992,0.333247,0.621127,0.479408,0.910937,1.4028,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,1.19208,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,1.34861,1.84176,0.302077,0.178088,0.0664621,0.103135,0.857198,0.133365,0.455644,0.93735,2.1244,0.199652,0.290467,0.299755,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,0.484323,0.413167,0.0207556
|tfbs_overrepresentation_jaspar=MA0003.1;0.0132247,MA0004.1;0.330313,MA0006.1;0.186435,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.0633827,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;2.65407,MA0038.1;1.16958,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.703657,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.199479,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;0.147394,MA0063.1;0,MA0066.1;1.1475,MA0067.1;1.08124,MA0068.1;0.735122,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.0672071,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;0.534411,MA0089.1;0,MA0090.1;0.299987,MA0091.1;1.62354,MA0092.1;0.300264,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.619698,MA0105.1;0.26272,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;0.446898,MA0115.1;0.84036,MA0116.1;1.04399,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;0.658164,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.452699,MA0145.1;0.0329586,MA0146.1;0.00490019,MA0147.1;0.475899,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.0791588,MA0035.2;0.412747,MA0039.2;0.143896,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;0.230686,MA0104.2;0.369356,MA0047.2;0.46201,MA0112.2;0.0329566,MA0065.2;0.133827,MA0150.1;0.849777,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.195907,MA0155.1;0.154271,MA0156.1;0.222905,MA0157.1;1.47574,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.103104,MA0163.1;1.46795,MA0164.1;1.11611,MA0080.2;0.609443,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;0.107903,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;0.455671,MA0442.1;0
}}
}}

Revision as of 12:06, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69843574..69843585,+p16@Dlg4
Mm9::chr15:101388830..101388853,-p@chr15:101388830..101388853
-
Mm9::chr16:65515435..65515440,-p@chr16:65515435..65515440
-
Mm9::chr17:71435502..71435539,+p@chr17:71435502..71435539
+
Mm9::chr1:72193472..72193482,-p@chr1:72193472..72193482
-
Mm9::chr1:72193489..72193505,-p@chr1:72193489..72193505
-
Mm9::chr2:157395240..157395251,-p@chr2:157395240..157395251
-
Mm9::chr2:174153059..174153076,+p13@Gnas
Mm9::chr2:174251791..174251796,+p2@Th1l
Mm9::chr6:3713618..3713624,-p1@Calcr
Mm9::chr7:119534709..119534724,+p@chr7:119534709..119534724
+


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:0030316osteoclast differentiation0.00278899719243379
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.00356662957471553
GO:0002573myeloid leukocyte differentiation0.00356662957471553
GO:0019897extrinsic to plasma membrane0.00356662957471553
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.00356662957471553
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.00356662957471553
GO:0019933cAMP-mediated signaling0.00356662957471553
GO:0019935cyclic-nucleotide-mediated signaling0.00356662957471553
GO:0019898extrinsic to membrane0.00380579321820146
GO:0030099myeloid cell differentiation0.00479373253711718
GO:0001503ossification0.00479373253711718
GO:0031214biomineral formation0.00479373253711718
GO:0031234extrinsic to internal side of plasma membrane0.00479373253711718
GO:0040032post-embryonic body morphogenesis0.00479373253711718
GO:0046849bone remodeling0.00509394126511799
GO:0048771tissue remodeling0.00639094300550725
GO:0019932second-messenger-mediated signaling0.00639094300550725
GO:0002521leukocyte differentiation0.00639094300550725
GO:0044460flagellum part0.00639094300550725
GO:0044442microtubule-based flagellum part0.00639094300550725
GO:0004948calcitonin receptor activity0.00639094300550725
GO:0001501skeletal development0.0105616541659634
