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MCL coexpression mm9:1402: Difference between revisions

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{{MCL_coexpression_mm9
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regulation of binding;0.0183440988746465;319757!GO:0043392;negative regulation of DNA binding;0.0183440988746465;319757!GO:0021938;smoothened signaling pathway in regulation of granule cell precursor cell proliferation;0.0183440988746465;319757!GO:0021937;Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation;0.0183440988746465;319757!GO:0002052;positive regulation of neuroblast proliferation;0.0183440988746465;319757!GO:0004727;prenylated protein tyrosine phosphatase activity;0.0183440988746465;19280!GO:0021940;positive regulation of granule cell precursor proliferation;0.0183440988746465;319757!GO:0021936;regulation of granule cell precursor proliferation;0.0183440988746465;319757!GO:0021534;cell proliferation in hindbrain;0.0183440988746465;319757!GO:0021924;cell proliferation in the external granule layer;0.0183440988746465;319757!GO:0021930;granule cell precursor proliferation;0.0183440988746465;319757!GO:0051101;regulation of DNA binding;0.0183440988746465;319757!GO:0004926;non-G-protein coupled 7TM receptor activity;0.0186252951044767;319757!GO:0021696;cerebellar cortex morphogenesis;0.0220056817904624;319757!GO:0021587;cerebellum morphogenesis;0.0220056817904624;319757!GO:0021575;hindbrain morphogenesis;0.0220056817904624;319757!GO:0021695;cerebellar cortex development;0.0229523844659907;319757!GO:0007185;transmembrane receptor protein tyrosine phosphatase signaling pathway;0.0229523844659907;19280!GO:0051098;regulation of binding;0.0229523844659907;319757!GO:0001755;neural crest cell migration;0.0229523844659907;319757!GO:0022037;metencephalon development;0.0229523844659907;319757!GO:0021549;cerebellum development;0.0229523844659907;319757!GO:0021953;central nervous system neuron differentiation;0.0229523844659907;319757!GO:0007405;neuroblast proliferation;0.0231659527747764;319757!GO:0001649;osteoblast 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|gostat_on_MCL_coexpression=GO:0051100;negative regulation of binding;0.0183440988746465;319757!GO:0043392;negative regulation of DNA binding;0.0183440988746465;319757!GO:0021938;smoothened signaling pathway in regulation of granule cell precursor cell proliferation;0.0183440988746465;319757!GO:0021937;Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation;0.0183440988746465;319757!GO:0002052;positive regulation of neuroblast proliferation;0.0183440988746465;319757!GO:0004727;prenylated protein tyrosine phosphatase activity;0.0183440988746465;19280!GO:0021940;positive regulation of granule cell precursor proliferation;0.0183440988746465;319757!GO:0021936;regulation of granule cell precursor proliferation;0.0183440988746465;319757!GO:0021534;cell proliferation in hindbrain;0.0183440988746465;319757!GO:0021924;cell proliferation in the external granule layer;0.0183440988746465;319757!GO:0021930;granule cell precursor proliferation;0.0183440988746465;319757!GO:0051101;regulation of DNA binding;0.0183440988746465;319757!GO:0004926;non-G-protein coupled 7TM receptor activity;0.0186252951044767;319757!GO:0021696;cerebellar cortex morphogenesis;0.0220056817904624;319757!GO:0021587;cerebellum morphogenesis;0.0220056817904624;319757!GO:0021575;hindbrain morphogenesis;0.0220056817904624;319757!GO:0021695;cerebellar cortex development;0.0229523844659907;319757!GO:0007185;transmembrane receptor protein tyrosine phosphatase signaling pathway;0.0229523844659907;19280!GO:0051098;regulation of binding;0.0229523844659907;319757!GO:0001755;neural crest cell migration;0.0229523844659907;319757!GO:0022037;metencephalon development;0.0229523844659907;319757!GO:0021549;cerebellum development;0.0229523844659907;319757!GO:0021953;central nervous system neuron differentiation;0.0229523844659907;319757!GO:0007405;neuroblast proliferation;0.0231659527747764;319757!GO:0001649;osteoblast differentiation;0.0231659527747764;319757!GO:0007224;smoothened signaling pathway;0.0231659527747764;319757!GO:0001570;vasculogenesis;0.0231659527747764;319757!GO:0014032;neural crest cell development;0.0231659527747764;319757!GO:0014033;neural crest cell differentiation;0.0231659527747764;319757!GO:0007368;determination of left/right symmetry;0.0231659527747764;319757!GO:0003007;heart morphogenesis;0.0231659527747764;319757!GO:0009799;determination of symmetry;0.0231659527747764;319757!GO:0009855;determination of bilateral symmetry;0.0231659527747764;319757!GO:0042475;odontogenesis of dentine-containing teeth;0.0231659527747764;319757!GO:0042476;odontogenesis;0.0231659527747764;319757!GO:0048762;mesenchymal cell differentiation;0.0231659527747764;319757!GO:0014031;mesenchymal cell development;0.0231659527747764;319757!GO:0030902;hindbrain development;0.0242267904896349;319757!GO:0009953;dorsal/ventral pattern formation;0.0242267904896349;319757!GO:0048589;developmental growth;0.0263605344081711;319757!GO:0005929;cilium;0.0358600873421324;319757!GO:0004725;protein tyrosine phosphatase activity;0.0448866127346977;19280!GO:0001503;ossification;0.0468114595328525;319757!GO:0031214;biomineral formation;0.0468114595328525;319757!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,1.32583,0.346849,0.550971,0.645383,0.247459,0.257202,1.48899,0.599767,0.632897,1.28144,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,0.713088,0.657163,0.345236,0.472505,0.686615,0.223823,1.40396,0.394364,0.181062,0.558142,2.20535,0.336199,0.589948,0.956447,0.607065,1.56842,0.629145,0.820134,0.27383,0.342638,0.56353,0.327433,0.366415,1.45501,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,1.93338,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,3.09546,1.156,1.7706,1.08629,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,3.86445,4.08047,0.0610418,0.534643,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.281222,0.685716,0.976308,0.775372,0.160254,0.871473,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,0.428007,0.484547,2.46589,0.431734,0.605144,1.33732,0.340765,2.46363,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.706252,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.183562,3.59715,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,5.38281
|tfbs_overrepresentation_jaspar=MA0003.1;2.70639,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;1.71935,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.161427,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.895081,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.827788,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;7.1726,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;22.9056,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.111145,MA0089.1;0,MA0090.1;2.16326,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;2.43957,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.944657,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.379391,MA0146.1;3.00399,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;2.61252,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;1.92909,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;3.86228,MA0163.1;3.72829,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;23.8813,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:56601566..56601666,-p2@Ptprs
Mm9::chr4:134108037..134108115,-p1@Sepn1
Mm9::chr6:29685471..29685547,+p1@Smo
Mm9::chr6:29685631..29685663,+p2@Smo
Mm9::chr6:29685667..29685680,+p3@Smo
Mm9::chr7:86860574..86860635,-p@chr7:86860574..86860635
-


