MCL coexpression mm9:2479: Difference between revisions
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{{MCL_coexpression_mm9| | 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cell fate specification;0.00657426176518929;16412!GO:0042684;cardioblast cell fate commitment;0.00657426176518929;16412!GO:0010002;cardioblast differentiation;0.00986085235671182;16412!GO:0002102;podosome;0.00986085235671182;326618!GO:0031941;filamentous actin;0.0165981967165556;326618!GO:0045214;sarcomere organization;0.0165981967165556;16412!GO:0031594;neuromuscular junction;0.0165981967165556;16412!GO:0030239;myofibril assembly;0.0165981967165556;16412!GO:0055002;striated muscle cell development;0.0165981967165556;16412!GO:0055001;muscle cell development;0.0165981967165556;16412!GO:0035051;cardiac cell differentiation;0.0165981967165556;16412!GO:0030863;cortical cytoskeleton;0.0165981967165556;326618!GO:0031032;actomyosin structure organization and biogenesis;0.0165981967165556;16412!GO:0048628;myoblast maturation;0.0165981967165556;16412!GO:0048627;myoblast development;0.0165981967165556;16412!GO:0005178;integrin binding;0.0165981967165556;16412!GO:0005884;actin filament;0.0165981967165556;326618!GO:0001708;cell fate specification;0.0165981967165556;16412!GO:0000082;G1/S transition of mitotic cell cycle;0.0165981967165556;16412!GO:0042383;sarcolemma;0.0173188502188161;16412!GO:0044448;cell cortex part;0.0173188502188161;326618!GO:0051146;striated muscle cell differentiation;0.0173188502188161;16412!GO:0008305;integrin complex;0.0194193766222151;16412!GO:0045445;myoblast differentiation;0.0197038751080447;16412!GO:0051325;interphase;0.0207114902502578;16412!GO:0051329;interphase of mitotic cell cycle;0.0207114902502578;16412!GO:0005938;cell cortex;0.0228593283850328;326618!GO:0032403;protein complex binding;0.0229796598781254;16412!GO:0019717;synaptosome;0.0235437237573873;16412!GO:0042692;muscle cell differentiation;0.0251245228129955;16412!GO:0007160;cell-matrix adhesion;0.0251245228129955;16412!GO:0048741;skeletal muscle fiber development;0.0251245228129955;16412!GO:0048747;muscle fiber development;0.0251245228129955;16412!GO:0043234;protein complex;0.0251245228129955;326618,16412!GO:0031589;cell-substrate adhesion;0.0251245228129955;16412!GO:0043235;receptor complex;0.0262444587297404;16412!GO:0048469;cell maturation;0.0262444587297404;16412!GO:0045596;negative regulation of cell differentiation;0.0293434924889218;16412!GO:0007229;integrin-mediated signaling pathway;0.029839141300271;16412!GO:0021700;developmental maturation;0.029839141300271;16412!GO:0007519;skeletal muscle development;0.0303876390862631;16412!GO:0045165;cell fate commitment;0.0312211055229063;16412!GO:0051093;negative regulation of developmental process;0.0315284890423223;16412!GO:0032991;macromolecular complex;0.0315284890423223;326618,16412!GO:0001701;in utero embryonic development;0.0346581434509376;16412!GO:0014706;striated muscle development;0.0347565801341027;16412!GO:0045595;regulation of cell differentiation;0.0420080360732898;16412!GO:0030036;actin cytoskeleton organization and biogenesis;0.0420080360732898;16412!GO:0030029;actin filament-based process;0.0434557838213296;16412!GO:0007517;muscle development;0.0434557838213296;16412!GO:0007507;heart development;0.0436255024541881;16412!GO:0008284;positive regulation of cell proliferation;0.0442893493205074;16412!GO:0015629;actin cytoskeleton;0.0468921679718131;326618!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004535!1.69e-07!23;UBERON:0001009!1.69e-07!23;UBERON:0004872!3.43e-07!33|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.0986756,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,2.04926,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.961641,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,2.01478,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,1.95555,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,1.85366,0.0824127|tfbs_overrepresentation_jaspar=MA0003.1;0.0356887,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;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,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;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;1.47308,MA0103.1;0.540576,MA0105.1;0.841866,MA0106.1;0.899777,MA0107.1;1.3208,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;0.817395,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;0.21199,MA0146.1;0.0944145,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.0220513,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;0.263609,MA0155.1;0.230016,MA0156.1;0.549102,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;1.91337,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.000201415,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0}} | ||
Latest revision as of 18:36, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr8:131256722..131256746,+ | p@chr8:131256722..131256746 + |
| Mm9::chr8:131256759..131256778,+ | p@chr8:131256759..131256778 + |
| Mm9::chr8:26061312..26061316,- | p@chr8:26061312..26061316 - |
| Mm9::chr8:74676495..74676509,+ | p@chr8:74676495..74676509 + |
