1B
strains<-c("N2", "rict-1(mg360)", "rict-1(ft7)", "sgk-1(ok538)", "akt-1(mg306)", "akt-2", "pkc-2")
foods <- "OP50"
TORC2<-read.csv(file.path(pathname, "extdata/1B_2D_rict-1_TORC2.csv"), header=TRUE) %>% dauergut::format_dauer(p.dauer = "non") #including partial/pd as non-dauer due to excess zeros.
lm <- TORC2 %>% dauer_ANOVA()
#stan
stan.glmm <- TORC2 %>% dauergut::run_dauer_stan()
contrasts<-dauergut::dunnett_contrasts(lm, ref.index = 1, "genotype")
mixed<-dauergut::getStan_CIs(stan.glmm, type = "dauer")
plot.contrasts<-c("",contrasts$prange[1:6])
labels = c("WT", "rict-1(mg360)", "rict-1(ft7)", "sgk-1(ok538)", "akt-1(mg306)", "akt-2(ok393)", "pkc-2(ok328)") %>% stringr::str_wrap(width = 10)
(p<-dauergut::plot_CIs(TORC2, title='TORC2 prevents high temperature dauer formation', plot.contrasts, ypos = 1.075, type = "dauer", labels = labels))
Figure 1B
TORC2 controls high temperature-induced dauer formation. Increased dauer formation occurs in TORC2-specific rict-1 mutants, as well as in mutants of TORC2 targets sgk-1 and akt-1. Plot shows proportion of dauers formed by animals of the indicated genotypes at 27°C. Each black dot indicates the proportion of dauers formed in a single assay. Arrested L3 and/or partial/post dauers are included as non-dauers due to excess arrest in rict-1(ft7). Horizontal black bar indicates median. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the number of independent experiments with at least 25 and 9 animals each scored for non-transgenic and transgenic animals, respectively. For transgenic rescues, data are combined from 2 independent lines, with the exception of ges-1p constructs, in which one line was analyzed. ***
- P<0.001 compared to wild-type (ANOVA with Dunnett-type multivariate-t adjustment for 1B and Tukey-type multivariate-t adjustment for 1C); ***
- P<0.001 compared to corresponding mutant animals. P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively.
library(sjPlot)
sjt.lm(lm, depvar.labels = "proportion of dauers (ANOVA)", show.se = TRUE)
|
|
proportion of dauers (ANOVA)
|
|
|
B
|
CI
|
std. Error
|
p
|
(Intercept)
|
|
0.27
|
0.21 – 0.33
|
0.03
|
<.001
|
genotype
|
rict-1(mg360)
|
|
0.67
|
0.58 – 0.76
|
0.05
|
<.001
|
rict-1(ft7)
|
|
0.63
|
0.50 – 0.76
|
0.06
|
<.001
|
sgk-1(ok538)
|
|
0.34
|
0.22 – 0.45
|
0.06
|
<.001
|
akt-1(mg306)
|
|
0.68
|
0.56 – 0.81
|
0.06
|
<.001
|
akt-2
|
|
0.03
|
-0.11 – 0.17
|
0.07
|
.660
|
pkc-2
|
|
-0.25
|
-0.36 – -0.13
|
0.06
|
<.001
|
Observations
|
|
69
|
R2 / adj. R2
|
|
.877 / .865
|
pairwise comparisons (Dunnett)
rict-1(mg360) - N2 |
0.6680907 |
0.0457575 |
62 |
14.6006908 |
0.0000000 |
*** |
rict-1(ft7) - N2 |
0.6293179 |
0.0635012 |
62 |
9.9103326 |
0.0000000 |
*** |
sgk-1(ok538) - N2 |
0.3375392 |
0.0570696 |
62 |
5.9145186 |
0.0000008 |
*** |
akt-1(mg306) - N2 |
0.6835682 |
0.0635012 |
62 |
10.7646523 |
0.0000000 |
*** |
akt-2 - N2 |
0.0301690 |
0.0682112 |
62 |
0.4422887 |
0.9975895 |
p~1 |
pkc-2 - N2 |
-0.2467089 |
0.0570696 |
62 |
-4.3229489 |
0.0003475 |
*** |
Bayesian credible intervals
N2 |
0.2941140 |
0.1685863 |
