# HG changeset patch # User luca_milaz # Date 1758635304 0 # Node ID e0bcc61b2febfb25e86a8ef60194046867e20b60 # Parent 6b8a7e1e8efad325e082b227b6be89104c496d1d Uploaded diff -r 6b8a7e1e8efa -r e0bcc61b2feb COBRAxy/marea_macros.xml --- a/COBRAxy/marea_macros.xml Tue Sep 23 13:48:06 2025 +0000 +++ b/COBRAxy/marea_macros.xml Tue Sep 23 13:48:24 2025 +0000 @@ -1,203 +1,210 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -+--------------------+-------------------------------+ -| id | rule (with entrez-id) | -+====================+===============================+ -| SHMT1 | 155060 or 10357 | -+--------------------+-------------------------------+ -| NIT2 | 155060 or 100134869 | -+--------------------+-------------------------------+ -| GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 | -+--------------------+-------------------------------+ - -| - - - - - -+------------+------------+------------+------------+ -| Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 | -+============+============+============+============+ -| HGNC:24086 | 0.523167 | 0.371355 | 0.925661 | -+------------+------------+------------+------------+ -| HGNC:24086 | 0.568765 | 0.765567 | 0.456789 | -+------------+------------+------------+------------+ -| HGNC:9876 | 0.876545 | 0.768933 | 0.987654 | -+------------+------------+------------+------------+ -| HGNC:9 | 0.456788 | 0.876543 | 0.876542 | -+------------+------------+------------+------------+ -| HGNC:23 | 0.876543 | 0.786543 | 0.897654 | -+------------+------------+------------+------------+ - -| - - - - - -+-------------+------------+------------+------------+ -| Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 | -+=============+============+============+============+ -| A1BG | 0.523167 | 0.371355 | 0.925661 | -+-------------+------------+------------+------------+ -| A1CF | 0.568765 | 0.765567 | 0.456789 | -+-------------+------------+------------+------------+ -| A2M | 0.876545 | 0.768933 | 0.987654 | -+-------------+------------+------------+------------+ -| A4GALT | 0.456788 | 0.876543 | 0.876542 | -+-------------+------------+------------+------------+ -| M664Y65 | 0.876543 | 0.786543 | 0.897654 | -+-------------+------------+------------+------------+ - -| - - - - - -This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. - -.. _BIMIB: https://bimib.disco.unimib.it/index.php/Home -.. _Department of Informatics, Systems and Communications: https://www.disco.unimib.it/en -.. _University of Milan - Bicocca: https://en.unimib.it/ - - - - - - - @article{graudenzi2018integration, - title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power}, - 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}, - journal={Journal of biomedical informatics}, - volume={87}, - pages={37--49}, - year={2018}, - publisher={Elsevier}, - url = {https://doi.org/10.1016/j.jbi.2018.09.010}, - } - - - @article{damiani2020marea4galaxy, - title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy}, - 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}, - journal={Computational and Structural Biotechnology Journal}, - volume={18}, - pages={993}, - year={2020}, - publisher={Research Network of Computational and Structural Biotechnology}, - url = {https://doi.org/10.1016/j.csbj.2020.04.008}, - } - - - @article{ebrahim2013cobrapy, - title={COBRApy: constraints-based reconstruction and analysis for python}, - author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R}, - journal={BMC systems biology}, - volume={7}, - pages={1--6}, - year={2013}, - publisher={Springer} - } - - - - - - - - @article{galuzzi2024adjusting, - title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis}, - author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara}, - journal={Journal of Biomedical Informatics}, - volume={150}, - pages={104597}, - year={2024}, - publisher={Elsevier} - } - - - @inproceedings{galuzzi2022best, - title={Best practices in flux sampling of constrained-based models}, - author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara}, - booktitle={International Conference on Machine Learning, Optimization, and Data Science}, - pages={234--248}, - year={2022}, - organization={Springer} - } - - - @article{ebrahim2013cobrapy, - title={COBRApy: constraints-based reconstruction and analysis for python}, - author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R}, - journal={BMC systems biology}, - volume={7}, - pages={1--6}, - year={2013}, - publisher={Springer} - } - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ++--------------------+-------------------------------+ +| id | rule (with entrez-id) | ++====================+===============================+ +| SHMT1 | 155060 or 10357 | ++--------------------+-------------------------------+ +| NIT2 | 155060 or 100134869 | ++--------------------+-------------------------------+ +| GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 | ++--------------------+-------------------------------+ + +| + + + + + ++------------+------------+------------+------------+ +| Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 | ++============+============+============+============+ +| HGNC:24086 | 0.523167 | 0.371355 | 0.925661 | ++------------+------------+------------+------------+ +| HGNC:24086 | 0.568765 | 0.765567 | 0.456789 | ++------------+------------+------------+------------+ +| HGNC:9876 | 0.876545 | 0.768933 | 0.987654 | ++------------+------------+------------+------------+ +| HGNC:9 | 0.456788 | 0.876543 | 0.876542 | ++------------+------------+------------+------------+ +| HGNC:23 | 0.876543 | 0.786543 | 0.897654 | ++------------+------------+------------+------------+ + +| + + + + + ++-------------+------------+------------+------------+ +| Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 | ++=============+============+============+============+ +| A1BG | 0.523167 | 0.371355 | 0.925661 | ++-------------+------------+------------+------------+ +| A1CF | 0.568765 | 0.765567 | 0.456789 | ++-------------+------------+------------+------------+ +| A2M | 0.876545 | 0.768933 | 0.987654 | ++-------------+------------+------------+------------+ +| A4GALT | 0.456788 | 0.876543 | 0.876542 | ++-------------+------------+------------+------------+ +| M664Y65 | 0.876543 | 0.786543 | 0.897654 | ++-------------+------------+------------+------------+ + +| + + + + + +This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. + +.. _BIMIB: https://bimib.disco.unimib.it/index.php/Home +.. _Department of Informatics, Systems and Communications: https://www.disco.unimib.it/en +.. _University of Milan - Bicocca: https://en.unimib.it/ + + + + + + + @article{graudenzi2018integration, + title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power}, + 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}, + journal={Journal of biomedical informatics}, + volume={87}, + pages={37--49}, + year={2018}, + publisher={Elsevier}, + url = {https://doi.org/10.1016/j.jbi.2018.09.010}, + } + + + @article{damiani2020marea4galaxy, + title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy}, + 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}, + journal={Computational and Structural Biotechnology Journal}, + volume={18}, + pages={993}, + year={2020}, + publisher={Research Network of Computational and Structural Biotechnology}, + url = {https://doi.org/10.1016/j.csbj.2020.04.008}, + } + + + @article{ebrahim2013cobrapy, + title={COBRApy: constraints-based reconstruction and analysis for python}, + author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R}, + journal={BMC systems biology}, + volume={7}, + pages={1--6}, + year={2013}, + publisher={Springer} + } + + + + + + + + @article{galuzzi2024adjusting, + title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis}, + author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara}, + journal={Journal of Biomedical Informatics}, + volume={150}, + pages={104597}, + year={2024}, + publisher={Elsevier} + } + + + @inproceedings{galuzzi2022best, + title={Best practices in flux sampling of constrained-based models}, + author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara}, + booktitle={International Conference on Machine Learning, Optimization, and Data Science}, + pages={234--248}, + year={2022}, + organization={Springer} + } + + + @article{ebrahim2013cobrapy, + title={COBRApy: constraints-based reconstruction and analysis for python}, + author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R}, + journal={BMC systems biology}, + volume={7}, + pages={1--6}, + year={2013}, + publisher={Springer} + } + + + + + +