To reduce the amount of missing data in the final matrix, we included genes that were represented by at least half (10) of the taxa in this study.
We included the matrix type column in this table for providing details of the comparisons to the readers.
As IL-1β also antagonizes the matrix-producing action of BMP7, we included it in this experimental set as a control.
The weight matrix W we used included the reciprocal of the maximum concentration of the corresponding metabolite in all the time points.
These homography matrices are included in the dataset [34].
To test for overrepresentation of motifs, we used a set of 1038 position weight matrices, including matrices from JASPAR [ 52] and PLACE [ 53] and followed the procedure in [ 35].
For metabolites measured in common by both NMR and MS, correlation matrices included data measured by NMR.
When CMI = 5, all matrices included in the test are congruent.
The matrices included 171 MM, 136 FF dyads, and 323 MF dyads.
However, these latter matrices included a few more positions, generating PSSMs of 14 and 16 columns (Table 1).