0.4714586 |
0.2446274 |
0.3467727 |
rict-1(mg360) |
0.9633932 |
0.8927355 |
0.9875899 |
0.9473462 |
0.9747217 |
rict-1(ft7) |
0.8996555 |
0.6630829 |
0.9750949 |
0.8448562 |
0.9372747 |
sgk-1(ok538) |
0.6039456 |
0.2861732 |
0.8526753 |
0.4971906 |
0.7019556 |
akt-1(mg306) |
0.9649093 |
0.8472189 |
0.9927722 |
0.9419640 |
0.9791813 |
akt-2 |
0.2714936 |
0.0730530 |
0.6266923 |
0.1837610 |
0.3822809 |
pkc-2 |
0.0119781 |
0.0023949 |
0.0490971 |
0.0073032 |
0.0201653 |
1C
strains<-c("N2","rict-1(mg360)",
"rict-1(mg360); ex[ges1]",
"rict-1(mg360); ex[gpa4]",
"rict-1(ft7)",
"rict-1(ft7); ex[ges1]",
"rict-1(ft7); ex[elt2]",
"rict-1(ft7); ex[ifb2]",
"sgk-1(ok538)",
"sgk-1(ok538); ex[ges1]",
"akt-1(mg306)",
"akt-1(mg306); ex[ges1]")
foods = "OP50"
gutresc<-read.csv(file.path(pathname, "extdata/1C_ges-1_rescue_rict_sgk.csv")) %>% dauergut::format_dauer(p.dauer = "non") %>%
mutate(allele = factor(allele, levels = c("WT","mg360","ft7","ok538","mg306")))
gutresc %<>% dplyr::mutate(adj.pct = case_when(.$pct == 0 ~ 0.01, .$pct == 1 ~ 0.99, TRUE ~ .$pct))
lm <- gutresc %>% dauer_ANOVA()
stan.glmm <- gutresc %>% dauergut::run_dauer_stan()
contrasts<-dauergut::tukey_contrasts(lm, "genotype")
mixed<-stan.glmm %>% dauergut::getStan_CIs(type="dauer")
plot.contrasts<-c("",contrasts$prange[1], "", "", contrasts$prange[4], "","","", contrasts$prange[8],"",contrasts$prange[10],"")
plot.contrasts.2<-c("", "",contrasts$prange[12:13],"",contrasts$prange[39:41],"", contrasts$prange[61],"", contrasts$prange[66])
labels <- c("WT","rict-1(mg360)",
"rict-1(mg360); +ges-1p::rict-1",
"rict-1(mg360); +gpa-4p::rict-1",
"rict-1(ft7)",
"rict-1(ft7); +ges-1p::rict-1",
"rict-1(ft7); +elt-2p::rict-1",
"rict-1(ft7); +ifb-2p::rict-1",
"sgk-1(ok538)",
"sgk-1(ok538); +ges-1p::sgk-1",
"akt-1(mg306)",
"akt-1(mg306); +ges-1p::akt-1") %>% stringr::str_wrap(width=10)
(p<-dauergut::plot_CIs(gutresc, title="TORC2 components act in the intestine to regulate dauer formation", plot.contrasts, plot.contrasts.2=plot.contrasts.2, ypos = 1.075,type = "dauer", offset = 0, labels = labels))
Figure 1C
mTORC2 acts in the intestine to inhibit high-temperature dauer formation. Increased dauer formation of rict-1 and sgk-1 mutants is rescued by intestinal-specific expression. akt-1 mutants were not rescued using this promoter. Dauers formed by animals of the indicated genotypes at 27°C. Each black dot indicates the proportion of dauers formed in a single assay. Horizontal black bar indicates median. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the number of independent experiments with at least 25 and 9 animals each scored for non-transgenic and transgenic animals, respectively. For transgenic rescues, data are combined from 2 independent lines, with the exception of ges-1p constructs, in which one line was analyzed. ***
- P<0.001 compared to wild-type (ANOVA with Dunnett-type multivariate-t adjustment for 1B and Tukey-type multivariate-t adjustment for 1C); ***
- P<0.001 compared to corresponding mutant animals. P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively.
