Contains data and code necessary to reproduce analyses that appear in “Temporal Multi-Omic Analysis Uncovers Sex-Biased Molecular Programs Underlying Muscle Adaptation to Endurance Training”
Differential analysis of transcriptomics, proteomics, phosphoproteomics,
and metabolomics subcutaneous white adipose tissue -omics datasets.
Enrichment analyses (FGSEA or KSEA) for each -ome. Weighted Gene
Co-expression Network Analysis for all -omes excluding proteomics. The
data-raw/ folder contains code to reproduce all analyses. Most R
script names match the objects they create, though some scripts create
multiple objects, and so are given more general names. Code to reproduce
figures are found in vigenttes for all of the gene set enrichment
analysis, and in the Other Figures folders. If you would like to
recreate the entire project from scratch, like in the case of a new
genome annotation, refer to the script regenerate_figures.sh, because
some files rely on others in the order of generation.
The vignettes in the package cover visualizations that describe the number of genes/proteins/metabolites found to be differentially abundant as a result of exercise training, as well as the sets that they are enriched in.
devtools::install_github("MoTrPAC/MotrpacRatTraining6moMuscleData")or, to get vignettes:
devtools::install_github("MoTrPAC/MotrpacRatTraining6moMuscleData", build_vignettes = TRUE)For questions, bug reporting, and data requests for this package, please submit a new issue and include as many details as possible.
MoTrPAC is supported by the National Institutes of Health (NIH) Common Fund through cooperative agreements managed by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of Arthritis and Musculoskeletal Diseases (NIAMS), and National Institute on Aging (NIA).
Specifically, the MoTrPAC Study is supported by NIH grants U24OD026629 (Bioinformatics Center), U24DK112349, U24DK112342, U24DK112340, U24DK112341, U24DK112326, U24DK112331, U24DK112348 (Chemical Analysis Sites), U01AR071133, U01AR071130, U01AR071124, U01AR071128, U01AR071150, U01AR071160, U01AR071158 (Clinical Centers), U24AR071113 (Consortium Coordinating Center), U01AG055133, U01AG055137 and U01AG055135 (PASS/Animal Sites).
Recipients and their Agents agree that in publications using any data from MoTrPAC public-use data sets they will acknowledge MoTrPAC as the source of data, including the version number of the data sets used, e.g.:
- Data used in the preparation of this article were obtained from the Molecular Transducers of Physical Activity Consortium (MoTrPAC) database, which is available for public access at motrpac-data.org.
- Data used in the preparation of this article were obtained from the Molecular Transducers of Physical Activity Consortium (MoTrPAC) MotrpacRatTraining6moMuscleData R package [0.1.1.0].