Yeast_Ionome_Metabolome

This repository contains materials for the paper [Extraction and integration of genetic networks from short-profile omic datasets], by J. Iacovacci et al..

Scripts

• multilink_analysis.m : script to compute a basic multilink analysis of the Yeast Ionome-Metabolome multiplex network.

• cosM.m : function to measure the Mahalanobis cosine between the N observations of M correlated variables in a dataset (N>>M).

• cosH.m : function to measure the hybrid-Mahalanobis cosine between the N observations of M correlated variables in a dataset (N>>M).

Networks

The following files included in the repository contain the Yeast Ionome-Metabolome multiplex network:

• yeast_ionome_metabolome_multiplex_cosM.txt : edge lists of the layers of the Yeast Ionome-Metabolome multiplex network (ionome knockout, ionome oevrexpression, metabolome amino acids) extracted by using the Mahalanobis cosine. Link weights correspond to the rank of the correlation values.

• yeast_ionome_metabolome_multiplex_cosH.txt : edge lists of the layers of the Yeast Ionome-Metabolome multiplex network (ionome knockout, ionome oevrexpression, metabolome amino acids) extracted by using the hybrid-Mahalanobis cosine. Link weights correspond to the rank of the correlation values.

• yeast_ionome_metabolome_multiplex_cos.txt : edge lists of the layers of the Yeast Ionome-Metabolome multiplex network (ionome knockout, ionome oevrexpression, metabolome amino acids) extracted by using the cosine. Link weights correspond to the rank of the correlation values.

• yeast_ionome_metabolome_multiplex_PCC.txt : edge lists of the layers of the Yeast Ionome-Metabolome multiplex network (ionome knockout, ionome oevrexpression, metabolome amino acids) extracted by using the Pearson's coefficient. Link weights correspond to the rank of the correlation values.

• nodes_list.txt : contains the gene names (ORFs) corresponding to the nodes in the multiplex networks.

Data

The following data folders and files included in the repository contain datasets:

• zprofiles_all_datasets : contains z-score profiles for all mutants in the ionome and metabolome datasets.

• Synthetic_data : contains the files correspondng to the synthetic datasets generated for the analysis.