library(sjPlot)
sjt.lm(lm, depvar.labels = "proportion of dauers (ANOVA)", show.se = TRUE)
|
|
proportion of dauers (ANOVA)
|
|
|
B
|
CI
|
std. Error
|
p
|
(Intercept)
|
|
0.27
|
0.22 – 0.32
|
0.02
|
<.001
|
genotype
|
rict-1(mg360)
|
|
0.69
|
0.59 – 0.79
|
0.05
|
<.001
|
rict-1(mg360); ex[ges1]
|
|
-0.12
|
-0.22 – -0.03
|
0.05
|
.011
|
rict-1(mg360); ex[gpa4]
|
|
0.66
|
0.57 – 0.75
|
0.05
|
<.001
|
rict-1(ft7)
|
|
0.66
|
0.57 – 0.75
|
0.05
|
<.001
|
rict-1(ft7); ex[ges1]
|
|
-0.03
|
-0.13 – 0.07
|
0.05
|
.556
|
rict-1(ft7); ex[elt2]
|
|
0.13
|
0.02 – 0.23
|
0.05
|
.017
|
rict-1(ft7); ex[ifb2]
|
|
0.06
|
-0.06 – 0.17
|
0.06
|
.344
|
sgk-1(ok538)
|
|
0.44
|
0.33 – 0.56
|
0.06
|
<.001
|
sgk-1(ok538); ex[ges1]
|
|
-0.08
|
-0.20 – 0.03
|
0.06
|
.155
|
akt-1(mg306)
|
|
0.71
|
0.60 – 0.83
|
0.06
|
<.001
|
akt-1(mg306); ex[ges1]
|
|
0.72
|
0.60 – 0.83
|
0.06
|
<.001
|
Observations
|
|
112
|
R2 / adj. R2
|
|
.884 / .871
|
pairwise comparisons (Tukey)
N2 - rict-1(mg360) |
-0.6909880 |
0.0518355 |
100 |
-13.3303901 |
0.0000000 |
*** |
N2 - rict-1(mg360); ex[ges1] |
0.1241772 |
0.0476694 |
100 |
2.6049685 |
0.0155310 |
p~0.016 |
N2 - rict-1(mg360); ex[gpa4] |
-0.6605064 |
0.0460611 |
100 |
-14.3397941 |
0.0000000 |
*** |
N2 - rict-1(ft7) |
-0.6599220 |
0.0476694 |
100 |
-13.8437300 |
0.0000000 |
*** |
N2 - rict-1(ft7); ex[ges1] |
0.0305997 |
0.0518355 |
100 |
0.5903222 |
0.6119370 |
p~0.61 |
N2 - rict-1(ft7); ex[elt2] |
-0.1258822 |
0.0518355 |
100 |
-2.4284924 |
0.0237990 |
p~0.024 |
N2 - rict-1(ft7); ex[ifb2] |
-0.0552211 |
0.0581192 |
100 |
-0.9501352 |
0.4287936 |
p~0.43 |
N2 - sgk-1(ok538) |
-0.4428609 |
0.0581192 |
100 |
-7.6198664 |
0.0000000 |
*** |
N2 - sgk-1(ok538); ex[ges1] |
0.0831857 |
0.0581192 |
100 |
1.4312943 |
0.2052121 |
p~0.21 |
N2 - akt-1(mg306) |
-0.7145009 |
0.0581192 |
100 |
-12.2937048 |
0.0000000 |
*** |
N2 - akt-1(mg306); ex[ges1] |
-0.7176764 |
0.0581192 |
100 |
-12.3483425 |
0.0000000 |
*** |
rict-1(mg360) - rict-1(mg360); ex[ges1] |
0.8151652 |
0.0610818 |
100 |
13.3454703 |
0.0000000 |
*** |
rict-1(mg360) - rict-1(mg360); ex[gpa4] |
0.0304817 |
0.0598351 |
100 |
0.5094278 |
0.6516490 |
p~0.65 |
rict-1(mg360) - rict-1(ft7) |