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:0051100negative regulation of binding0.0183440988746465
GO:0043392negative regulation of DNA binding0.0183440988746465
GO:0021938smoothened signaling pathway in regulation of granule cell precursor cell proliferation0.0183440988746465
GO:0021937Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation0.0183440988746465
GO:0002052positive regulation of neuroblast proliferation0.0183440988746465
GO:0004727prenylated protein tyrosine phosphatase activity0.0183440988746465
GO:0021940positive regulation of granule cell precursor proliferation0.0183440988746465
GO:0021936regulation of granule cell precursor proliferation0.0183440988746465
GO:0021534cell proliferation in hindbrain0.0183440988746465
GO:0021924cell proliferation in the external granule layer0.0183440988746465
GO:0021930granule cell precursor proliferation0.0183440988746465
GO:0051101regulation of DNA binding0.0183440988746465
GO:0004926non-G-protein coupled 7TM receptor activity0.0186252951044767
GO:0021696cerebellar cortex morphogenesis0.0220056817904624
GO:0021587cerebellum morphogenesis0.0220056817904624
GO:0021575hindbrain morphogenesis0.0220056817904624
GO:0021695cerebellar cortex development0.0229523844659907
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0229523844659907
GO:0051098regulation of binding0.0229523844659907
GO:0001755neural crest cell migration0.0229523844659907
GO:0022037metencephalon development0.0229523844659907
GO:0021549cerebellum development0.0229523844659907
GO:0021953central nervous system neuron differentiation0.0229523844659907
GO:0007405neuroblast proliferation0.0231659527747764
GO:0001649osteoblast differentiation0.0231659527747764
GO:0007224smoothened signaling pathway0.0231659527747764
GO:0001570vasculogenesis0.0231659527747764
GO:0014032neural crest cell development0.0231659527747764
GO:0014033neural crest cell differentiation0.0231659527747764
GO:0007368determination of left/right symmetry0.0231659527747764
GO:0003007heart morphogenesis0.0231659527747764
GO:0009799determination of symmetry0.0231659527747764
GO:0009855determination of bilateral symmetry0.0231659527747764
GO:0042475odontogenesis of dentine-containing teeth0.0231659527747764
GO:0042476odontogenesis0.0231659527747764
GO:0048762mesenchymal cell differentiation0.0231659527747764
GO:0014031mesenchymal cell development0.0231659527747764
GO:0030902hindbrain development0.0242267904896349
GO:0009953dorsal/ventral pattern formation0.0242267904896349
GO:0048589developmental growth0.0263605344081711
GO:0005929cilium0.0358600873421324
GO:0004725protein tyrosine phosphatase activity0.0448866127346977
GO:0001503ossification0.0468114595328525
GO:0031214biomineral formation0.0468114595328525



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><br><br>


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)
MA0003.12.70639
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.11.71935
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.827788
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.17.1726
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.122.9056
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.12.16326
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.12.43957
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.944657
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.13.00399
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.22.61252
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.11.92909
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.13.86228
MA0163.13.72829
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.223.8813
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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