% Notation % Supplemental Table: over-occurence p-values % The first value is the empirical p-value, % the second is based on a Gamma distribution. % Both valuies are log10(p-value). Model=Imodel Peak cutoff=0.50 Fix mode= condition Tchn3:FwdOnOff Tchn3:FwdOffOn Tchn3:BwdOnOff Tchn3:BwdOffOn Tchn4:FwdOnOff Tchn4:FwdOffOn Tchn4:BwdOnOff Tchn4:BwdOffOn Gasch00 1M sorbitol 0.97,0.87 0.18,0.24 0.27,0.47 0.09,0.14 0.98,1.21 0.00,0.00 0.00,0.00 0.00,0.00 Gasch00 1 5 mM diamide 1.23,1.07 0.09,0.28 0.31,0.35 0.20,0.33 0.37,0.86 0.00,0.00 0.57,0.91 0.00,0.00 Gasch00 1 mM Menadione 0.00,0.00 0.08,0.17 0.27,0.66 0.30,0.36 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 Gasch00 25C 0.36,0.79 1.10,1.24 0.62,0.79 0.80,0.89 0.00,0.00 1.33,1.15 0.00,0.00 0.24,0.68 Gasch00 2 5mM DTT 0.00,0.00 0.00,0.02 1.09,1.24 0.37,0.36 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 Gasch00 adenine starvation 0.06,0.07 0.24,0.61 0.13,0.13 0.40,0.67 0.15,0.60 0.64,1.09 0.48,0.80 0.00,0.00 Gasch00 Hypo osmotic shock 0.28,0.37 0.54,0.68 0.00,0.02 1.60,1.21 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 Gasch00 Nitrogen Depletion 0.20,0.48 0.00,0.00 0.02,0.17 0.61,0.93 0.44,0.92 0.00,0.00 0.00,0.00 0.95,1.23 Gasch00 constant 0 32 mM H2O2 0.25,0.47 1.23,1.18 0.20,0.39 0.75,0.71 0.97,1.18 0.96,1.10 0.00,0.00 0.33,0.76 Gasch00 dtt 0.16,0.16 0.54,0.64 0.86,0.90 0.80,0.77 0.38,0.85 0.00,0.00 1.10,1.20 0.00,0.00 Gasch00 heat shock 2.27,2.30 0.27,0.54 1.24,1.26 0.31,0.57 0.70,0.93 0.00,0.00 0.30,0.71 0.00,0.00 Gasch01 DES459 mec1 0 02 MMS 0.07,0.42 0.35,0.54 0.05,0.36 0.09,0.31 0.00,0.00 0.43,0.93 0.00,0.00 0.00,0.00 Gasch01 DES460 0 02 MMS 0.49,0.73 0.00,0.00 0.42,0.66 0.23,0.67 0.77,1.16 0.00,0.00 0.00,0.00 0.00,0.00 Gasch01 mec1 plus gamma 0.27,0.31 0.04,0.18 0.13,0.20 1.42,1.08 0.00,0.00 0.00,0.00 0.00,0.00 0.64,0.95 Gasch01 wt plus gamma 1.00,0.77 0.17,0.43 0.33,0.32 0.33,0.58 0.75,0.97 0.00,0.00 0.00,0.00 0.00,0.00 DeRisi97 diauxic shift 0.25,0.78 0.00,0.00 1.10,1.13 0.42,0.81 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 Rando05 SD 0.19,0.18 0.86,0.81 0.15,0.16 0.59,0.66 0.00,0.00 0.70,1.13 0.19,0.63 0.64,1.03 Rando05 