0.0310660 |
0.0610818 |
100 |
0.5085968 |
0.6516490 |
p~0.65 |
rict-1(mg360) - rict-1(ft7); ex[ges1] |
0.7215877 |
0.0643859 |
100 |
11.2072381 |
0.0000000 |
*** |
rict-1(mg360) - rict-1(ft7); ex[elt2] |
0.5651058 |
0.0643859 |
100 |
8.7768615 |
0.0000000 |
*** |
rict-1(mg360) - rict-1(ft7); ex[ifb2] |
0.6357669 |
0.0695447 |
100 |
9.1418477 |
0.0000000 |
*** |
rict-1(mg360) - sgk-1(ok538) |
0.2481271 |
0.0695447 |
100 |
3.5678807 |
0.0009148 |
*** |
rict-1(mg360) - sgk-1(ok538); ex[ges1] |
0.7741738 |
0.0695447 |
100 |
11.1320344 |
0.0000000 |
*** |
rict-1(mg360) - akt-1(mg306) |
-0.0235128 |
0.0695447 |
100 |
-0.3380969 |
0.7589989 |
p~0.76 |
rict-1(mg360) - akt-1(mg306); ex[ges1] |
-0.0266883 |
0.0695447 |
100 |
-0.3837582 |
0.7353996 |
p~0.74 |
rict-1(mg360); ex[ges1] - rict-1(mg360); ex[gpa4] |
-0.7846836 |
0.0562644 |
100 |
-13.9463561 |
0.0000000 |
*** |
rict-1(mg360); ex[ges1] - rict-1(ft7) |
-0.7840992 |
0.0575885 |
100 |
-13.6155604 |
0.0000000 |
*** |
rict-1(mg360); ex[ges1] - rict-1(ft7); ex[ges1] |
-0.0935776 |
0.0610818 |
100 |
-1.5320041 |
0.1733227 |
p~0.173 |
rict-1(mg360); ex[ges1] - rict-1(ft7); ex[elt2] |
-0.2500595 |
0.0610818 |
100 |
-4.0938460 |
0.0001537 |
*** |
rict-1(mg360); ex[ges1] - rict-1(ft7); ex[ifb2] |
-0.1793984 |
0.0664974 |
100 |
-2.6978240 |
0.0122898 |
p~0.012 |
rict-1(mg360); ex[ges1] - sgk-1(ok538) |
-0.5670381 |
0.0664974 |
100 |
-8.5272183 |
0.0000000 |
*** |
rict-1(mg360); ex[ges1] - sgk-1(ok538); ex[ges1] |
-0.0409915 |
0.0664974 |
100 |
-0.6164370 |
0.6029569 |
p~0.6 |
rict-1(mg360); ex[ges1] - akt-1(mg306) |
-0.8386781 |
0.0664974 |
100 |
-12.6121875 |
0.0000000 |
*** |
rict-1(mg360); ex[ges1] - akt-1(mg306); ex[ges1] |
-0.8418536 |
0.0664974 |
100 |
-12.6599413 |
0.0000000 |
*** |
rict-1(mg360); ex[gpa4] - rict-1(ft7) |
0.0005843 |
0.0562644 |
100 |
0.0103857 |
0.9917342 |
p~1 |
rict-1(mg360); ex[gpa4] - rict-1(ft7); ex[ges1] |
0.6911060 |
0.0598351 |
100 |
11.5501788 |
0.0000000 |
*** |
rict-1(mg360); ex[gpa4] - rict-1(ft7); ex[elt2] |
0.5346241 |
0.0598351 |
100 |
8.9349594 |
0.0000000 |
*** |
rict-1(mg360); ex[gpa4] - rict-1(ft7); ex[ifb2] |
0.6052852 |
0.0653541 |
100 |
9.2616222 |
