time    gene    value
A1.01   TMCS09g1008676  0.423176672
A1.02   TMCS09g1008676  0.911415197
A1.03   TMCS09g1008676  1.042786687
A1.04   TMCS09g1008676  0.859630996
A1.05   TMCS09g1008676  0.624891793
A1.01   TMCS09g1008677  0.304568066
A1.02   TMCS09g1008677  1.134582618
A1.03   TMCS09g1008677  1.626528999
A1.04   TMCS09g1008677  1.778379422
A1.05   TMCS09g1008677  1.922418792
A1.01   TMCS09g1008678  0.312127815
A1.02   TMCS09g1008678  0.567599868
A1.03   TMCS09g1008678  1.37594692
A1.04   TMCS09g1008678  1.655878776
A1.05   TMCS09g1008678  1.720470659

ggplot(mydata, aes(as.factor(time), value)) +
geom_hline(yintercept = 0, linetype = 2, color = "red") +
# Line for each gene
geom_line(aes(group = gene), size = 0.5, alpha = 0.3, color = "blue") +
# Trend line
geom_smooth(size = 2, se = FALSE, color = "orange") +
scale_x_continuous(breaks = factor(prova$time)) +
theme_classic()