MCL coexpression mm9:977: Difference between revisions
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{{MCL_coexpression_mm9| | 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receptor protein tyrosine kinase signaling pathway;0.0078468093272825;18596,16948!GO:0007167;enzyme linked receptor protein signaling pathway;0.0104734073596937;18596,16948!GO:0048251;elastic fiber assembly;0.010846937592383;16948!GO:0004720;protein-lysine 6-oxidase activity;0.0162690691681711;16948!GO:0005021;vascular endothelial growth factor receptor activity;0.0216897149435109;18596!GO:0030199;collagen fibril organization;0.0247841703113544;16948!GO:0016641;oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;0.0247841703113544;16948!GO:0016638;oxidoreductase activity, acting on the CH-NH2 group of donors;0.0271047146771474;16948!GO:0050730;regulation of peptidyl-tyrosine phosphorylation;0.0306023212323308;18596!GO:0005581;collagen;0.0306023212323308;16948!GO:0001932;regulation of protein amino acid phosphorylation;0.0306023212323308;18596!GO:0033238;regulation of amine metabolic process;0.0306023212323308;18596!GO:0006521;regulation of amino acid metabolic process;0.0306023212323308;18596!GO:0005507;copper ion binding;0.0306023212323308;16948!GO:0018212;peptidyl-tyrosine modification;0.0306023212323308;18596!GO:0042325;regulation of phosphorylation;0.0306023212323308;18596!GO:0018108;peptidyl-tyrosine phosphorylation;0.0306023212323308;18596!GO:0051174;regulation of phosphorus metabolic process;0.0306023212323308;18596!GO:0019220;regulation of phosphate metabolic process;0.0306023212323308;18596!GO:0030198;extracellular matrix organization and biogenesis;0.0306023212323308;16948!GO:0004714;transmembrane receptor protein tyrosine kinase activity;0.0306023212323308;18596!GO:0030324;lung development;0.0306023212323308;16948!GO:0030323;respiratory tube development;0.0306023212323308;16948!GO:0019199;transmembrane receptor protein kinase activity;0.0329294981744104;18596!GO:0044420;extracellular matrix part;0.0387029986977406;16948!GO:0018193;peptidyl-amino acid modification;0.0387029986977406;18596!GO:0043062;extracellular structure organization and biogenesis;0.0396675041538477;16948!GO:0005615;extracellular space;0.0411665423765647;18596,16948!GO:0044421;extracellular region part;0.04465246371108;18596,16948!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,1.13872,0.538088,0.515265,1.02512,0.687027,0.494602,0.526159,0.173454,1.35627,0.756943,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.485665,0.549359,0.258745,0.374936,0.577606,0.909128,1.18318,0.303071,0.757024,1.15331,0.843667,0.250677,0.136998,0.757987,4.29115,0.242032,0.522578,0.221921,2.41256,0.256422,0.460258,0.450632,0.27776,0.403938,0.423266,0.662995,1.21655,0.687215,0.305876,0.725127,0.604356,1.2032,0.985264,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,1.92541,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.527912,0.0665967,2.35974,0.140213,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.501608,0.920903,0.108172,0.540827,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,0.332938,0.242106,3.25899,0.967837,0.725721,0.724668,0.459825,0.784351,2.09671,0.340849,2.41655,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,2.45994,0.854131,1.70776,2.03014,0.666107,1.9792,0.403515,0.261837,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.94732,0.524587