GO:0045672positive regulation of osteoclast differentiation0.0116678601829111
GO:0030097hemopoiesis0.0128976887068827
GO:0010171body morphogenesis0.0129005470206413
GO:0016188synaptic vesicle maturation0.0129005470206413
GO:0048534hemopoietic or lymphoid organ development0.0134150987537201
GO:0048701embryonic cranial skeleton morphogenesis0.0134150987537201
GO:0002763positive regulation of myeloid leukocyte differentiation0.0134150987537201
GO:0009898internal side of plasma membrane0.0134150987537201
GO:0002520immune system development0.0138081472602439
GO:0045669positive regulation of osteoblast differentiation0.0138081472602439
GO:0042043neurexin binding0.0138081472602439
GO:0007191dopamine receptor, adenylate cyclase activating pathway0.0138081472602439
GO:0009886post-embryonic morphogenesis0.0144996312881903
GO:0048488synaptic vesicle endocytosis0.0144996312881903
GO:0001958endochondral ossification0.0144996312881903
GO:0009888tissue development0.0147190492066304
GO:0042220response to cocaine0.0147190492066304
GO:0030279negative regulation of ossification0.0147190492066304
GO:0014073response to tropane0.0147190492066304
GO:0048704embryonic skeletal morphogenesis0.0170588006539819
GO:0048169regulation of long-term neuronal synaptic plasticity0.0170588006539819
GO:0016050vesicle organization and biogenesis0.0170588006539819
GO:0014069postsynaptic density0.0170588006539819
GO:0045667regulation of osteoblast differentiation0.0170588006539819
GO:0032982myosin filament0.0170588006539819
GO:0045639positive regulation of myeloid cell differentiation0.0170588006539819
GO:0043488regulation of mRNA stability0.0170588006539819
GO:0005863striated muscle thick filament0.0170588006539819
GO:0046851negative regulation of bone remodeling0.0170588006539819
GO:0042995cell projection0.0170588006539819
GO:0035116embryonic hindlimb morphogenesis0.0170588006539819
GO:0005859muscle myosin complex0.0170588006539819
GO:0048168regulation of neuronal synaptic plasticity0.0170588006539819
GO:0043487regulation of RNA stability0.0176340456221715
GO:0045670regulation of osteoclast differentiation0.0176340456221715
GO:0016460myosin II complex0.0178672081809556
GO:0048706embryonic skeletal development0.0178672081809556
GO:0014070response to organic cyclic substance0.0178672081809556
GO:0043279response to alkaloid0.0180779318978345
GO:0007204elevation of cytosolic calcium ion concentration0.0180779318978345
GO:0051252regulation of RNA metabolic process0.0180779318978345
GO:0001633secretin-like receptor activity0.0182692766514566
GO:0002761regulation of myeloid leukocyte differentiation0.0182692766514566
GO:0007212dopamine receptor signaling pathway0.0182692766514566
GO:0042221response to chemical stimulus0.0187045269489132
GO:0051480cytosolic calcium ion homeostasis0.0187150020818881
GO:0005624membrane fraction0.0200895987969162
GO:0048167regulation of synaptic plasticity0.0200895987969162
GO:0048705skeletal morphogenesis0.0205315340201663
GO:0035137hindlimb morphogenesis0.0205315340201663
GO:0050803regulation of synapse structure and activity0.0205315340201663
GO:0048489synaptic vesicle transport0.0205315340201663
GO:0009434microtubule-based flagellum0.0205315340201663
GO:0001669acrosome0.0208654498178503
GO:0030278regulation of ossification0.0208654498178503
GO:0000267cell fraction0.0219201197674251
GO:0001649osteoblast differentiation0.0228718415783858
GO:0044430cytoskeletal part0.0230987240562656
GO:0051241negative regulation of multicellular organismal process0.0230987240562656
GO:0006941striated muscle contraction0.0230987240562656
GO:0046850regulation of bone remodeling0.0230987240562656
GO:0010033response to organic substance0.0230987240562656
GO:0042493response to drug0.0234803036591527
GO:0065007biological regulation0.0234803036591527
GO:0009791post-embryonic development0.023835075809622
GO:0005834heterotrimeric G-protein complex0.0250540014560574
GO:0032501multicellular organismal process0.0250540014560574
GO:0006112energy reserve metabolic process0.0257164125055754
