Published April 28, 2020
| Version v1
Journal article
Open
metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes
Creators
- 1. BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
- 2. Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- 3. Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- 4. Department of Medical Genetics and BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
- 5. Department of Pediatics, BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada and Department of Pediatrics, Radboud University Medical Center, Nijmegen, the Netherlands
- 6. Department of Medical Genetics and Department of Statistics, University of British Columbia, Vancouver, Canada
Description
These files were used in a manuscript submitted to npj Genomic Medicine titled “metPropagate: metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes”. De-identified raw LC/MS metabolomic data for all patients and controls in addition to processed patient-specific gene lists are provided here.
For details on processing, see the manuscript or contact:
ejgraham3 AT wisc DOT edu
Description of files
Sample mapping
- 20200428_meta_data.csv
- This file maps ID with causative gene and patient-specific HPO terms for each patient.
- For all patients and controls, we also map patient ID with metabolomics file names.
Untargeted metabolomics data from TIDEX study
- 20200428_LCMS_data.zip
- contains raw metabolomics data generated through the TIDEX study (Tarailo-Graovac et al, 2016). The mapping file above maps file names to patient IDs. Each patient/control has two files: one analyzed in ESI+ and one analyzed in ESI- mode.
Genetic data from TIDEX study
- 20200428_Gene_lists.zip
- per-gene Exomiser scores for each patient. To generate these files, singleton VCFs produced by DeepVariant and patient-specific HPO terms available in the sample mapping file were provided to Exomiser as input. Genomic location of specific variants are not included to protect patient privacy. See the manuscript for more details.