TABLE 2.
Inferred human–chimp expression evolution parameters from probe-set data
| Data set | HC | HCR | HCO | HCRO |
|---|---|---|---|---|
| t1a | 1.42 (1.25–1.65) | 1.19 (1.10–1.31) | 1.20 (1.11–1.33) | 0.82 (0.77–0.88) |
| t2 | 0.42 (0.33–0.52) | 0.42 (0.36–0.48) | 0.28 (0.23–0.33) | 0.32 (0.29–0.35) |
| t3 | 0.95 (0.81–1.08) | 0.28 (0.16–0.41) | 1.77 (1.66–1.88) | |
| t4 | 1.31 (1.15–1.48) | 2.34 (2.09–2.62) | 0.15 (0.10–0.19) | |
| t5 | 1.0 (0.9–1.1) | |||
| t6 | 0.34 (0.26–0.41) | |||
| σ | 0.07 (0.05–0.12) | 0.08 (0.05–0.11) | 0.08 (0.05–0.13) | 0.27 (0.25–0.30) |
| a | 0.58 (0.53–0.62) | 0.44 (0.41–0.46) | 0.45 (0.42–0.47) | −0.43 (−0.45–0.41) |
| p | 0.01 (0–0.01) | 0.01 (0.01–0.01) | 0.01 (0.00–0.01) | 0.49 (0.03–0.97) |
| var | 0.34 (0.29–0.40) | 0.20 (0.18–0.22) | 0.21 (0.19–0.23) | 0.26 (0.25–0.28) |
| div × var | 0.63 (0.59–0.67) | 0.32 (0.30–0.34) | 0.31 (0.29–0.33) | 0.30 (0.29–0.31) |
| log2(t1/t2) | 1.8 (1.4–2.2) | 1.5 (1.3–1.8) | 2.1 (1.8–2.4) | 1.4 (1.2–1.6) |
| t1/t2 | 3.4 (2.7–4.4) | 2.9 (2.4–3.4) | 4.3 (3.5–5.4) | 2.6 (2.3–3.0) |
| n | 9,806 | 8,303 | 9,273 | 10,427 |
| ESS | 951 | 536 | 334 | 354 |
Estimates (posterior medians and 95% credible intervals) of branch lengths and model parameters from probe-set level data, using various choices of outgroups: none (HC, human–chimp), one outgroup (rhesus macaque, HCR; or orangutan, HCO), or two outgroup species (HCRO). For inferences from data without quantile–quantile normalization see supplemental Table 4.
t1, length of human branch; t2, length of chimpanzee branch; a and σ, shape parameters of the distribution of change magnitudes; p, proportion of outliers; var, event variance (a2 + σ2); div, expected number of events between human and chimpanzee (t1 + t2); n, number of probe sets in the data set; ESS, effective sample size for t1.