GO:0045637regulation of myeloid cell differentiation0.0257164125055754
GO:0065008regulation of biological quality0.0277652728956135
GO:0019861flagellum0.0280268974902848
GO:0045597positive regulation of cell differentiation0.0326806139258294
GO:0051216cartilage development0.0337351525317492
GO:0019717synaptosome0.0360562520975677
GO:0002376immune system process0.0360562520975677
GO:0016459myosin complex0.0387958709503544
GO:0006874cellular calcium ion homeostasis0.0395436774545312
GO:0044446intracellular organelle part0.0395436774545312
GO:0044422organelle part0.0395436774545312
GO:0055074calcium ion homeostasis0.0398727348824259
GO:0030326embryonic limb morphogenesis0.0403792631809752
GO:0035113embryonic appendage morphogenesis0.0403792631809752
GO:0006875cellular metal ion homeostasis0.0411025309070273
GO:0030017sarcomere0.0411025309070273
GO:0015980energy derivation by oxidation of organic compounds0.0411025309070273
GO:0055065metal ion homeostasis0.0414087142460823
GO:0044463cell projection part0.0414087142460823
GO:0044449contractile fiber part0.0414087142460823
GO:0051094positive regulation of developmental process0.0414087142460823
GO:0005856cytoskeleton0.0439894213510667
GO:0030016myofibril0.0439894213510667
GO:0035107appendage morphogenesis0.0439894213510667
GO:0035108limb morphogenesis0.0439894213510667
GO:0043292contractile fiber0.0440124119882475
GO:0048519negative regulation of biological process0.0440124119882475
GO:0060173limb development0.0441743181315497
GO:0048736appendage development0.0441743181315497
GO:0003012muscle system process0.0456238660318506
GO:0006936muscle contraction0.0456238660318506
GO:0005200structural constituent of cytoskeleton0.047949518323782



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
pituitary gland3.38e-568
gland of diencephalon3.38e-568
neuroendocrine gland3.38e-568
diencephalon4.52e-4510
future diencephalon4.52e-4510
regional part of forebrain8.16e-1239
forebrain8.16e-1239
future forebrain8.16e-1239
anterior neural tube1.59e-1140
regional part of brain4.79e-1046
brain7.77e-1047
future brain7.77e-1047
pre-chordal neural plate1.93e-0949
neural tube6.63e-0952
neural rod6.63e-0952
future spinal cord6.63e-0952
neural keel6.63e-0952
regional part of nervous system1.40e-0854
endocrine gland9.83e-0860
neurectoderm2.95e-0764
neural plate2.95e-0764
presumptive neural plate2.95e-0764
gland3.81e-0765


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)
MA0003.10.0132247
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.10.0633827
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.12.65407
MA0038.11.16958
MA0040.10.755433
MA0041.10.263922
MA0042.10.703657
MA0043.10.837621
MA0046.10.778239
MA0048.10.199479
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
MA0061.10.147394
MA0063.10
MA0066.11.1475
MA0067.11.08124
MA0068.10.735122
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.0672071
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.534411
MA0089.10
MA0090.10.299987
MA0091.11.62354
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.619698
MA0105.10.26272
MA0106.10.509454
MA0107.10.607721
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.446898
MA0115.10.84036
MA0116.11.04399
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
MA0141.10.658164
MA0142.10.63775
MA0143.10.49828
MA0144.10.452699
MA0145.10.0329586
MA0146.10.00490019
MA0147.10.475899
MA0148.10.344843
MA0149.10.269772
MA0062.20.0791588
MA0035.20.412747
MA0039.20.143896
MA0138.20.555696
MA0002.20.105469
MA0137.20.230686
MA0104.20.369356
MA0047.20.46201
MA0112.20.0329566
MA0065.20.133827
MA0150.10.849777
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.195907
MA0155.10.154271
MA0156.10.222905
MA0157.11.47574
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.103104
MA0163.11.46795
MA0164.11.11611
MA0080.20.609443
MA0018.20.446948
MA0099.20.549696
MA0079.20.107903
MA0102.21.45844
MA0258.10.135621
MA0259.10.455671
MA0442.10
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