MCL coexpression mm9:2050: Difference between revisions
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{{MCL_coexpression_mm9| | 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coupled proton transport, down electrochemical gradient;0.0417526751697796;66144!GO:0015986;ATP synthesis coupled proton transport;0.0417526751697796;66144!GO:0006754;ATP biosynthetic process;0.0417526751697796;66144!GO:0006753;nucleoside phosphate metabolic process;0.0417526751697796;66144!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.0417526751697796;66144!GO:0016469;proton-transporting two-sector ATPase complex;0.0417526751697796;66144!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.0417526751697796;66144!GO:0044249;cellular biosynthetic process;0.0417526751697796;66144,67994!GO:0046034;ATP metabolic process;0.0417526751697796;66144!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0019829;cation-transporting ATPase activity;0.0417526751697796;66144!GO:0009142;nucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009199;ribonucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009144;purine nucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0006119;oxidative phosphorylation;0.0417526751697796;66144!GO:0015992;proton transport;0.0417526751697796;66144!GO:0006752;group transfer coenzyme metabolic process;0.0417526751697796;66144!GO:0009141;nucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009152;purine ribonucleotide biosynthetic process;0.0417526751697796;66144!GO:0006818;hydrogen transport;0.0417526751697796;66144!GO:0009260;ribonucleotide biosynthetic process;0.0417526751697796;66144!GO:0009150;purine ribonucleotide metabolic process;0.0417526751697796;66144!GO:0006164;purine nucleotide biosynthetic process;0.0417526751697796;66144!GO:0009058;biosynthetic process;0.0417526751697796;66144,67994!GO:0009259;ribonucleotide metabolic process;0.0417526751697796;66144!GO:0006163;purine nucleotide metabolic process;0.0426071727823965;66144!GO:0042625;ATPase activity, coupled to transmembrane movement of ions;0.0446838862837438;66144!GO:0009108;coenzyme biosynthetic process;0.0446838862837438;66144!GO:0015078;hydrogen ion transmembrane transporter activity;0.0470887349534143;66144!GO:0015077;monovalent inorganic cation transmembrane transporter activity;0.0470887349534143;66144!GO:0051188;cofactor biosynthetic process;0.0470887349534143;66144!|ontology_enrichment_celltype=CL:0000055!3.40e-23!49;CL:0000221!1.70e-21!44;CL:0000133!1.70e-21!44;CL:0002319!2.51e-21!43;CL:0000393!1.33e-16!39;CL:0000211!1.33e-16!39;CL:0002371!2.91e-15!118;CL:0000540!7.76e-15!33;CL:0000047!7.76e-15!33;CL:0000031!7.76e-15!33;CL:0000404!7.76e-15!33;CL:0000723!1.69e-14!91;CL:0000048!1.69e-14!91;CL:0000548!2.75e-14!115;CL:0000255!2.75e-14!115;CL:0002321!3.51e-14!70;CL:0000034!5.61e-14!97;CL:0000117!5.15e-13!23;CL:0000337!5.15e-13!23;CL:0000333!1.58e-07!10;CL:0000095!1.58e-07!10;CL:0000243!1.58e-07!10;CL:0000123!1.58e-07!10;CL:0000125!1.58e-07!10;CL:0000030!1.58e-07!10;CL:0000339!1.58e-07!10|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001016!1.45e-31!75;UBERON:0001017!2.49e-30!73;UBERON:0004121!4.94e-22!95;UBERON:0000924!4.94e-22!95;UBERON:0006601!4.94e-22!95;UBERON:0000073!5.17e-22!54;UBERON:0001049!8.56e-21!52;UBERON:0005068!8.56e-21!52;UBERON:0006241!8.56e-21!52;UBERON:0007135!8.56e-21!52;UBERON:0002346!3.22e-19!64;UBERON:0003075!3.22e-19!64;UBERON:0007284!3.22e-19!64;UBERON:0010314!3.66e-19!92;UBERON:0000955!4.25e-18!47;UBERON:0006238!4.25e-18!47;UBERON:0002616!9.28e-18!46;UBERON:0002020!1.70e-16!34;UBERON:0003080!7.11e-16!40;UBERON:0002780!8.74e-16!39;UBERON:0001890!8.74e-16!39;UBERON:0006240!8.74e-16!39;UBERON:0010371!1.97e-14!73;UBERON:0003528!5.90e-14!29;UBERON:0002791!5.90e-14!29;UBERON:0001893!5.90e-14!29;UBERON:0003056!2.20e-13!49;UBERON:0000956!7.47e-10!21;UBERON:0001869