Raw and Intermediate data associated with "Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multiomics integration"

Data and intermediate structures for "Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multiomics integration"

The project involves the comparison of gene expression data and estimated flux across over 44 million models of HMO biosynthesis. Here we provide intermediate objects to simplify the task of reproducing our calculations.

• Raw/Input data (raw.zip); data_HMO.xlsx is the central dataset including HMO concentrations and gene expression data.  Other files are .csv exports from data_HMO.xlsx to circumvent a temporary bug in the xlsx reading package. They should not differ from the original file and are provided to facilitate code readability.
• (models_split.zip) HMO biosynthesis models generated through network generation ( /code/1.flux/A) and enumeration (/code/1.flux/B)
• (scores_spllit.zip) Correlation (R) and correlation p-values (P) between estimated flux and observed gene expression for corresponding genes (/code/1.flux/C)
• (big_mat.<bin/desc>.zip) Intermediate matrixes containing gene-linkage scores, models score, model classifications and other information generated/used by the Flux-Expression Comparision code (/code/3.flux_expression)