Group-level modular topology was spatially investigated by obtaining a "benchmark" healthy modular subdivision, that is, averaging all controls' matrices and performing modularity analysis on this averaged matrix as described previously.
The released carbohydrates were analyzed both in a positive-ion mode using the super-DHB solution (Bruker Daltonik) as a matrix and in a negative-ion mode using 2′,4′,6′-trihydroxyacetophenon (THAP) as a matrix as described previously (Papac et al. 1996; Kanda et al. 2006).
For yeast and human dataset, randomization testing was carried out straightforwardly by shuffling gene labels in the expression matrix as described previously [60].
The intra-specific variations and inter-specific divergences of congeneric species in the dicotyledons, monocotyledons, gymnosperms, ferns, mosses, and animals were calculated using a K2P distance matrix, as described previously [11], [31], [32].
Primary chondrocytes were isolated from the surrounding matrix as described previously [ 2].
The principal modes of structural variation are determined upon principal component analysis (PCA) of the covariance matrix, as described previously (Bakan and Bahar, 2009).
All measured congeners were normalized to PCB 153 and transformed by the natural logarithm prior to PCA analysis to obtain a unitless profile matrix as described previously [ 10].
An internal amplification control targeting bacteriophage lambda DNA was included to determine inhibitory effects of the sample matrix as described previously [ 11].
Confidence intervals of the estimated parameters were calculated from the square root of the diagonal of the covariance matrix, as described previously [ 25].
Similar to the Zscore method, we define a robust standardization (Rscore) of the X matrix as described previously [ 10]: (4) Rscor e ij = x ij − median x i mad x i where the mad function is the median absolute deviation.