!7.47e-10!21;UBERON:0000203!7.47e-10!21;UBERON:0002619!2.15e-08!17|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,0.471365,0.318879,1.2563,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,1.61988,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,1.44172,0.377213,1.75657,1.32691,1.55806,0.310084,0.318792,0.926147,1.08947,0.575233,0.986898,1.04072,0.884013,0.362446,1.20828,1.24129,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,1.70541,1.06633,0.740267,1.42067,0.57247,0.633483,1.25851,0.576517,1.79716,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.79777,0.542121,1.27621,1.069,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293|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;0.276754,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;1.1032,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;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,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;0.313734,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.856416,MA0035.2;0.788288,MA0039.2;0.45096,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;0.609584,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,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;0.34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| ||
Latest revision as of 17:55, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr12:8928823..8928834,+ | p@chr12:8928823..8928834 + |
| Mm9::chr2:118305373..118305423,- | p1@LOC100504988 p1@Srp14 |
| Mm9::chr6:29417733..29417764,+ | p2@Atp6v1f |
| Mm9::chr7:85928189..85928227,+ | p2@Mrps11 |
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:0015985 | energy coupled proton transport, down electrochemical gradient | 0.0417526751697796 |
| GO:0015986 | ATP synthesis coupled proton transport | 0.0417526751697796 |
| GO:0006754 | ATP biosynthetic process | 0.0417526751697796 |
| GO:0006753 | nucleoside phosphate metabolic process | 0.0417526751697796 |
| GO:0046933 | hydrogen ion transporting ATP synthase activity, rotational mechanism | 0.0417526751697796 |
| GO:0016469 | proton-transporting two-sector ATPase complex | 0.0417526751697796 |
| GO:0046961 | hydrogen ion transporting ATPase activity, rotational mechanism | 0.0417526751697796 |
| GO:0044249 | cellular biosynthetic process | 0.0417526751697796 |
| GO:0046034 | ATP metabolic process | 0.0417526751697796 |
| GO:0009206 | purine ribonucleoside triphosphate biosynthetic process | 0.0417526751697796 |
| GO:0009201 | ribonucleoside triphosphate biosynthetic process | 0.0417526751697796 |
| GO:0009145 | purine nucleoside triphosphate biosynthetic process | 0.0417526751697796 |
| GO:0019829 | cation-transporting ATPase activity | 0.0417526751697796 |
| GO:0009142 | nucleoside triphosphate biosynthetic process | 0.0417526751697796 |
| GO:0009205 | purine ribonucleoside triphosphate metabolic process | 0.0417526751697796 |
| GO:0009199 | ribonucleoside triphosphate metabolic process | 0.0417526751697796 |
| GO:0009144 | purine nucleoside triphosphate metabolic process | 0.0417526751697796 |
| GO:0006119 | oxidative phosphorylation | 0.0417526751697796 |
| GO:0015992 | proton transport | 0.0417526751697796 |
| GO:0006752 | group transfer coenzyme metabolic process | 0.0417526751697796 |
| GO:0009141 | nucleoside triphosphate metabolic process | 0.0417526751697796 |
| GO:0009152 | purine ribonucleotide biosynthetic process | 0.0417526751697796 |
| GO:0006818 | hydrogen transport | 0.0417526751697796 |
| GO:0009260 | ribonucleotide biosynthetic process | 0.0417526751697796 |
| GO:0009150 | purine ribonucleotide metabolic process | 0.0417526751697796 |
| GO:0006164 | purine nucleotide biosynthetic process | 0.0417526751697796 |
| GO:0009058 | biosynthetic process | 0.0417526751697796 |
| GO:0009259 | ribonucleotide metabolic process | 0.0417526751697796 |