0.0000000 |
*** |
rict-1(mg360); ex[gpa4] - sgk-1(ok538) |
0.2176455 |
0.0653541 |
100 |
3.3302483 |
0.0019578 |
** |
rict-1(mg360); ex[gpa4] - sgk-1(ok538); ex[ges1] |
0.7436921 |
0.0653541 |
100 |
11.3794210 |
0.0000000 |
*** |
rict-1(mg360); ex[gpa4] - akt-1(mg306) |
-0.0539945 |
0.0653541 |
100 |
-0.8261836 |
0.4790578 |
p~0.48 |
rict-1(mg360); ex[gpa4] - akt-1(mg306); ex[ges1] |
-0.0571700 |
0.0653541 |
100 |
-0.8747727 |
0.4646272 |
p~0.46 |
rict-1(ft7) - rict-1(ft7); ex[ges1] |
0.6905217 |
0.0610818 |
100 |
11.3048694 |
0.0000000 |
*** |
rict-1(ft7) - rict-1(ft7); ex[elt2] |
0.5340398 |
0.0610818 |
100 |
8.7430275 |
0.0000000 |
*** |
rict-1(ft7) - rict-1(ft7); ex[ifb2] |
0.6047009 |
0.0664974 |
100 |
9.0935972 |
0.0000000 |
*** |
rict-1(ft7) - sgk-1(ok538) |
0.2170611 |
0.0664974 |
100 |
3.2642030 |
0.0023622 |
** |
rict-1(ft7) - sgk-1(ok538); ex[ges1] |
0.7431078 |
0.0664974 |
100 |
11.1749842 |
0.0000000 |
*** |
rict-1(ft7) - akt-1(mg306) |
-0.0545788 |
0.0664974 |
100 |
-0.8207663 |
0.4790578 |
p~0.48 |
rict-1(ft7) - akt-1(mg306); ex[ges1] |
-0.0577544 |
0.0664974 |
100 |
-0.8685200 |
0.4646272 |
p~0.46 |
rict-1(ft7); ex[ges1] - rict-1(ft7); ex[elt2] |
-0.1564819 |
0.0643859 |
100 |
-2.4303767 |
0.0237990 |
p~0.024 |
rict-1(ft7); ex[ges1] - rict-1(ft7); ex[ifb2] |
-0.0858208 |
0.0695447 |
100 |
-1.2340386 |
0.2848105 |
p~0.28 |
rict-1(ft7); ex[ges1] - sgk-1(ok538) |
-0.4734606 |
0.0695447 |
100 |
-6.8080056 |
0.0000000 |
*** |
rict-1(ft7); ex[ges1] - sgk-1(ok538); ex[ges1] |
0.0525861 |
0.0695447 |
100 |
0.7561481 |
0.5135916 |
p~0.51 |
rict-1(ft7); ex[ges1] - akt-1(mg306) |
-0.7451005 |
0.0695447 |
100 |
-10.7139833 |
0.0000000 |
*** |
rict-1(ft7); ex[ges1] - akt-1(mg306); ex[ges1] |
-0.7482760 |
0.0695447 |
100 |
-10.7596446 |
0.0000000 |
*** |
rict-1(ft7); ex[elt2] - rict-1(ft7); ex[ifb2] |
0.0706611 |
0.0695447 |
100 |
1.0160530 |
0.3960713 |
p~0.4 |
rict-1(ft7); ex[elt2] - sgk-1(ok538) |
-0.3169787 |
0.0695447 |
100 |
-4.5579140 |
0.0000269 |
*** |
rict-1(ft7); ex[elt2] - sgk-1(ok538); ex[ges1] |
0.2090680 |
0.0695447 |
100 |
3.0062396 |
0.0051334 |
** |
rict-1(ft7); ex[elt2] - akt-1(mg306) |
-0.5886186 |
0.0695447 |
