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1
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1 <macros>
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2
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3 <xml name="options">
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4 <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
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5 <option value="HMRcore" selected="true">HMRcore rules</option>
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6 <option value="Recon">Recon 2.2 rules</option>
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7 <option value="Custom">Custom rules</option>
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8 </param>
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9 </xml>
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10
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11 <token name="@CUSTOM_RULES_EXEMPLE@">
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12
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13 +--------------------+-------------------------------+
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14 | id | rule (with entrez-id) |
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15 +====================+===============================+
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16 | SHMT1 | 155060 or 10357 |
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17 +--------------------+-------------------------------+
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18 | NIT2 | 155060 or 100134869 |
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19 +--------------------+-------------------------------+
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20 | GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 |
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21 +--------------------+-------------------------------+
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22
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23 |
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24
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25 </token>
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26
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27 <token name="@DATASET_EXEMPLE1@">
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28
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29 +------------+------------+------------+------------+
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30 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
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31 +============+============+============+============+
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32 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
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33 +------------+------------+------------+------------+
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34 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
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35 +------------+------------+------------+------------+
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36 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
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37 +------------+------------+------------+------------+
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38 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
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39 +------------+------------+------------+------------+
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40 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
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41 +------------+------------+------------+------------+
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42
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43 |
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44
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45 </token>
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46
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47 <token name="@DATASET_EXEMPLE2@">
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48
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49 +-------------+------------+------------+------------+
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50 | Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
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51 +=============+============+============+============+
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52 | A1BG | 0.523167 | 0.371355 | 0.925661 |
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53 +-------------+------------+------------+------------+
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54 | A1CF | 0.568765 | 0.765567 | 0.456789 |
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55 +-------------+------------+------------+------------+
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56 | A2M | 0.876545 | 0.768933 | 0.987654 |
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57 +-------------+------------+------------+------------+
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58 | A4GALT | 0.456788 | 0.876543 | 0.876542 |
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59 +-------------+------------+------------+------------+
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60 | M664Y65 | 0.876543 | 0.786543 | 0.897654 |
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61 +-------------+------------+------------+------------+
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62
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63 |
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64
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65 </token>
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66
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67 <token name="@REFERENCE@">
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68
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13
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69 This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_.
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1
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70
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70
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71 .. _BIMIB: https://bimib.disco.unimib.it/index.php/Home
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72
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72 .. _Department of Informatics, Systems and Communications: https://www.disco.unimib.it/en
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73 .. _University of Milan - Bicocca: https://en.unimib.it/
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1
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74
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75 </token>
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76
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77 <xml name="citations">
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78 <citations> <!--esempio di citazione-->
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79 <citation type="bibtex">
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70
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80 @article{graudenzi2018integration,
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81 title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power},
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82 author={Graudenzi, Alex and Maspero, Davide and Di Filippo, Marzia and Gnugnoli, Marco and Isella, Claudio and Mauri, Giancarlo and Medico, Enzo and Antoniotti, Marco and Damiani, Chiara},
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83 journal={Journal of biomedical informatics},
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84 volume={87},
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85 pages={37--49},
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86 year={2018},
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87 publisher={Elsevier},
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74
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88 url = {https://doi.org/10.1016/j.jbi.2018.09.010},
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70
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89 }
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90 </citation>
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91 <citation type="bibtex">
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92 @article{damiani2020marea4galaxy,
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93 title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy},
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94 author={Damiani, Chiara and Rovida, Lorenzo and Maspero, Davide and Sala, Irene and Rosato, Luca and Di Filippo, Marzia and Pescini, Dario and Graudenzi, Alex and Antoniotti, Marco and Mauri, Giancarlo},
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95 journal={Computational and Structural Biotechnology Journal},
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96 volume={18},
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97 pages={993},
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98 year={2020},
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99 publisher={Research Network of Computational and Structural Biotechnology},
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74
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100 url = {https://doi.org/10.1016/j.csbj.2020.04.008},
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70
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101 }
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1
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102 </citation>
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103 </citations>
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104 </xml>
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105
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106 </macros>
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