MCL coexpression mm9:2285: Difference between revisions
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{{MCL_coexpression_mm9| | 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protein nuclear translocation;0.0103613104695119;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.0103613104695119;20742!GO:0000060;protein import into nucleus, translocation;0.0103613104695119;20742!GO:0051016;barbed-end actin filament capping;0.0103613104695119;20742!GO:0051693;actin filament capping;0.0103613104695119;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0103613104695119;20742!GO:0030834;regulation of actin filament depolymerization;0.0103613104695119;20742!GO:0030042;actin filament depolymerization;0.0103613104695119;20742!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0103613104695119;20742!GO:0051261;protein depolymerization;0.0103613104695119;20742!GO:0032535;regulation of cellular component size;0.0103613104695119;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0103613104695119;20742!GO:0030832;regulation of actin filament length;0.0103613104695119;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0103613104695119;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0103613104695119;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0103613104695119;20742!GO:0008154;actin polymerization and/or depolymerization;0.0114727313157225;20742!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0124606609567986;20742!GO:0051128;regulation of cellular component organization and biogenesis;0.0132346150534941;20742!GO:0006606;protein import into nucleus;0.0132346150534941;20742!GO:0051170;nuclear import;0.0132346150534941;20742!GO:0017038;protein import;0.0141844678085296;20742!GO:0051248;negative regulation of protein metabolic process;0.0144157363054078;20742!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0160498730802243;20742!GO:0006913;nucleocytoplasmic transport;0.017440757894382;20742!GO:0051169;nuclear transport;0.017440757894382;20742!GO:0005516;calmodulin binding;0.0193230539474992;20742!GO:0030036;actin cytoskeleton organization and biogenesis;0.0268175094505013;20742!GO:0030029;actin filament-based process;0.027742251155691;20742!GO:0006605;protein targeting;0.0305557077375409;20742!GO:0051246;regulation of protein metabolic process;0.0361761124552217;20742!GO:0003779;actin binding;0.0368740754944393;20742!GO:0007167;enzyme linked receptor protein signaling pathway;0.0393027962194675;20742!GO:0009892;negative regulation of metabolic process;0.0465301202933373;20742!GO:0008092;cytoskeletal protein binding;0.0465301202933373;20742!|ontology_enrichment_celltype=CL:0002563!1.89e-07!9;CL:0002251!1.89e-07!9|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000160!1.45e-22!31;UBERON:0005409!2.02e-22!47;UBERON:0000344!6.84e-12!15;UBERON:0001242!1.98e-10!13;UBERON:0000060!1.98e-10!13;UBERON:0001262!1.98e-10!13;UBERON:0004786!1.98e-10!13;UBERON:0001007!1.57e-08!116;UBERON:0001555!1.57e-08!116;UBERON:0007026!1.57e-08!116;UBERON:0004119!2.22e-08!118;UBERON:0000925!2.22e-08!118;UBERON:0006595!2.22e-08!118;UBERON:0004921!1.16e-07!114;UBERON:0003350!1.89e-07!9;UBERON:0004808!1.89e-07!9;UBERON:0001277!1.89e-07!9|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,1.2551,0,1.02248,0.473993,0.928768,0.24402,0.570433,1.71244,0.815872,1.20979,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,1.04032,0.504971,0.0986756,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,1.40995,1.2746,1.29252,0.82458,0.549352,1.82858,0.882473,0.822375,1.10737,0.885556,1.02399,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,2.34289,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,1.34553,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,1.79716,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,1.87995,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,2.03331|tfbs_overrepresentation_jaspar=MA0003.1;0.600426,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