Journal: NAR Genomics and Bioinformatics
Article Title: GEMCAT—a new algorithm for gene expression-based prediction of metabolic alterations
doi: 10.1093/nargab/lqaf003
Figure Lengend Snippet: Comparison of predicted and measured changes in the abundance of metabolites in SLC25A51 -deficient (293- SLC25A51 -ko) cells relative to parental HEK293 cells. ( A ) A histogram showing the distribution of changes predicted in the abundance of 8399 metabolites in the HMM (Recon3D model) using RNA-seq data from three replicates. ( B ) A scatter plot showing the distribution of the mean of predicted metabolic changes calculated based on the integration of RNA-seq data from three replicates in comparison to the mean of the experimentally measured changes in metabolite concentrations in 293- SLC25A51 -ko relative to parental HEK293 cells from five replicates (for details see the ‘Materials and methods’ section). The dashed lines are used to divide the plot into four quadrants. The upper right and lower left quadrants show metabolites, whose concentration changes are predicted correctly. In each quadrant, the percentage and names of metabolites corresponding to it are shown. Metabolite abbreviations: AMP, adenosine monophosphate; ATP, adenosine triphosphate; cAMP, cyclic AMP; 2,3-DPG, 2,3-diphosphoglyceric acid; 6PG, 6-phosphogluconic acid; S7P, d -sedoheptulose 7-phosphate; F16BP, fructose 1,6-bisphosphate; F6P, fructose 6-phosphate; G1P, glucose 1-phosphate; G6P, glucose 6-phosphate; PEP, phosphoenolpyruvic acid; SAM, S -adenosylmethionine; NAA, N -acetyl- l -aspartic acid; 3OHKYN, hydroxykynurenine.
Article Snippet: Cells (293- SLC25A51 -ko [ ] and parental HEK293) were cultivated in Dulbecco’s modified Eagle medium, high glucose (Merck/Sigma, D5671) supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM l -glutamine, 1 mM sodium pyruvate, and penicillin/streptomycin at 37°C in humidified atmosphere with 5% CO 2 .
Techniques: Comparison, RNA Sequencing Assay, Concentration Assay