Assuming that I am understanding what you are wanting, this formula is going to be in one column where each subsequent row will have a higher number (3,4,5,...) If that is the case, unlock your formula to read:
=INDEX(gdsc_en_input_w2!$A$1:$YE$13848,MATCH("AKT2",gdsc_en_input_w2!$A$1:$A$13848,0),MATCH($A3,gdsc_en_input_w2!$A$1:$YE$1,0)) (I removed the $ in-front of the 3)
Paste that into the whatever your starting cell is, then auto-fill