Table 1 Positive validation set. The list of the protein pairs that our known to interact. This list was used to evaluate PIPE's accuracy to detect protein interactions.

YAL021C

YNR052C

YDR394W

YOR117W

YJL187C

YBR133C

YAL032C

YDR416W

YDR416W

YKL095W

YJR068W

YBR087W

YAR003W

YBR175W

YDR477W

YGL115W

YJR076C

YHR107C

YBL007C

YHR016C

YDR490C

YPL004C

YJR093C

YPR107C

YBL045C

YPR191W

YDR490C

YGR086C

YJR093C

YMR061W

YBL056W

YDR071C

YEL037C

YER162C

YKL028W

YDR311W

YBR102C

YLR166C

YER027C

YDR477W

YKL135C

YPR029C

YBR102C

YDR166C

YER027C

YGL115W

YKL135C

YPL259C

YBR103W

YIL112W

YER081W

YIL074C

YKL135C

YHL019C

YBR123C

YOR110W

YER095W

YML032C

YKL139W

YJL006C

YBR125C

YDR071C

YFL039C

YNL138W

YKR046C

YLR291C

YBR126C

YMR261C

YFR004W

YOR261C

YKR048C

YCL024W

YBR126C

YML100W

YGL112C

YBR198C

YKR068C

YBR254C

YBR135W

YDL155W

YGL190C

YML109W

YKR068C

YDR472W

YBR154C

YOR116C

YGL195W

YFR009W

YLR103C

YLR274W

YBR160W

YBR135W

YGL208W

YGL115W

YLR103C

YBR202W

YBR170C

YGR048W

YGL237C

YOR358W

YLR166C

YPR055W

YBR200W

YER114C

YGR040W

YDL159W

YLR226W

YPR161C

YBR200W

YAL041W

YGR040W

YPL049C

YLR274W

YBR202W

YBR254C

YDR472W

YGR240C

YMR205C

YLR291C

YGR083C

YCR052W

YFR037C

YGR261C

YBR288C

YLR371W

YDL203C

YCR077C

YDL160C

YHR148W

YJR002W

YLR423C

YBR217W

YCR093W

YPR072W

YHR166C

YBL084C

YLR423C

YNL182C

YDL002C

YER092W

YHR172W

YNL126W

YLR423C

YGL237C

YDL002C

YGL150C

YHR172W

YLR212C

YML077W

YDR472W

YDL092W

YKL122C

YIL021W

YOL005C

YML094W

YLR200W

YDL126C

YKL213C

YIL033C

YKL166C

YML098W

YML015C

YDL126C

YBR170C

YIL033C

YJL164C

YMR091C

YFR037C

YDL147W

YDR179C

YIL038C

YPR072W

YMR146C

YDR429C

YDL216C

YMR025W

YIL062C

YKL013C

YMR167W

YNL082W

YDR074W

YMR261C

YJL005W

YNL138W

YMR231W

YDL077C

YDR074W

YML100W

YJL008C

YOR117W

YNL126W

YLR212C

YDR148C

YFR049W

YJL124C

YBL026W

YNR006W

YHL002W

YDR179C

YMR025W