PTB_Metabs_2021

Analyses pertaining to the manuscruipt Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome

William F. Kindschuh^1*, Federico Baldini^1*, Martin C. Liu^1,2*, Jingqiu Liao¹, Yoli Meydan¹, Harry H.Lee¹, Almut Heinken³, Ines Thiele^3,4,5,6, Maayan Levy⁷&, Tal Korem^1,8,9&

Author affiliations:

1 Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY

2 Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY

3 School of Medicine, National University of Ireland, Galway, Galway, Ireland

4 Discipline of Microbiology, National University of Galway, Galway, Ireland

5 Ryan Institute, National University of Galway, Galway, Ireland

6 APC Microbiome Ireland, University College Cork, Cork, Ireland

7 Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA

8 Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY

9 CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada

• • these authors contributed equally to this work

& - corresponding authors, Tal Korem ([email protected]) and Maayan Levy ([email protected])

Instructions for running code:

To install required dependencies run the following command: "conda env create -f ptb_metabs.yml"

To reproduce the analyses and panels run the following commands: "python generate_figures.py" "python generate_prediction_figures.py"

Note - in order to avoid having to regenerate the null distributions of p-values required for the msea (extended data figure 5d) you will need to unzip the zipped p-value files contained within data/msea