Table 2.
Partial correlation analyses between the distances in codon usage frequencies and distances of all other variables.
| Test variable | Control variables | Partial correlation with distances in absCUFs frequency (distances calculated by Euclidean distance method) | Partial correlation with distances in absCUFs frequency (distances calculated by Bray-Curtis dissimilarity method) |
|---|---|---|---|
| AminoAcid frequency | GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer |
ρ = −0.3; P = 0.00E + 00 |
ρ = −0.394; P = 0.00E + 00 |
| GO-BP | GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid |
ρ = 0.088; P = 1.73E−153 |
ρ = 0.352; P = 0.00E + 00 |
| GO-CC | GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP |
ρ = 0.19; P = 0.00E + 00 |
-------- |
| GO-MF | family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC |
ρ = 0.037; P = 7.36E−28 |
ρ = −0.342; P = 0.00E + 00 |
| Family | genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF |
ρ = 0.017; P = 2.44E−07 |
ρ = 0.029; P = 1.06E−17 |
| Genus | order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family |
ρ = 0.101; P = 4.12E−200 |
ρ = −0.001; P = 8.10E−01 |
| Order | phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus |
ρ = 0.101; P = 1.64E-198 |
ρ = 0.037; P = 5.10E−28 |
| Phylum | GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order |
ρ = −0.147; P = 0.00E + 00 |
ρ = −0.12; P = 1.57E−281 |
| GC-distance | k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum |
ρ = 0.613; P = 0.00E + 00 |
ρ = 0.306; P = 0.00E + 00 |
| k2-mer | k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance |
ρ = 0.09; P = 3.27E−158 |
ρ = 0.038; P = 1.71E−30 |
| k4-mer | k5-mer & k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer |
ρ = 0.1; P = 1.36E−196 |
ρ = 0.194; P = 0.00E + 00 |
| k5-mer | k6-mer & k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer |
ρ = 0.308; P = 0.00E + 00 |
ρ = 0.005; P = 1.03E−01 |
| k6-mer | k7-mer & k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer |
ρ = −0.197; P = 0.00E + 00 |
ρ = 0.097; P = 7.38E−184 |
| k7-mer | k8-mer & k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer |
ρ = −0.011; P = 8.20E−04 |
ρ = −0.143; P = 0.00E + 00 |
| k8-mer | k9-mer & k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer |
ρ = 0.08; P = 2.76E−126 |
ρ = 0.105; P = 2.55E−214 |
| k9-mer | k10-mer & AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer |
ρ = 0.021; P = 2.73E−10 |
ρ = 0.049; P = 1.18E−48 |
| k10-mer | AminoAcid & GO-BP & GO-CC & GO-MF & family & genus & order & phylum & GC-distance & k2-mer & k4-mer & k5-mer & k6-mer & k7-mer & k8-mer & k9-mer |
ρ = −0.074; P = 2.90E−108 |
ρ = −0.05; P = 4.94E−50 |
Partial correlations were conducted between two variables controlling the effects of all other variables where the one variable is distances in codon usage frequencies (absCUFs) and the other variable is either distances in GC content or amino acid usage or k-mer frequencies or distances in GO terms’ abundance or in taxonomic abundance. Distances in Gene Ontology (GO) terms’ frequencies among the samples were calculated considering the relative abundance of 500 GO biological process, 500 GO molecular function, and 100 GO cellular component terms separately. Taxonomic distances among the samples were calculated considering relative abundance of selected taxons under four taxonomic ranks (order, phylum, family, genus) separately (see main text). All the distances were calculated following two methods, (i) Euclidean, and (ii) BC dissimilarity methods. Correlation values were tested considering the distances calculated by each of these two methods separately. Therefore, there are two columns for correlation values (one for Euclidean distance and another for Bray-Curtis dissimilarity). Here ρ stands for correlation coefficient and significance levels were shown with P-values.