Table I

Comparison of TAP-MudPIT analyses using different bipartite affinity tags to Gcn5p

Samples were prepared and analyzed as described in “Experimental Procedures.” The column “Gene product” represents the name of the gene product recovered and known to interact with Gcn5p according to GRID, MIPS, and YPD. “Exp. 1–3” represent three independent affinity purifications of Gcn5p-HPM. “TAP tag” and “Modified TAP tag” represent TAP-MudPIT experiments performed with strains in which the GCN5 locus was tagged with either the TAP (13) or modified TAP tag from (10). The numbers of unique peptides from each open reading frame that were sequenced are shown (with the total number of sequenced peptides in parentheses). The last column lists the frequency with which the gene product is found in the entire dataset (n = 22). For example, a gene product found in association with a single bait has a frequency of 4.55% (1/22). The GRID, MIPS, and YPD interaction databases contain 83 additional gene products classified as interacting with Gcn5p, but not recovered in our analyses.

Gene productHPM tagTAP tagModified TAP tagFrequency in ref. set
Exp. 1Exp. 2Exp. 3
Gcn5p41 (41)25 (25)65 (65)19 (19)21 (21)4.55%
Ada2p22 (22)15 (15)36 (36)22 (22)36 (36)4.55%
Adh1p6 (8)10 (14)2 (4)86.36%
Ahc1p16 (16)7 (7)22 (22)7 (7)31 (31)4.55%
Clu1p5 (5)45.45%
Eno2p3 (7)2 (3)22.73%
Fba1p6 (6)9 (9)68.18%
Hfi1p9 (9)3 (3)23 (23)20 (20)23 (23)4.55%
Ngg1p30 (30)29 (29)53 (53)43 (43)68 (68)4.55%
Pfk2p2 (2)3 (3)36.36%
Pgk1p4 (4)0.00%
Rpg1p5 (5)0.00%
Sgf29p19 (19)4 (4)17 (17)21 (21)32 (32)4.55%
Sgf73p10 (10)4 (4)18 (18)25 (25)29 (29)4.55%
Spt20p8 (8)6 (6)26 (26)26 (26)29 (29)4.55%
Spt3p4 (4)12 (12)12 (12)8 (8)4.55%
Spt7p9 (9)10 (10)28 (28)49 (49)52 (53)4.55%
Spt8p11 (11)6 (6)23 (23)18 (18)20 (20)4.55%
Swi1p3 (3)9.09%
Taf10p4 (4)9 (9)7 (7)11 (11)4.55%
Taf12p7 (7)6 (6)16 (16)28 (28)23 (23)4.55%
Taf5p16 (16)10 (10)35 (35)46 (46)37 (37)4.55%
Taf6p6 (6)5 (5)23 (23)24 (24)26 (26)4.55%
Taf9p2 (2)2 (2)7 (7)7 (7)15 (15)4.55%
Tra1p11 (11)7 (7)35 (35)82 (82)99 (99)4.55%
Ubp8p13 (13)17 (17)18 (18)4.55%
Yap1p6 (6)12 (12)0.00%