SysBioM001Paper

This repository includes the main code used in our M001/M004 paper.

Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers.
Kengo Watanabe, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Gonzalo G. Garcia, Michael R. Hoopmann, Mukul K. Midha, David H. Baxter, Michal Maes, Seamus R. Morrone, Kelly M. Crebs, Charu Kapil, Ulrike Kusebauch, Jack Wiedrick, Jodi Lapidus, Lance Pflieger, Christopher Lausted, Jared C. Roach, Gwênlyn Glusman, Steven R. Cummings, Nicholas J. Schork, Nathan D. Price, Leroy Hood, Richard A. Miller, Robert L. Moritz and Noa Rappaport.
Commun. Biol. 6, 768 (2023), DOI: https://doi.org/10.1038/s42003-023-05128-y

Preprint version:
Systems-level patterns in biological processes are changed under prolongevity interventions and across biological age.
Kengo Watanabe, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Gonzalo G. Garcia, Michael R. Hoopmann, Mukul K. Midha, David H. Baxter, Michal Maes, Seamus R. Morrone, Kelly M. Crebs, Charu Kapil, Ulrike Kusebauch, Jack Wiedrick, Jodi Lapidus, Jennifer C. Lovejoy, Andrew T. Magis, Christopher Lausted, Jared C. Roach, Gustavo Glusman, Steven R. Cummings, Nicholas J. Schork, Nathan D. Price, Leroy Hood, Richard A. Miller, Robert L. Moritz, and Noa Rappaport.
medRxiv 2022.07.11.22277435 (2022), DOI: https://doi.org/10.1101/2022.07.11.22277435

Correspondence to Leroy Hood (lee.hood@isbscience.org) and Noa Rappaport (noa.rappaport@isbscience.org).

Overview

The below figure numbers correspond to the published paper version.

1. DIRAC

This directory includes the main code for the differential rank conservation (DIRAC; Eddy, J.A. et al. PLoS Comput. Biol. 2010) analyses, corresponding to:

• Figure 2
• Figure 3f–i
• Figure 4
• Figure 5
• Supplementary Figure 1
• Supplementary Figure 2
• Supplementary Figure 3e, f
• Supplementary Figure 4
• Supplementary Data 1
• Supplementary Data 4
• Supplementary Data 5
• Supplementary Data 6
• Supplementary Data 7

2. WGCNA

This directory includes the main code for the weighted gene correlation network analysis (WGCNA; Langfelder, P. & Horvath, S. BMC Bioinform. 2008), corresponding to:

• Figure 3b–e
• Supplementary Figure 3a–d
• Supplementary Data 2
• Supplementary Data 3

3. GEM

This directory includes the main code for the mouse genome-scale metabolic model (GEM; Khodaee, S. et al. Sci. Rep. 2020) reconstruction analysis, corresponding to:

• Figure 6
• Supplementary Data 8

Log

Last update on Jul 24, 2023

• 2022-07-19 The repository was generated.
• 2022-07-22 The code files were uploaded and README was edited.
• 2023-06-03 The code files and README were updated based on the revised manuscript (1st revision).
• 2023-06-30 Two code files were added to the DIRAC directory and READMEs (figure numbers) were updated based on the revised manuscript (2nd revision).
• 2023-07-24 README was updated after publication.