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 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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0051100 | negative regulation of binding | 0.0183440988746465 |
| GO:0043392 | negative regulation of DNA binding | 0.0183440988746465 |
| GO:0021938 | smoothened signaling pathway in regulation of granule cell precursor cell proliferation | 0.0183440988746465 |
| GO:0021937 | Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation | 0.0183440988746465 |
| GO:0002052 | positive regulation of neuroblast proliferation | 0.0183440988746465 |
| GO:0004727 | prenylated protein tyrosine phosphatase activity | 0.0183440988746465 |
| GO:0021940 | positive regulation of granule cell precursor proliferation | 0.0183440988746465 |
| GO:0021936 | regulation of granule cell precursor proliferation | 0.0183440988746465 |
| GO:0021534 | cell proliferation in hindbrain | 0.0183440988746465 |
| GO:0021924 | cell proliferation in the external granule layer | 0.0183440988746465 |
| GO:0021930 | granule cell precursor proliferation | 0.0183440988746465 |
| GO:0051101 | regulation of DNA binding | 0.0183440988746465 |
| GO:0004926 | non-G-protein coupled 7TM receptor activity | 0.0186252951044767 |
| GO:0021696 | cerebellar cortex morphogenesis | 0.0220056817904624 |
| GO:0021587 | cerebellum morphogenesis | 0.0220056817904624 |
| GO:0021575 | hindbrain morphogenesis | 0.0220056817904624 |
| GO:0021695 | cerebellar cortex development | 0.0229523844659907 |
| GO:0007185 | transmembrane receptor protein tyrosine phosphatase signaling pathway | 0.0229523844659907 |
| GO:0051098 | regulation of binding | 0.0229523844659907 |
| GO:0001755 | neural crest cell migration | 0.0229523844659907 |
| GO:0022037 | metencephalon development | 0.0229523844659907 |
| GO:0021549 | cerebellum development | 0.0229523844659907 |
| GO:0021953 | central nervous system neuron differentiation | 0.0229523844659907 |
| GO:0007405 | neuroblast proliferation | 0.0231659527747764 |
| GO:0001649 | osteoblast differentiation | 0.0231659527747764 |
| GO:0007224 | smoothened signaling pathway | 0.0231659527747764 |
| GO:0001570 | vasculogenesis | 0.0231659527747764 |
| GO:0014032 | neural crest cell development | 0.0231659527747764 |
| GO:0014033 | neural crest cell differentiation | 0.0231659527747764 |
| GO:0007368 | determination of left/right symmetry | 0.0231659527747764 |
| GO:0003007 | heart morphogenesis | 0.0231659527747764 |
| GO:0009799 | determination of symmetry | 0.0231659527747764 |
| GO:0009855 | determination of bilateral symmetry | 0.0231659527747764 |
| GO:0042475 | odontogenesis of dentine-containing teeth | 0.0231659527747764 |
| GO:0042476 | odontogenesis | 0.0231659527747764 |
| GO:0048762 | mesenchymal cell differentiation | 0.0231659527747764 |
| GO:0014031 | mesenchymal cell development | 0.0231659527747764 |
| GO:0030902 | hindbrain development | 0.0242267904896349 |
| GO:0009953 | dorsal/ventral pattern formation | 0.0242267904896349 |
| GO:0048589 | developmental growth | 0.0263605344081711 |
| GO:0005929 | cilium | 0.0358600873421324 |
| GO:0004725 | protein tyrosine phosphatase activity | 0.0448866127346977 |
| GO:0001503 | ossification | 0.0468114595328525 |
| GO:0031214 | biomineral formation | 0.0468114595328525 |
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) |
|---|---|
| MA0003.1 | 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 |
