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MCL coexpression mm9:339: Difference between revisions

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{{MCL_coexpression_mm9
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organismal development;0.021161115316747;17450,16873,54427,330890!GO:0032502;developmental process;0.021161115316747;17450,16873,54427,330890!GO:0021937;Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation;0.021161115316747;16873!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.021161115316747;16873!GO:0021940;positive regulation of granule cell precursor proliferation;0.021161115316747;16873!GO:0021694;cerebellar Purkinje cell layer formation;0.021161115316747;16873!GO:0021936;regulation of granule cell precursor proliferation;0.021161115316747;16873!GO:0021702;cerebellar Purkinje cell differentiation;0.021161115316747;16873!GO:0021534;cell proliferation in hindbrain;0.021161115316747;16873!GO:0021930;granule cell precursor proliferation;0.021161115316747;16873!GO:0021924;cell proliferation in the external granule layer;0.021161115316747;16873!GO:0032501;multicellular organismal process;0.021161115316747;17450,16873,54427,330890!GO:0021697;cerebellar cortex formation;0.021161115316747;16873!GO:0021533;cell differentiation in hindbrain;0.021161115316747;16873!GO:0021680;cerebellar Purkinje cell layer development;0.0233375147164997;16873!GO:0021696;cerebellar cortex morphogenesis;0.0235599773010943;16873!GO:0021587;cerebellum morphogenesis;0.0237560075770642;16873!GO:0021575;hindbrain morphogenesis;0.0239300109561331;16873!GO:0008270;zinc ion binding;0.0242251532587318;17450,16873,54427!GO:0021695;cerebellar cortex development;0.0242251532587318;16873!GO:0005720;nuclear heterochromatin;0.0269057763554648;54427!GO:0022037;metencephalon development;0.0269057763554648;16873!GO:0021549;cerebellum development;0.0269057763554648;16873!GO:0000794;condensed nuclear chromosome;0.0313771730989331;54427!GO:0000790;nuclear chromatin;0.0332211727732593;54427!GO:0046914;transition metal ion binding;0.0332211727732593;17450,16873,54427!GO:0000792;heterochromatin;0.0358360502863889;54427!GO:0030902;hindbrain development;0.0402956744087905;16873!GO:0000793;condensed chromosome;0.0407521414766671;54427!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000473!1.21e-49!14;UBERON:0003135!2.35e-46!15;UBERON:0003101!1.78e-43!16;UBERON:0000079!1.78e-43!16;UBERON:0004176!6.20e-41!17;UBERON:0009196!6.20e-41!17;UBERON:0009117!6.20e-41!17;UBERON:0000991!1.13e-38!18;UBERON:0005564!1.13e-38!18;UBERON:0003133!4.66e-29!24;UBERON:0005156!7.77e-27!26;UBERON:0000990!7.77e-27!26;UBERON:0002323!6.84e-19!37;UBERON:0004458!6.84e-19!37;UBERON:0003886!2.14e-18!38;UBERON:0002553!6.32e-18!39;UBERON:0000464!2.88e-12!57;UBERON:0000466!7.96e-09!79|tfbs_overrepresentation_for_novel_motifs=0.724006,0.0500441,0.320091,0.831798,0.0463074,0.869459,0.588187,0.401523,1.41898,0.0991086,0.173735,0.195161,0.208457,1.14547,0.195204,0,0.359959,0.166842,0.598894,0.925769,0.0783992,0.4442,0.211409,0.392821,0.330779,0.23172,0.169642,0.475256,0.0645727,0.906199,1.42648,0.444875,0.164341,0.489293,0.4339,0.749497,0.0394039,0.19269,0.0323669,1.12251,0.171229,0.151372,0.0676595,0.197591,0.247603,0.802976,0.803276,0.500261,0.451223,0.234067,0.345732,1.29548,0.212927,0.569522,0.585246,1.16504,0.525548,0.547424,0.0579051,1.15945,0.427748,0.258489,0.464178,0.33663,0.22505,0.36962,0.710311,1.04299,0.423773,0.901202,0.293888,0.684784,0.0913601,0.615662,0.504228,1.35982,0.285478,0.287424,0.413185,0.0804202,0.0876452,0.374245,0.25741,0.383247,0.512157,0.0813617