| GO:0006163 | purine nucleotide metabolic process | 0.0426071727823965 |
| GO:0042625 | ATPase activity, coupled to transmembrane movement of ions | 0.0446838862837438 |
| GO:0009108 | coenzyme biosynthetic process | 0.0446838862837438 |
| GO:0015078 | hydrogen ion transmembrane transporter activity | 0.0470887349534143 |
| GO:0015077 | monovalent inorganic cation transmembrane transporter activity | 0.0470887349534143 |
| GO:0051188 | cofactor biosynthetic process | 0.0470887349534143 |
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 |
|---|---|---|
| non-terminally differentiated cell | 3.40e-23 | 49 |
| ectodermal cell | 1.70e-21 | 44 |
| neurectodermal cell | 1.70e-21 | 44 |
| neural cell | 2.51e-21 | 43 |
| electrically responsive cell | 1.33e-16 | 39 |
| electrically active cell | 1.33e-16 | 39 |
| somatic cell | 2.91e-15 | 118 |
| neuron | 7.76e-15 | 33 |
| neuronal stem cell | 7.76e-15 | 33 |
| neuroblast | 7.76e-15 | 33 |
| electrically signaling cell | 7.76e-15 | 33 |
| somatic stem cell | 1.69e-14 | 91 |
| multi fate stem cell | 1.69e-14 | 91 |
| animal cell | 2.75e-14 | 115 |
| eukaryotic cell | 2.75e-14 | 115 |
| embryonic cell | 3.51e-14 | 70 |
| stem cell | 5.61e-14 | 97 |
| CNS neuron (sensu Vertebrata) | 5.15e-13 | 23 |
| neuroblast (sensu Vertebrata) | 5.15e-13 | 23 |
| migratory neural crest cell | 1.58e-07 | 10 |
| neuron associated cell | 1.58e-07 | 10 |
| glial cell (sensu Vertebrata) | 1.58e-07 | 10 |
| neuron associated cell (sensu Vertebrata) | 1.58e-07 | 10 |
| glial cell | 1.58e-07 | 10 |
| glioblast | 1.58e-07 | 10 |
| glioblast (sensu Vertebrata) | 1.58e-07 | 10 |
| Ontology term | p-value | n |
|---|---|---|
| nervous system | 1.45e-31 | 75 |
| central nervous system | 2.49e-30 | 73 |
| ectoderm-derived structure | 4.94e-22 | 95 |
| ectoderm | 4.94e-22 | 95 |
| presumptive ectoderm | 4.94e-22 | 95 |
| regional part of nervous system | 5.17e-22 | 54 |
| neural tube | 8.56e-21 | 52 |
| neural rod | 8.56e-21 | 52 |
| future spinal cord | 8.56e-21 | 52 |
| neural keel | 8.56e-21 | 52 |
| neurectoderm | 3.22e-19 | 64 |
| neural plate | 3.22e-19 | 64 |
| presumptive neural plate | 3.22e-19 | 64 |
| structure with developmental contribution from neural crest | 3.66e-19 | 92 |
| brain | 4.25e-18 | 47 |
| future brain | 4.25e-18 | 47 |
| regional part of brain | 9.28e-18 | 46 |
| gray matter | 1.70e-16 | 34 |
| anterior neural tube | 7.11e-16 | 40 |
| regional part of forebrain | 8.74e-16 | 39 |
| forebrain | 8.74e-16 | 39 |
| future forebrain | 8.74e-16 | 39 |
| ecto-epithelium | 1.97e-14 | 73 |
| brain grey matter | 5.90e-14 | 29 |
| regional part of telencephalon | 5.90e-14 | 29 |
| telencephalon | 5.90e-14 | 29 |
| pre-chordal neural plate | 2.20e-13 | 49 |
| cerebral cortex | 7.47e-10 | 21 |
| cerebral hemisphere | 7.47e-10 | 21 |
| pallium | 7.47e-10 | 21 |
| regional part of cerebral cortex | 2.15e-08 | 17 |
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 | 0.276754 |
| 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 | 1.1032 |
| 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 | 0.313353 |
| MA0106.1 | 0.899777 |
| MA0107.1 | 0.533522 |
| 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 | 0.313734 |
| MA0147.1 | 0.453952 |
| MA0148.1 | 0.706718 |
| MA0149.1 | 0.611881 |
| MA0062.2 | 0.856416 |
| MA0035.2 | 0.788288 |
| MA0039.2 | 0.45096 |
| 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 | 0.609584 |
| MA0150.1 | 0.67206 |
| MA0151.1 | 0 |
| MA0152.1 | 0.84577 |
| MA0153.1 | 1.31015 |
| MA0154.1 | 0.728853 |
| 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 | 0.346529 |
| MA0163.1 | 0.327769 |
| MA0164.1 | 0.817786 |
| MA0080.2 | 0.534538 |
| MA0018.2 | 0.828253 |
| MA0099.2 | 0.944966 |
| MA0079.2 | 0.0234849 |
| MA0102.2 | 1.8929 |
| MA0258.1 | 0.419871 |
| MA0259.1 | 0.441366 |
| MA0442.1 | 0 |