100 |
-8.4638917 |
0.0000000 |
*** |
rict-1(ft7); ex[elt2] - akt-1(mg306); ex[ges1] |
-0.5917941 |
0.0695447 |
100 |
-8.5095530 |
0.0000000 |
*** |
rict-1(ft7); ex[ifb2] - sgk-1(ok538) |
-0.3876397 |
0.0743464 |
100 |
-5.2139687 |
0.0000019 |
*** |
rict-1(ft7); ex[ifb2] - sgk-1(ok538); ex[ges1] |
0.1384069 |
0.0743464 |
100 |
1.8616491 |
0.0901854 |
p~0.09 |
rict-1(ft7); ex[ifb2] - akt-1(mg306) |
-0.6592797 |
0.0743464 |
100 |
-8.8676763 |
0.0000000 |
*** |
rict-1(ft7); ex[ifb2] - akt-1(mg306); ex[ges1] |
-0.6624552 |
0.0743464 |
100 |
-8.9103885 |
0.0000000 |
*** |
sgk-1(ok538) - sgk-1(ok538); ex[ges1] |
0.5260466 |
0.0743464 |
100 |
7.0756178 |
0.0000000 |
*** |
sgk-1(ok538) - akt-1(mg306) |
-0.2716400 |
0.0743464 |
100 |
-3.6537076 |
0.0007003 |
*** |
sgk-1(ok538) - akt-1(mg306); ex[ges1] |
-0.2748155 |
0.0743464 |
100 |
-3.6964198 |
0.0006203 |
*** |
sgk-1(ok538); ex[ges1] - akt-1(mg306) |
-0.7976866 |
0.0743464 |
100 |
-10.7293254 |
0.0000000 |
*** |
sgk-1(ok538); ex[ges1] - akt-1(mg306); ex[ges1] |
-0.8008621 |
0.0743464 |
100 |
-10.7720376 |
0.0000000 |
*** |
akt-1(mg306) - akt-1(mg306); ex[ges1] |
-0.0031755 |
0.0743464 |
100 |
-0.0427122 |
0.9808779 |
p~0.98 |
Bayesian credible intervals
N2 |
0.2793225 |
0.1833459 |
0.4066347 |
0.2431513 |
0.3185055 |
rict-1(mg360) |
0.9627715 |
0.8815987 |
0.9885193 |
0.9450084 |
0.9752851 |
rict-1(mg360); ex[ges1] |
0.1296133 |
0.0457332 |
0.3034522 |
0.0935004 |
0.1785384 |
rict-1(mg360); ex[gpa4] |
0.9170733 |
0.7598877 |
0.9740302 |
0.8811744 |
0.9436661 |
rict-1(ft7) |
0.9420074 |
0.8443246 |
0.9802061 |
0.9171760 |
0.9596365 |
rict-1(ft7); ex[ges1] |
0.2671974 |
0.0875506 |
0.5767962 |
0.1894259 |
0.3626919 |
rict-1(ft7); ex[elt2] |
0.3800157 |
0.1172738 |
0.7357145 |
0.2715965 |
0.5027534 |
rict-1(ft7); ex[ifb2] |
0.4023557 |
0.1275289 |
0.7527617 |
0.2873637 |
0.5301470 |
sgk-1(ok538) |
0.6903346 |
0.3638554 |
0.8856750 |
0.5950865 |
0.7766973 |
sgk-1(ok538); ex[ges1] |
0.1641085 |
0.0480079 |
0.4154684 |
0.1131033 |
0.2367389 |
akt-1(mg306) |
0.9881795 |
0.9461830 |
0.9977387 |
0.9794053 |
0.9930754 |
akt-1(mg306); ex[ges1] |
0.9875661 |
0.9235693 |
0.9985239 |
0.9752865 |
0.9933613 |