,0.00710275,2.4496,0.300065,1.20106,0.775527,0.516553,0.455893,2.07999,0.301769,0.799569,0.0798092,1.16009,1.46082,0.027214,0.637194,0.444635,0.553884,0.346214,0.34536,1.44426,1.02179,0.164518,0.995592,0.272087,0.706247,0.555481,0.276856,1.00732,0.78216,0.383607,0.0105339,0.137389,0.361025,2.39688,0.620583,0.319864,0.233041,0.286725,0.833329,0.416312,1.13425,0.450055,0.7089,0.415597,0.53872,0.812917,0.68148,1.20252,0.802533,0.159824,0.369821,1.45123,0.75625,1.56412,1.1699,0.714696,1.25936,0.45388,0.340119,0.902267,0.298675,1.52485,0.373295,0.177804,0.411919,0.0665125,0.570933,0.115918,0.226192,0.645175,0.2522,0.209661,1.18163,0.11537,0.765175,0.511402,0.416689,0.105725,0.337452,0.220885,0.988101,0.565716,0.103435|tfbs_overrepresentation_jaspar=MA0003.1;0.0379965,MA0004.1;1.34839,MA0006.1;0.423045,MA0007.1;0.39838,MA0009.1;2.05352,MA0014.1;0.0989421,MA0017.1;0.222109,MA0019.1;0.315968,MA0024.1;0.430047,MA0025.1;0.677312,MA0027.1;2.06014,MA0028.1;0.202369,MA0029.1;0.411611,MA0030.1;0.417163,MA0031.1;1.00584,MA0038.1;0.65478,MA0040.1;0.478574,MA0041.1;0.0931678,MA0042.1;0.609486,MA0043.1;0.552986,MA0046.1;0.499059,MA0048.1;0.00492967,MA0050.1;0.159414,MA0051.1;0.238165,MA0052.1;1.21868,MA0055.1;0.268845,MA0056.1;0,MA0057.1;0.293333,MA0058.1;1.48544,MA0059.1;1.04256,MA0060.1;0.483231,MA0061.1;0.57688,MA0063.1;0,MA0066.1;0.223752,MA0067.1;0.78096,MA0068.1;0.306744,MA0069.1;0.485904,MA0070.1;0.477443,MA0071.1;0.158881,MA0072.1;0.470071,MA0073.1;8.52779,MA0074.1;0.576444,MA0076.1;0.0701228,MA0077.1;0.451332,MA0078.1;0.262644,MA0081.1;0.332119,MA0083.1;0.552276,MA0084.1;1.09535,MA0087.1;0.513946,MA0088.1;1.50052,MA0089.1;0,MA0090.1;0.745255,MA0091.1;0.867225,MA0092.1;1.2227,MA0093.1;1.22621,MA0095.1;0,MA0098.1;0,MA0100.1;0.557457,MA0101.1;1.07479,MA0103.1;0.235667,MA0105.1;2.21619,MA0106.1;0.740097,MA0107.1;0.493454,MA0108.2;3.33294,MA0109.1;0,MA0111.1;1.27377,MA0113.1;0.247414,MA0114.1;0.311671,MA0115.1;0.555491,MA0116.1;1.13813,MA0117.1;0.526724,MA0119.1;1.59029,MA0122.1;0.544387,MA0124.1;0.731064,MA0125.1;0.662359,MA0130.1;0,MA0131.1;0.839673,MA0132.1;0,MA0133.1;0,MA0135.1;0.585739,MA0136.1;0.609426,MA0139.1;0.957166,MA0140.1;0.557269,MA0141.1;0.26113,MA0142.1;0.979417,MA0143.1;0.259584,MA0144.1;0.912796,MA0145.1;0.0410716,MA0146.1;0.0828399,MA0147.1;0.1482,MA0148.1;0.445966,MA0149.1;0.658346,MA0062.2;0.0515767,MA0035.2;0.193764,MA0039.2;1.73903,MA0138.2;0.306125,MA0002.2;0.0179261,MA0137.2;2.52068,MA0104.2;0.231733,MA0047.2;0.231108,MA0112.2;0.0996805,MA0065.2;0.731364,MA0150.1;0.39821,MA0151.1;0,MA0152.1;1.21903,MA0153.1;0.600798,MA0154.1;0.763143,MA0155.1;0.838236,MA0156.1;0.525036,MA0157.1;0.921385,MA0158.1;0,MA0159.1;0.159102,MA0160.1;0.450623,MA0161.1;0,MA0162.1;3.112,MA0163.1;4.97402,MA0164.1;1.14784,MA0080.2;0.495494,MA0018.2;0.219518,MA0099.2;0.301184,MA0079.2;3.09131,MA0102.2;1.14642,MA0258.1;0.11888,MA0259.1;0.584304,MA0442.1;0}}
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10760681
|gostat_on_MCL_coexpression=GO:0007275;multicellular organismal development;0.021161115316747;17450,16873,54427,330890!GO:0032502;developmental process;0.021161115316747;17450,16873,54427,330890!GO:0021937;Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation;0.021161115316747;16873!