reSeArcH Article
Extended Data Fig. 8 | Significant covariation among multi-omic
components of the gut microbiome and host interactors in IBD
(adjusted). Detailed labelling of the association network in Fig. 4c
(intended for magnification). 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 adjusted network, Spearman correlations were
calculated using HAllA from the residuals of a mixed-effects model with
subjects as random effects (or a simple linear model without the random
effects when only baseline samples were used) after adjusting for age, sex,
diagnosis, dysbiosis status, recruitment site, and antibiotics (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 35, sample counts in Fig. 1b, c.