CORGIAS experimental datasets
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2025
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| _version_ | 1866902321727799296 |
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| author | Nishimura, Yuki Omae, Kimiho Tominaga, Kento Iwasaki, Wataru |
| author_facet | Nishimura, Yuki Omae, Kimiho Tominaga, Kento Iwasaki, Wataru |
| contents | <p>The dataset accompaies to the manuscript "<a href="https://doi.org/10.1101/2025.05.07.652372"><strong>CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset</strong></a>"</p> <p>The results in the manuscript can be reproduced by this dataset and the code provide <a href="https://github.com/ynishimuraLv/corgias_data">here</a>.</p> <p><strong>archaea, mycobacteriales and pseudomonadales zip include the following:</strong></p> <p>Input files for analysis:</p> <ul> <li>COG_table.csv: A presence/absence table of all COGs found in either genomes in the datasets.</li> <li>COG_table99.csv: A presence/absence tableof COGs shared in 1-99% genomes in the datasets.</li> <li>hq_tree.tre: A phylogenetic tree used in the analyses.</li> <li>COG_table4evoweaver.csv: Same as COG_table99.csv but for <a href="https://doi.org/10.1038/s41467-025-59175-6">EvoWeaver</a>.</li> <li>hq_tree4evoweaver.tree: Same as hq_tree.tre but for <a href="https://doi.org/10.1038/s41467-025-59175-6">EvoWeaver</a>.</li> </ul> <p>The results of phylogenetic profiling are as follows:</p> <ul> <li>naive.csv</li> <li>rle.csv</li> <li>cwa.csv</li> <li>cotr.csv</li> <li>asa_*.csv</li> <li>asawo.csv</li> <li>sev.csv</li> <li>evoweaver.csv</li> </ul> <p>The prefix of each file name represents the phylogenetic profiling method used.<br>ASA and SEV require ancestral state reconstruction (ASR), and * in their file names indicates how ASR was performed.<br>asawo.csv is the result of ASA without considering branch length.<br>evoweaver.csv is the result of four phylogenetic profiling methods implemented in <a href="https://doi.org/10.1038/s41467-025-59175-6">EvoWeaver</a>. </p> <p>The results of statistical tests of above files are recorded in *_stat.csv except for evoweaver.csv, as it contains scores combining p-value.</p> <p>The data for comparing phylogenetic methods as follows:</p> <ul> <li>scaled_pvalues.csv: A table showing the minmax-scaled p-values for each method of CORGIAS and scores for EvoWeaver. </li> <li>tp_pairs.txt: A list of true positive (functionally related) COG pairs detected by either method at TPR = 0.5</li> <li>evolCCM.csv: Results from evolCCM for the COG pairs listed in tpr07_pairs.txt</li> <li>tp_stat*<em>.</em>csv: A concatenated table combining evolCCM.csv, COG information, and presence/absence changes during evolution.* in tp_stat files indicates True positive rate (TPR) threshold. </li> </ul> <p><strong>ipynb.zip includes Jupyter notebook version of .py, which are deposited at https://github.com/ynishimuraLv/CORGIAS_data</strong></p> <p><strong>COG.links.wo_cooccurence.txt includes STRING scores of the COG pairs recalculated without cooccurrence score. <br></strong>Original files is available at <a href="https://string-db.org/cgi/download?sessionId=betqaSoThzqj">STRING database</a> and recalculation can be reproduced in <a title="1_Prepare_dataset.py" href="https://github.com/ynishimuraLv/corgias_data/blob/main/1_Prepare_dataset.py">1_Prepare_dataset.py</a>.</p> <p><strong>Table S8-S10 included the pairs detected only by weighted methods with varying TPRs.</strong></p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15496141 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | CORGIAS experimental datasets Nishimura, Yuki Omae, Kimiho Tominaga, Kento Iwasaki, Wataru <p>The dataset accompaies to the manuscript "<a href="https://doi.org/10.1101/2025.05.07.652372"><strong>CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset</strong></a>"</p> <p>The results in the manuscript can be reproduced by this dataset and the code provide <a href="https://github.com/ynishimuraLv/corgias_data">here</a>.</p> <p><strong>archaea, mycobacteriales and pseudomonadales zip include the following:</strong></p> <p>Input files for analysis:</p> <ul> <li>COG_table.csv: A presence/absence table of all COGs found in either genomes in the datasets.</li> <li>COG_table99.csv: A presence/absence tableof COGs shared in 1-99% genomes in the datasets.</li> <li>hq_tree.tre: A phylogenetic tree used in the analyses.</li> <li>COG_table4evoweaver.csv: Same as COG_table99.csv but for <a href="https://doi.org/10.1038/s41467-025-59175-6">EvoWeaver</a>.</li> <li>hq_tree4evoweaver.tree: Same as hq_tree.tre but for <a href="https://doi.org/10.1038/s41467-025-59175-6">EvoWeaver</a>.</li> </ul> <p>The results of phylogenetic profiling are as follows:</p> <ul> <li>naive.csv</li> <li>rle.csv</li> <li>cwa.csv</li> <li>cotr.csv</li> <li>asa_*.csv</li> <li>asawo.csv</li> <li>sev.csv</li> <li>evoweaver.csv</li> </ul> <p>The prefix of each file name represents the phylogenetic profiling method used.<br>ASA and SEV require ancestral state reconstruction (ASR), and * in their file names indicates how ASR was performed.<br>asawo.csv is the result of ASA without considering branch length.<br>evoweaver.csv is the result of four phylogenetic profiling methods implemented in <a href="https://doi.org/10.1038/s41467-025-59175-6">EvoWeaver</a>. </p> <p>The results of statistical tests of above files are recorded in *_stat.csv except for evoweaver.csv, as it contains scores combining p-value.</p> <p>The data for comparing phylogenetic methods as follows:</p> <ul> <li>scaled_pvalues.csv: A table showing the minmax-scaled p-values for each method of CORGIAS and scores for EvoWeaver. </li> <li>tp_pairs.txt: A list of true positive (functionally related) COG pairs detected by either method at TPR = 0.5</li> <li>evolCCM.csv: Results from evolCCM for the COG pairs listed in tpr07_pairs.txt</li> <li>tp_stat*<em>.</em>csv: A concatenated table combining evolCCM.csv, COG information, and presence/absence changes during evolution.* in tp_stat files indicates True positive rate (TPR) threshold. </li> </ul> <p><strong>ipynb.zip includes Jupyter notebook version of .py, which are deposited at https://github.com/ynishimuraLv/CORGIAS_data</strong></p> <p><strong>COG.links.wo_cooccurence.txt includes STRING scores of the COG pairs recalculated without cooccurrence score. <br></strong>Original files is available at <a href="https://string-db.org/cgi/download?sessionId=betqaSoThzqj">STRING database</a> and recalculation can be reproduced in <a title="1_Prepare_dataset.py" href="https://github.com/ynishimuraLv/corgias_data/blob/main/1_Prepare_dataset.py">1_Prepare_dataset.py</a>.</p> <p><strong>Table S8-S10 included the pairs detected only by weighted methods with varying TPRs.</strong></p> |
| title | CORGIAS experimental datasets |
| url | https://doi.org/10.5281/zenodo.15496141 |