Table 3.
SLACa Predicted Sites of Positive Selection in Brain and Lymphoid Tissue
| |
|
Consensus amino acid (frequency)b |
|
|||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Codon (NL4-3 residue #) | Tissue | MACS1 | MACS2 | MACS3 | UK6 | p Valuec | ||||
| 10 (10) | Brain | L | (10/10) | V | (7/7) | V | (6/6) | M | (4/7) | 0.0049 |
| Lymphoid | S | (7/7) | G | (25/26) | L | (25/28) | K | (5/6) | ||
| 22 (22) | Brain | R | (10/10) | R | (7/7) | R | (6/6) | R | (7/7) | 0.0935 |
| Lymphoid | R | (7/7) | R | (23/26) | R | (25/28) | Q | (4/6) | ||
| 32 (28) | Brain | D | (10/10) | D | (6/7) | A | (6/6) | D | (6/7) | 0.0672 |
| Lymphoid | D | (6/10) | E | (26/26) | A | (27/28) | D | (6/6) | ||
| 158 (152) | Brain | E | (10/10) | E | (7/7) | Q | (4/6) | K | (7/7) | 0.0868 |
| Lymphoid | E | (6/10) | K | (26/26) | Q | (15/28) | K | (6/6) | ||
| 194 (188) | Brain | R | (10/10) | R | (7/7) | R | (6/6) | L | (7/7) | 0.0932 |
| Lymphoid | L | (10/10) | H | (12/26) | R | (27/28) | T | (5/6) | ||
| Q | (11/26) | |||||||||
Single Likelihood Ancestor Counting (HyPhy software package) was used to reconstruct ancestral sequences at each node of the phylogenetic tree shown in Fig. 1. Substitutions are calculated at each branch and terminal node. Wherever a variation occurs, the dS and dN were calculated.
Consensus amino acid is the residue at that position in >60% of sequences. Where no consensus residue was apparent, the two most frequent residues are shown. Frequency indicates the fraction of total sequences from the tissue of each patient in which the residue occurred.
p Values are based on a two-tailed binomial distribution that measures how likely the observed proportion of synonymous substitutions differs from the expected value derived from a global dN/dS ratio fitted to reconstructed ancestral states at each patient-specific node of the maximum likelihood phylogenetic tree. p-values < 0.1 were considered significant.