.0809287,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;1.29714,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;3.96212,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.00221226,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;2.56224,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.582815,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;1.56822,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;4.90831,MA0103.1;0.540576,MA0105.1;4.16446,MA0106.1;0.899777,MA0107.1;3.34176,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;1.91256,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.608454,MA0146.1;2.82479,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.856416,MA0035.2;0.788288,MA0039.2;0.0959929,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;1.61189,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;1.21457,MA0156.1;2.32242,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;1.32296,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;1.90618,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0}} | ||
Latest revision as of 18:17, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr1:137155026..137155042,- | p1@Elf3 |
| Mm9::chr2:132771764..132771778,- | p3@Fermt1 |
| Mm9::chr2:132771788..132771802,- | p2@Fermt1 |
| Mm9::chr2:132771819..132771830,- | p10@Fermt1 |
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:0007184 | SMAD protein nuclear translocation | 0.0103613104695119 |
| GO:0007182 | common-partner SMAD protein phosphorylation | 0.0103613104695119 |
| GO:0000060 | protein import into nucleus, translocation | 0.0103613104695119 |
| GO:0051016 | barbed-end actin filament capping | 0.0103613104695119 |
| GO:0051693 | actin filament capping | 0.0103613104695119 |
| GO:0030835 | negative regulation of actin filament depolymerization | 0.0103613104695119 |
| GO:0030834 | regulation of actin filament depolymerization | 0.0103613104695119 |
| GO:0030042 | actin filament depolymerization | 0.0103613104695119 |
| GO:0008064 | regulation of actin polymerization and/or depolymerization | 0.0103613104695119 |
| GO:0051261 | protein depolymerization | 0.0103613104695119 |
| GO:0032535 | regulation of cellular component size | 0.0103613104695119 |
| GO:0032956 | regulation of actin cytoskeleton organization and biogenesis | 0.0103613104695119 |
| GO:0030832 | regulation of actin filament length | 0.0103613104695119 |
| GO:0051493 | regulation of cytoskeleton organization and biogenesis | 0.0103613104695119 |
| GO:0033043 | regulation of organelle organization and biogenesis | 0.0103613104695119 |
| GO:0051129 | negative regulation of cellular component organization and biogenesis | 0.0103613104695119 |
| GO:0008154 | actin polymerization and/or depolymerization | 0.0114727313157225 |
| GO:0007179 | transforming growth factor beta receptor signaling pathway | 0.0124606609567986 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.0132346150534941 |
| GO:0006606 | protein import into nucleus | 0.0132346150534941 |
| GO:0051170 | nuclear import | 0.0132346150534941 |
| GO:0017038 | protein import | 0.0141844678085296 |
| GO:0051248 | negative regulation of protein metabolic process | 0.0144157363054078 |
| GO:0007178 | transmembrane receptor protein serine/threonine kinase signaling pathway | 0.0160498730802243 |
| GO:0006913 | nucleocytoplasmic transport | 0.017440757894382 |
| GO:0051169 | nuclear transport | 0.017440757894382 |
| GO:0005516 | calmodulin binding | 0.0193230539474992 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.0268175094505013 |
| GO:0030029 | actin filament-based process | 0.027742251155691 |
| GO:0006605 | protein targeting | 0.0305557077375409 |
| GO:0051246 | regulation of protein metabolic process | 0.0361761124552217 |
| GO:0003779 | actin binding | 0.0368740754944393 |
| GO:0007167 | enzyme linked receptor protein signaling pathway | 0.0393027962194675 |
