Yes, you can use a colon to present the two types of tissue. To make the association clear, you should add "respectively":
In contrast, X and Y expression increased in only one tissue [in each case]: pancreas and pituitary, respectively.
Note that I deleted an instance of "in" and changed the phrase to "expression increased," which is a much more common expression in the literature.
The addition of "in each case" further clarifies your meaning, as would a preceding sentence that reads something like "Expression of A, B, and C increased in both E and G."
You could also use, for example,
A, B, and C expression was elevated in multiple tissue types. In contrast, X and Y expression increased only in the pancreas and in the pituitary, respectively.
Expression of A, B, and C increased in both pancreas and pituitary tissue. In contrast, X expression increased only in the pancreas, and Y expression only in the pituitary.