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:0042685 | cardioblast cell fate specification | 0.00657426176518929 |
| GO:0042684 | cardioblast cell fate commitment | 0.00657426176518929 |
| GO:0010002 | cardioblast differentiation | 0.00986085235671182 |
| GO:0002102 | podosome | 0.00986085235671182 |
| GO:0031941 | filamentous actin | 0.0165981967165556 |
| GO:0045214 | sarcomere organization | 0.0165981967165556 |
| GO:0031594 | neuromuscular junction | 0.0165981967165556 |
| GO:0030239 | myofibril assembly | 0.0165981967165556 |
| GO:0055002 | striated muscle cell development | 0.0165981967165556 |
| GO:0055001 | muscle cell development | 0.0165981967165556 |
| GO:0035051 | cardiac cell differentiation | 0.0165981967165556 |
| GO:0030863 | cortical cytoskeleton | 0.0165981967165556 |
| GO:0031032 | actomyosin structure organization and biogenesis | 0.0165981967165556 |
| GO:0048628 | myoblast maturation | 0.0165981967165556 |
| GO:0048627 | myoblast development | 0.0165981967165556 |
| GO:0005178 | integrin binding | 0.0165981967165556 |
| GO:0005884 | actin filament | 0.0165981967165556 |
| GO:0001708 | cell fate specification | 0.0165981967165556 |
| GO:0000082 | G1/S transition of mitotic cell cycle | 0.0165981967165556 |
| GO:0042383 | sarcolemma | 0.0173188502188161 |
| GO:0044448 | cell cortex part | 0.0173188502188161 |
| GO:0051146 | striated muscle cell differentiation | 0.0173188502188161 |
| GO:0008305 | integrin complex | 0.0194193766222151 |
| GO:0045445 | myoblast differentiation | 0.0197038751080447 |
| GO:0051325 | interphase | 0.0207114902502578 |
| GO:0051329 | interphase of mitotic cell cycle | 0.0207114902502578 |
| GO:0005938 | cell cortex | 0.0228593283850328 |
| GO:0032403 | protein complex binding | 0.0229796598781254 |
| GO:0019717 | synaptosome | 0.0235437237573873 |
| GO:0042692 | muscle cell differentiation | 0.0251245228129955 |
| GO:0007160 | cell-matrix adhesion | 0.0251245228129955 |
| GO:0048741 | skeletal muscle fiber development | 0.0251245228129955 |
| GO:0048747 | muscle fiber development | 0.0251245228129955 |
| GO:0043234 | protein complex | 0.0251245228129955 |
| GO:0031589 | cell-substrate adhesion | 0.0251245228129955 |
| GO:0043235 | receptor complex | 0.0262444587297404 |
| GO:0048469 | cell maturation | 0.0262444587297404 |
| GO:0045596 | negative regulation of cell differentiation | 0.0293434924889218 |
| GO:0007229 | integrin-mediated signaling pathway | 0.029839141300271 |
| GO:0021700 | developmental maturation | 0.029839141300271 |
| GO:0007519 | skeletal muscle development | 0.0303876390862631 |
| GO:0045165 | cell fate commitment | 0.0312211055229063 |
| GO:0051093 | negative regulation of developmental process | 0.0315284890423223 |
| GO:0032991 | macromolecular complex | 0.0315284890423223 |
| GO:0001701 | in utero embryonic development | 0.0346581434509376 |
| GO:0014706 | striated muscle development | 0.0347565801341027 |
| GO:0045595 | regulation of cell differentiation | 0.0420080360732898 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.0420080360732898 |
| GO:0030029 | actin filament-based process | 0.0434557838213296 |
| GO:0007517 | muscle development | 0.0434557838213296 |
| GO:0007507 | heart development | 0.0436255024541881 |
| GO:0008284 | positive regulation of cell proliferation | 0.0442893493205074 |
| GO:0015629 | actin cytoskeleton | 0.0468921679718131 |
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>
| Ontology term | p-value | n |
|---|---|---|
| cardiovascular system | 1.69e-07 | 23 |
| circulatory system | 1.69e-07 | 23 |
| splanchnic layer of lateral plate mesoderm | 3.43e-07 | 33 |
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 | 0.0356887 |
| 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 | 0.251896 |
| MA0058.1 | 0.581673 |
| MA0059.1 | 0.59559 |
| MA0060.1 | 0.403071 |
| MA0061.1 | 0.438628 |
| MA0063.1 | 0 |
| MA0066.1 | 0.834648 |
| MA0067.1 | 1.50873 |
| MA0068.1 | 0.256913 |
| 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 | 1.13603 |
| MA0078.1 | 0.891476 |
| MA0081.1 | 0.621611 |
| MA0083.1 | 1.25482 |
| MA0084.1 | 1.84013 |
| MA0087.1 | 1.21037 |
| MA0088.1 | 0.201215 |
| MA0089.1 | 0 |
| MA0090.1 | 0.650768 |
| MA0091.1 | 0.703314 |
| MA0092.1 | 0.651119 |
| MA0093.1 | 0.519148 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.783305 |
| MA0101.1 | 1.47308 |
| MA0103.1 | 0.540576 |
| MA0105.1 | 0.841866 |
| MA0106.1 | 0.899777 |
| MA0107.1 | 1.3208 |
| 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 | 0.817395 |
| 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 | 0.21199 |
| MA0146.1 | 0.0944145 |
| MA0147.1 | 0.453952 |
| MA0148.1 | 0.706718 |
| MA0149.1 | 0.611881 |
| MA0062.2 | 0.319836 |
| MA0035.2 | 0.788288 |
| MA0039.2 | 0.0220513 |
| 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 | 0.263609 |
| MA0155.1 | 0.230016 |
| MA0156.1 | 0.549102 |
| 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 | 1.91337 |
| MA0080.2 | 0.534538 |
| MA0018.2 | 0.828253 |
| MA0099.2 | 0.944966 |
| MA0079.2 | 0.000201415 |
| MA0102.2 | 1.8929 |
| MA0258.1 | 0.419871 |
| MA0259.1 | 0.441366 |
| MA0442.1 | 0 |