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.021161115316747;16873!GO:0021940;positive regulation of granule cell precursor proliferation;0.021161115316747;16873!GO:0021694;cerebellar Purkinje cell layer formation;0.021161115316747;16873!GO:0021936;regulation of granule cell precursor proliferation;0.021161115316747;16873!GO:0021702;cerebellar Purkinje cell differentiation;0.021161115316747;16873!GO:0021534;cell proliferation in hindbrain;0.021161115316747;16873!GO:0021930;granule cell precursor proliferation;0.021161115316747;16873!GO:0021924;cell proliferation in the external granule layer;0.021161115316747;16873!GO:0032501;multicellular organismal process;0.021161115316747;17450,16873,54427,330890!GO:0021697;cerebellar cortex formation;0.021161115316747;16873!GO:0021533;cell differentiation in hindbrain;0.021161115316747;16873!GO:0021680;cerebellar Purkinje cell layer development;0.0233375147164997;16873!GO:0021696;cerebellar cortex morphogenesis;0.0235599773010943;16873!GO:0021587;cerebellum morphogenesis;0.0237560075770642;16873!GO:0021575;hindbrain morphogenesis;0.0239300109561331;16873!GO:0008270;zinc ion binding;0.0242251532587318;17450,16873,54427!GO:0021695;cerebellar cortex development;0.0242251532587318;16873!GO:0005720;nuclear heterochromatin;0.0269057763554648;54427!GO:0022037;metencephalon development;0.0269057763554648;16873!GO:0021549;cerebellum development;0.0269057763554648;16873!GO:0000794;condensed nuclear chromosome;0.0313771730989331;54427!GO:0000790;nuclear chromatin;0.0332211727732593;54427!GO:0046914;transition metal ion binding;0.0332211727732593;17450,16873,54427!GO:0000792;heterochromatin;0.0358360502863889;54427!GO:0030902;hindbrain development;0.0402956744087905;16873!GO:0000793;condensed chromosome;0.0407521414766671;54427!
}}

Latest revision as of 15:07, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:77512581..77512592,+p3@Dnmt3l
Mm9::chr10:77512605..77512612,+p7@Dnmt3l
Mm9::chr12:3871355..3871364,+p@chr12:3871355..3871364
+
Mm9::chr13:47139250..47139274,+p@chr13:47139250..47139274
+
Mm9::chr15:13062678..13062684,-p@chr15:13062678..13062684
-
Mm9::chr15:97929103..97929108,-p@chr15:97929103..97929108
-
Mm9::chr16:48431443..48431452,+p2@Morc1
Mm9::chr19:46745201..46745211,-p@chr19:46745201..46745211
-
Mm9::chr2:169058730..169058732,-p@chr2:169058730..169058732
-
Mm9::chr3:136950856..136950861,+p@chr3:136950856..136950861
+
Mm9::chr4:129606011..129606014,+p@chr4:129606011..129606014
+
Mm9::chr4:129606033..129606044,+p@chr4:129606033..129606044
+
Mm9::chr7:12573893..12573904,-p@chr7:12573893..12573904
-
Mm9::chr7:12573906..12573931,-p@chr7:12573906..12573931
-
Mm9::chr7:50683014..50683022,+p4@Lim2
Mm9::chr7:50683034..50683049,+p3@Lim2
Mm9::chr8:73125228..73125269,-p@chr8:73125228..73125269
-
Mm9::chr8:74241107..74241116,-p@chr8:74241107..74241116
-
Mm9::chr9:14545062..14545068,-p7@Piwil4
Mm9::chr9:14545086..14545097,-p4@Piwil4
Mm9::chr9:14545110..14545121,-p1@Piwil4
Mm9::chr9:14545135..14545140,-p6@Piwil4
Mm9::chr9:55139944..55139951,-p@chr9:55139944..55139951
-


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:0007275multicellular organismal development0.021161115316747
GO:0032502developmental process0.021161115316747
GO:0021937Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation0.021161115316747
GO:0021692cerebellar Purkinje cell layer morphogenesis0.021161115316747
GO:0021940positive regulation of granule cell precursor proliferation0.021161115316747
GO:0021694cerebellar Purkinje cell layer formation0.021161115316747
GO:0021936regulation of granule cell precursor proliferation0.021161115316747
GO:0021702cerebellar Purkinje cell differentiation0.021161115316747
GO:0021534cell proliferation in hindbrain0.021161115316747
GO:0021930granule cell precursor proliferation0.021161115316747
GO:0021924cell proliferation in the external granule layer0.021161115316747
GO:0032501multicellular organismal process0.021161115316747