,0.558175|tfbs_overrepresentation_jaspar=MA0003.1;0.016751,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;8.85639,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.282934,MA0056.1;0,MA0057.1;5.88339,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;1.61305,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;9.15579,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;5.11227,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;3.50866,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.0701568,MA0146.1;0.0771944,MA0147.1;0.236889,MA0148.1;1.14345,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;2.04793,MA0138.2;0.675599,MA0002.2;0.988033,MA0137.2;0.32312,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.90045,MA0065.2;0.528619,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.978338,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;1.276,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0211019,MA0163.1;0.669601,MA0164.1;1.35808,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;17.893,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.227035,MA0442.1;0}} | ||
Latest revision as of 16:12, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr18:52689249..52689272,- | p1@Lox |
| Mm9::chr18:52689284..52689297,- | p3@Lox |
| Mm9::chr18:52689310..52689327,- | p2@Lox |
| Mm9::chr18:52689346..52689363,- | p4@Lox |
| Mm9::chr18:52689457..52689483,- | p6@Lox |
| Mm9::chr18:61204893..61204902,+ | p6@Pdgfrb |
| Mm9::chr2:30297583..30297598,+ | p@chr2:30297583..30297598 + |
| Mm9::chr6:113640950..113640970,+ | p@chr6:113640950..113640970 + |
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:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 0.0078468093272825 |
| GO:0007167 | enzyme linked receptor protein signaling pathway | 0.0104734073596937 |
| GO:0048251 | elastic fiber assembly | 0.010846937592383 |
| GO:0004720 | protein-lysine 6-oxidase activity | 0.0162690691681711 |
| GO:0005021 | vascular endothelial growth factor receptor activity | 0.0216897149435109 |
| GO:0030199 | collagen fibril organization | 0.0247841703113544 |
| GO:0016641 | oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor | 0.0247841703113544 |
| GO:0016638 | oxidoreductase activity, acting on the CH-NH2 group of donors | 0.0271047146771474 |
| GO:0050730 | regulation of peptidyl-tyrosine phosphorylation | 0.0306023212323308 |
| GO:0005581 | collagen | 0.0306023212323308 |
| GO:0001932 | regulation of protein amino acid phosphorylation | 0.0306023212323308 |
| GO:0033238 | regulation of amine metabolic process | 0.0306023212323308 |
| GO:0006521 | regulation of amino acid metabolic process | 0.0306023212323308 |
| GO:0005507 | copper ion binding | 0.0306023212323308 |
| GO:0018212 | peptidyl-tyrosine modification | 0.0306023212323308 |
| GO:0042325 | regulation of phosphorylation | 0.0306023212323308 |
| GO:0018108 | peptidyl-tyrosine phosphorylation | 0.0306023212323308 |
| GO:0051174 | regulation of phosphorus metabolic process | 0.0306023212323308 |
| GO:0019220 | regulation of phosphate metabolic process | 0.0306023212323308 |
| GO:0030198 | extracellular matrix organization and biogenesis | 0.0306023212323308 |
| GO:0004714 | transmembrane receptor protein tyrosine kinase activity | 0.0306023212323308 |
| GO:0030324 | lung development | 0.0306023212323308 |
| GO:0030323 | respiratory tube development | 0.0306023212323308 |