| GO:0009892 | negative regulation of metabolic process | 0.0465301202933373 |
| GO:0008092 | cytoskeletal protein binding | 0.0465301202933373 |
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>
| Ontology term | p-value | n |
|---|---|---|
| intestinal epithelial cell | 1.89e-07 | 9 |
| epithelial cell of alimentary canal | 1.89e-07 | 9 |
| Ontology term | p-value | n |
|---|---|---|
| intestine | 1.45e-22 | 31 |
| gastrointestinal system | 2.02e-22 | 47 |
| mucosa | 6.84e-12 | 15 |
| intestinal mucosa | 1.98e-10 | 13 |
| anatomical wall | 1.98e-10 | 13 |
| wall of intestine | 1.98e-10 | 13 |
| gastrointestinal system mucosa | 1.98e-10 | 13 |
| digestive system | 1.57e-08 | 116 |
| digestive tract | 1.57e-08 | 116 |
| primitive gut | 1.57e-08 | 116 |
| endoderm-derived structure | 2.22e-08 | 118 |
| endoderm | 2.22e-08 | 118 |
| presumptive endoderm | 2.22e-08 | 118 |
| subdivision of digestive tract | 1.16e-07 | 114 |
| epithelium of mucosa | 1.89e-07 | 9 |
| gastrointestinal system epithelium | 1.89e-07 | 9 |
| intestinal epithelium | 1.89e-07 | 9 |
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 | 0.600426 |
| MA0004.1 | 0.6888 |
| MA0006.1 | 0.497533 |
| MA0007.1 | 0.672186 |
| MA0009.1 | 1.15569 |
| MA0014.1 | 0.0809287 |
| MA0017.1 | 0.528196 |
| MA0019.1 | 0.964875 |
| MA0024.1 | 1.11019 |
| MA0025.1 | 1.39562 |
| MA0027.1 | 2.81824 |
| MA0028.1 | 0.509589 |
| MA0029.1 | 1.08753 |
| MA0030.1 | 1.09438 |
| MA0031.1 | 1.05719 |
| MA0038.1 | 0.846479 |
| MA0040.1 | 1.16866 |
| MA0041.1 | 0.604221 |
| MA0042.1 | 0.589368 |
| MA0043.1 | 1.25564 |
| MA0046.1 | 1.1929 |
| MA0048.1 | 0.266382 |
| MA0050.1 | 0.731539 |
| MA0051.1 | 0.856094 |
| MA0052.1 | 1.17701 |
| MA0055.1 | 0.125758 |
| MA0056.1 | 0 |
| MA0057.1 | 1.29714 |
| MA0058.1 | 0.581673 |
| MA0059.1 | 0.59559 |
| MA0060.1 | 0.403071 |
| MA0061.1 | 3.96212 |
| MA0063.1 | 0 |
| MA0066.1 | 0.834648 |
| MA0067.1 | 1.50873 |
| MA0068.1 | 0.713436 |
| MA0069.1 | 1.17737 |
| MA0070.1 | 1.16732 |
| MA0071.1 | 0.73062 |
| MA0072.1 | 1.15853 |
| MA0073.1 | 0.00221226 |
| MA0074.1 | 0.795862 |
| MA0076.1 | 0.550092 |
| MA0077.1 | 2.56224 |
| MA0078.1 | 0.891476 |
| MA0081.1 | 0.621611 |
| MA0083.1 | 1.25482 |
| MA0084.1 | 1.84013 |
| MA0087.1 | 1.21037 |
| MA0088.1 | 0.582815 |
| MA0089.1 | 0 |
| MA0090.1 | 0.650768 |
| MA0091.1 | 0.703314 |
| MA0092.1 | 1.56822 |
| MA0093.1 | 0.519148 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.783305 |
| MA0101.1 | 4.90831 |
| MA0103.1 | 0.540576 |
| MA0105.1 | 4.16446 |
| MA0106.1 | 0.899777 |
| MA0107.1 | 3.34176 |
| MA0108.2 | 0.989014 |
| MA0109.1 | 0 |
| MA0111.1 | 0.666525 |
| MA0113.1 | 0.869608 |
| MA0114.1 | 0.43587 |
| MA0115.1 | 1.25852 |
| MA0116.1 | 0.497293 |
| MA0117.1 | 1.22527 |
| MA0119.1 | 0.606338 |
| MA0122.1 | 1.24573 |
| MA0124.1 | 1.45461 |
| MA0125.1 | 1.37907 |
| MA0130.1 | 0 |
| MA0131.1 | 0.960068 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.29308 |
| MA0136.1 | 1.91256 |
| MA0139.1 | 0.365453 |
| MA0140.1 | 0.78318 |
| MA0141.1 | 0.563066 |
| MA0142.1 | 1.04199 |
| MA0143.1 | 0.887119 |
| MA0144.1 | 0.439506 |
| MA0145.1 | 0.608454 |
| MA0146.1 | 2.82479 |
| MA0147.1 | 0.453952 |
| MA0148.1 | 0.706718 |
| MA0149.1 | 0.611881 |
| MA0062.2 | 0.856416 |
| MA0035.2 | 0.788288 |
| MA0039.2 | 0.0959929 |
| MA0138.2 | 0.951653 |
| MA0002.2 | 0.368961 |
| MA0137.2 | 0.559766 |
| MA0104.2 | 0.386166 |
| MA0047.2 | 0.845655 |
| MA0112.2 | 0.211985 |
| MA0065.2 | 0.212467 |
| MA0150.1 | 1.61189 |
| MA0151.1 | 0 |
| MA0152.1 | 0.84577 |
| MA0153.1 | 1.31015 |
| MA0154.1 | 0.728853 |
| MA0155.1 | 1.21457 |
| MA0156.1 | 2.32242 |
| MA0157.1 | 1.0083 |
| MA0158.1 | 0 |
| MA0159.1 | 0.465802 |
| MA0160.1 | 0.71003 |
| MA0161.1 | 0 |
| MA0162.1 | 0.10667 |
| MA0163.1 | 0.0996272 |
| MA0164.1 | 0.817786 |
| MA0080.2 | 1.32296 |
| MA0018.2 | 0.828253 |
| MA0099.2 | 0.944966 |
| MA0079.2 | 1.90618 |
| MA0102.2 | 1.8929 |
| MA0258.1 | 0.419871 |
| MA0259.1 | 0.441366 |
| MA0442.1 | 0 |
