Article reSeArcH
Extended Data Fig. 9 | Significant covariation among multi-omic
components of the gut microbiome and host interactors in IBD
(unadjusted). The network was constructed from ten data sets:
metagenomic species, species-level transcription ratios, functional profiles
at the EC levels (MGX, MTX and MPX), metabolites, host transcription
(rectal and ileal separately), serology and faecal calprotectin. As in Fig. 4c,
measurement types were approximately matched in time with a maximum
separation between paired samples of four weeks. The top 300 significant
correlations (FDR P < 0.05) among correlations between features that
were differentially abundant in dysbiosis were used to construct the
network visualized here (for serology, a threshold of FDR P < 0.25 was
used). Nodes are coloured by the disease group in which they are ‘high’,
and edges are coloured by the sign and strength of the correlation. For this
unadjusted network, Spearman correlations were calculated using HAllA
from the residuals of the same model as in Extended Data Fig. 8, though
without adjusting for dysbiosis (see Methods). Appropriate normalization
and/or transformation for each measurement type was performed
independently before the model fitting (see Methods). Singleton
node pairs were pruned from the network. Source associations are in
Supplementary Table 36, sample counts in Fig. 1b, c.