df <- data.frame(G1=c("a","b","c","d","e"),
                 G2=c("a","c","b","d","e"),
                 G3=c("a","d","e","b","c"),
                 G4=c("a","b","c","d","e"))

rank <- data.frame(term=c("a","b","c","d","e"),
                   G1=c(1:5),
                   G2=c(1,3,2,4,5),
                   G3=c(1,4,5,2,3),
                   G4=c(1:3,4,5))

df <- data.frame(G1=c("bta-let-7a-1","bta-let-7b", "bta-mir-26a-1", "bta-mir-21"),
                 G2=c("bta-mir-21", "bta-let-7a-1", "bta-let-7b", "bta-mir-26a-1"),
                 G3=c("bta-mir-26a-1", "bta-mir-21", "bta-let-7a-1", "bta-let-7b"),
                 G4=c("bta-let-7b","bta-mir-26a-1", "bta-mir-21", "bta-let-7a-1"))

rank <- as.data.frame(lapply(df, as.integer))

as.data.frame(lapply(df, as.integer))
#  G1 G2 G3 G4
#1  1  1  1  1
#2  2  3  4  2
#3  3  2  5  3
#4  4  4  2  4
#5  5  5  3  5

as.data.frame(lapply(lapply(df, function(x)
                  factor(as.character(x), as.character(df$G1))), as.integer))