GO:0021697cerebellar cortex formation0.021161115316747
GO:0021533cell differentiation in hindbrain0.021161115316747
GO:0021680cerebellar Purkinje cell layer development0.0233375147164997
GO:0021696cerebellar cortex morphogenesis0.0235599773010943
GO:0021587cerebellum morphogenesis0.0237560075770642
GO:0021575hindbrain morphogenesis0.0239300109561331
GO:0008270zinc ion binding0.0242251532587318
GO:0021695cerebellar cortex development0.0242251532587318
GO:0005720nuclear heterochromatin0.0269057763554648
GO:0022037metencephalon development0.0269057763554648
GO:0021549cerebellum development0.0269057763554648
GO:0000794condensed nuclear chromosome0.0313771730989331
GO:0000790nuclear chromatin0.0332211727732593
GO:0046914transition metal ion binding0.0332211727732593
GO:0000792heterochromatin0.0358360502863889
GO:0030902hindbrain development0.0402956744087905
GO:0000793condensed chromosome0.0407521414766671



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
testis1.21e-4914
male reproductive organ2.35e-4615
male organism1.78e-4316
male reproductive system1.78e-4316
external genitalia6.20e-4117
indifferent external genitalia6.20e-4117
indifferent gonad6.20e-4117
gonad1.13e-3818
gonad primordium1.13e-3818
reproductive organ4.66e-2924
reproductive structure7.77e-2726
reproductive system7.77e-2726
body cavity6.84e-1937
body cavity or lining6.84e-1937
body cavity precursor2.14e-1838
anatomical cavity6.32e-1839
anatomical space2.88e-1257
immaterial anatomical entity7.96e-0979


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)
MA0003.10.0379965
MA0004.11.34839
MA0006.10.423045
MA0007.10.39838
MA0009.12.05352
MA0014.10.0989421
MA0017.10.222109
MA0019.10.315968
MA0024.10.430047
MA0025.10.677312
MA0027.12.06014
MA0028.10.202369
MA0029.10.411611
MA0030.10.417163
MA0031.11.00584
MA0038.10.65478
MA0040.10.478574
MA0041.10.0931678
MA0042.10.609486
MA0043.10.552986
MA0046.10.499059
MA0048.10.00492967
MA0050.10.159414
MA0051.10.238165
MA0052.11.21868
MA0055.10.268845
MA0056.10
MA0057.10.293333
MA0058.11.48544
MA0059.11.04256
MA0060.10.483231
MA0061.10.57688
MA0063.10
MA0066.10.223752
MA0067.10.78096
MA0068.10.306744
MA0069.10.485904
MA0070.10.477443
MA0071.10.158881
MA0072.10.470071
MA0073.18.52779
MA0074.10.576444
MA0076.10.0701228
MA0077.10.451332
MA0078.10.262644
MA0081.10.332119
MA0083.10.552276
MA0084.11.09535
MA0087.10.513946
MA0088.11.50052
MA0089.10
MA0090.10.745255
MA0091.10.867225
MA0092.11.2227
MA0093.11.22621
MA0095.10
MA0098.10
MA0100.10.557457
MA0101.11.07479
MA0103.10.235667
MA0105.12.21619
MA0106.10.740097
MA0107.10.493454
MA0108.23.33294
MA0109.10
MA0111.11.27377
MA0113.10.247414
MA0114.10.311671
MA0115.10.555491
MA0116.11.13813
MA0117.10.526724
MA0119.11.59029
MA0122.10.544387
MA0124.10.731064
MA0125.10.662359
MA0130.10
MA0131.10.839673
MA0132.10
MA0133.10
MA0135.10.585739
MA0136.10.609426
MA0139.10.957166
MA0140.10.557269
MA0141.10.26113
MA0142.10.979417
MA0143.10.259584
MA0144.10.912796
MA0145.10.0410716
MA0146.10.0828399
MA0147.10.1482
MA0148.10.445966
MA0149.10.658346
MA0062.20.0515767
MA0035.20.193764
MA0039.21.73903
MA0138.20.306125
MA0002.20.0179261
MA0137.22.52068
MA0104.20.231733
MA0047.20.231108
MA0112.20.0996805
MA0065.20.731364
MA0150.10.39821
MA0151.10
MA0152.11.21903
MA0153.10.600798
MA0154.10.763143
MA0155.10.838236
MA0156.10.525036
MA0157.10.921385
MA0158.10
MA0159.10.159102
MA0160.10.450623
MA0161.10
MA0162.13.112
MA0163.14.97402
MA0164.11.14784
MA0080.20.495494
MA0018.20.219518
MA0099.20.301184
MA0079.23.09131
MA0102.21.14642
MA0258.10.11888
MA0259.10.584304
MA0442.10
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