Extended Data Fig. 3: MOFA (multi-omics factor analysis) and MEFISTO (a method for the functional integration of spatial omics data) in allo-SCT patients.

a) Correlation between MOFA-identified Factors and normalized intestinal metabolite concentrations. Associations between Factor values and metabolites were analyzed via Pearson’s correlation. The correlation coefficient is indicated in the adjacent color legend. The p-values associated with the correlations were corrected for multiple testing with the FDR approach. b) Top 15 Features in bacteriome, virome and metabolites in Factor 4 in descending order according to Feature weight. Larger weights indicate a higher correlation with that Factor, while the positive or negative sign indicates the directionality of that variation, that is, ‘+’ indicates a positive association, ‘−’ a negative association. c) Bar plot of time scale parameters assigned to Factors 1 through 10 identified by MEFISTO. MEFISTO assigns a time scale value between 0 and 1 to each Factor, which reflects the degree to which that Factor is dependent on time. A value of 0 implies no time-dependency, a value of 1 strong time-dependency. Of note, results pertaining to the identified Factors, their weight/covariance structure, variance explained across omics entities and Factor values obtained by MEFISTO modelling were almost identical and thus comparable to the output of our original MOFA model. d) Heatmap of normalized abundance of viral contigs assigned to eukaryotic and prokaryotic viruses at time-points relative to allo-SCT. The number of samples is indicated.