| GO:0019199 | transmembrane receptor protein kinase activity | 0.0329294981744104 |
| GO:0044420 | extracellular matrix part | 0.0387029986977406 |
| GO:0018193 | peptidyl-amino acid modification | 0.0387029986977406 |
| GO:0043062 | extracellular structure organization and biogenesis | 0.0396675041538477 |
| GO:0005615 | extracellular space | 0.0411665423765647 |
| GO:0044421 | extracellular region part | 0.04465246371108 |
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 | 0.016751 |
| MA0004.1 | 0.434673 |
| MA0006.1 | 0.271714 |
| MA0007.1 | 0.419994 |
| MA0009.1 | 0.870101 |
| MA0014.1 | 8.85639 |
| MA0017.1 | 0.296816 |
| MA0019.1 | 0.688051 |
| MA0024.1 | 0.826339 |
| MA0025.1 | 1.10341 |
| MA0027.1 | 2.51754 |
| MA0028.1 | 0.281528 |
| MA0029.1 | 0.804619 |
| MA0030.1 | 0.811181 |
| MA0031.1 | 0.775627 |
| MA0038.1 | 0.577528 |
| MA0040.1 | 0.882616 |
| MA0041.1 | 0.360875 |
| MA0042.1 | 0.348174 |
| MA0043.1 | 0.966833 |
| MA0046.1 | 0.906029 |
| MA0048.1 | 0.102483 |
| MA0050.1 | 0.472794 |
| MA0051.1 | 0.586414 |
| MA0052.1 | 0.890676 |
| MA0055.1 | 0.282934 |
| MA0056.1 | 0 |
| MA0057.1 | 5.88339 |
| MA0058.1 | 0.341628 |
| MA0059.1 | 0.353484 |
| MA0060.1 | 0.197678 |
| MA0061.1 | 0.224905 |
| MA0063.1 | 0 |
| MA0066.1 | 0.566617 |
| MA0067.1 | 1.21448 |
| MA0068.1 | 1.61305 |
| MA0069.1 | 0.891016 |
| MA0070.1 | 0.881319 |
| MA0071.1 | 0.471969 |
| MA0072.1 | 0.872842 |
| MA0073.1 | 9.15579 |
| MA0074.1 | 0.531046 |
| MA0076.1 | 0.315013 |
| MA0077.1 | 0.851175 |
| MA0078.1 | 0.61926 |
| MA0081.1 | 0.375851 |
| MA0083.1 | 0.96604 |
| MA0084.1 | 1.54225 |
| MA0087.1 | 0.922929 |
| MA0088.1 | 5.11227 |
| MA0089.1 | 0 |
| MA0090.1 | 0.401197 |
| MA0091.1 | 0.447561 |
| MA0092.1 | 0.401504 |
| MA0093.1 | 0.289361 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.519598 |
| MA0101.1 | 0.362124 |
| MA0103.1 | 0.307078 |
| MA0105.1 | 0.133231 |
| MA0106.1 | 0.626997 |
| MA0107.1 | 0.301222 |
| MA0108.2 | 0.710846 |
| MA0109.1 | 0 |
| MA0111.1 | 0.415012 |
| MA0113.1 | 0.598933 |
| MA0114.1 | 0.222763 |
| MA0115.1 | 0.969632 |
| MA0116.1 | 0.27152 |
| MA0117.1 | 0.937363 |
| MA0119.1 | 3.50866 |
| MA0122.1 | 0.957212 |
| MA0124.1 | 1.16127 |
| MA0125.1 | 1.0872 |
| MA0130.1 | 0 |
| MA0131.1 | 0.683521 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.00325 |
| MA0136.1 | 0.550755 |
| MA0139.1 | 0.169849 |
| MA0140.1 | 0.519484 |
| MA0141.1 | 0.325895 |
| MA0142.1 | 0.761136 |
| MA0143.1 | 0.615203 |
| MA0144.1 | 0.225588 |
| MA0145.1 | 0.0701568 |
| MA0146.1 | 0.0771944 |
| MA0147.1 | 0.236889 |
| MA0148.1 | 1.14345 |
| MA0149.1 | 0.367458 |
| MA0062.2 | 0.137653 |
| MA0035.2 | 0.524137 |
| MA0039.2 | 2.04793 |
| MA0138.2 | 0.675599 |
| MA0002.2 | 0.988033 |
| MA0137.2 | 0.32312 |
| MA0104.2 | 0.18504 |
| MA0047.2 | 0.576767 |
| MA0112.2 | 0.90045 |
| MA0065.2 | 0.528619 |
| MA0150.1 | 0.419883 |
| MA0151.1 | 0 |
| MA0152.1 | 0.576873 |
| MA0153.1 | 1.01988 |
| MA0154.1 | 0.677425 |
| MA0155.1 | 0.978338 |
| MA0156.1 | 0.314185 |
| MA0157.1 | 0.729116 |
| MA0158.1 | 0 |
| MA0159.1 | 1.276 |
| MA0160.1 | 0.453546 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0211019 |
| MA0163.1 | 0.669601 |
| MA0164.1 | 1.35808 |
| MA0080.2 | 0.302064 |
| MA0018.2 | 0.560731 |
| MA0099.2 | 0.669311 |
| MA0079.2 | 17.893 |
| MA0102.2 | 1.59466 |
| MA0258.1 | 0.60477 |
| MA0259.1 | 0.227035 |
| MA0442.1 | 0 |
