There was some expected variation in certain profiles (supplementary fig. S2, Supplementary Material online), especially between environments with low numbers of RpsL, RpoB, and GyrA/ParC sequences, but overall, the phylogenetic profiles generated based on the three housekeeping genes were congruent with those generated based on all sequences within their environments.
Numbers indicate the fold change in activity caused by a mutation in a certain background (Supplementary file 2B F ).
We identified many gene families related to transposases and bacteriophages in the metagenomic data, but their over-representation was noted only in certain individuals (Supplementary Table S5).
Meanwhile with the highly efficient knockdown, the protein level of epithelial marker E-cadherin was increased, whereas the protein level of mesenchymal marker fibronectin was decreased to a certain extent (Supplementary Figure S4B, available at Carcinogenesis Online).
We also implemented the neighborhood and latent factor models, but according to our analysis their incorporation into the model does not improve the prediction accuracy significantly, although it might in certain cases (Supplementary Material).
Members within the modules are not restricted to a certain cellular localization (supplementary fig. 1, Supplementary Material online).
As development proceeds there is a gradual increase in the polyadenylation levels of certain maternal mRNAs (supplementary material Table S7), whereas others gradually become de-adenylated (supplementary material Table S8).
Hence, a certain number of supplementary equations are required.
The undistorted amplification curves for these quantitative PCR reactions indicate that the 2-fold elevation of DNA signal amplified by primer sets 2 6 reflects the presence of 2-fold greater genomic DNA before amplification rather than aberrant amplification efficiency in certain PCR reactions (Supplementary Fig. S1).
The predicted ORFs use all regular codons to encode the 20 standard amino acids, and no significant preference for certain codons was observed (supplementary table 1, Supplementary Material online).