SD+aa 0.57,0.64 0.05,0.16 0.83,0.71 0.49,0.53 0.34,0.89 0.00,0.00 0.37,0.80 0.00,0.00 Rando05 SD+aaAR+ino 0.13,0.23 0.91,0.88 0.14,0.15 0.47,0.57 0.24,0.72 1.07,1.29 0.17,0.62 0.00,0.00 Rando05 SD+aaLI+ino 0.55,0.53 0.13,0.60 0.03,0.06 0.27,0.65 0.54,0.90 0.00,0.00 0.00,0.00 0.00,0.00 Rando05 SD+ino 0.16,0.25 0.64,0.81 0.38,0.34 0.41,0.67 0.00,0.00 0.62,1.11 0.10,0.48 0.00,0.00 Rando05 SEtOH 0.00,0.00 0.00,0.00 2.46,1.79 0.00,0.00 0.00,0.00 0.00,0.00 2.36,2.49 0.00,0.00 Rando05 SEtOH+aa 0.78,1.10 0.00,0.00 4.50,3.38 0.00,0.00 0.00,0.00 0.00,0.00 4.50,4.78 0.00,0.00 Rando05 SEtOH+aa+ino 0.73,1.06 0.00,0.00 4.20,2.38 0.00,0.00 0.00,0.00 0.00,0.00 4.50,5.02 0.00,0.00 Rando05 SEtOH+ino 1.32,1.30 0.00,0.00 3.20,2.00 0.00,0.00 1.63,1.90 0.00,0.00 2.12,2.20 0.00,0.00 Rando05 Sgal 0.70,1.01 0.00,0.00 3.22,1.94 0.00,0.00 1.42,1.62 0.00,0.00 2.46,2.32 0.00,0.00 Rando05 Sgal+aa 0.00,0.00 0.00,0.00 1.60,1.48 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 Rando05 Sgal+aa+ino 0.61,0.98 0.00,0.00 1.18,1.19 0.00,0.00 0.00,0.00 0.00,0.00 2.12,2.05 0.00,0.00 Rando05 Sgal+ino 0.23,0.76 0.00,0.00 1.59,1.33 0.00,0.00 0.00,0.00 0.00,0.00 1.72,1.82 0.00,0.00 Causton01 Acid 0.43,0.49 1.04,0.90 0.46,0.48 0.22,0.49 0.00,0.00 0.00,0.00 0.68,0.97 0.00,0.00 Causton01 Alkali 0.08,0.37 0.96,0.85 0.57,0.64 0.21,0.39 0.00,0.00 0.34,0.81 0.00,0.00 0.41,0.88 Causton01 Heat 1.42,1.41 0.00,0.00 0.32,0.33 0.70,0.96 1.86,1.38 0.00,0.00 0.14,0.57 0.00,0.00 Causton01 NaCl 0.26,0.66 0.54,0.46 1.23,1.06 0.15,0.33 0.00,0.00 0.46,0.98 0.00,0.00 0.34,0.86 Causton01 Peroxide 0.39,0.71 0.21,0.23 0.18,0.68 0.04,0.04 0.00,0.00 0.29,0.62 0.00,0.00 0.07,0.42 Causton01 Sorbitol 0.41,0.69 0.05,0.07 1.40,1.18 0.45,0.47 0.00,0.00 0.22,0.66 0.61,1.06 0.38,0.72 ORourke03 ZT WT 0.0625MKCl 1.16,1.09 0.16,0.41 1.47,1.22 0.03,0.22 0.00,0.00 0.49,0.95 0.00,0.00 0.00,0.00 ORourke03 ZT WT 0.125MKCL 0.00,0.00 0.11,0.12 0.28,0.79 0.16,0.15 0.00,0.00 0.34,0.80 0.00,0.00 0.00,0.00 ORourke03 ZT WT 0.25MKCL 0.33,0.86 0.06,0.11 0.95,1.10 0.34,0.33 0.00,0.00 0.31,0.70 1.01,1.27 0.60,0.78 ORourke03 ZT WT 0.5MKCl 0.59,0.95 0.23,0.29 1.23,1.31 0.12,0.12 0.00,0.00 0.00,0.00 0.00,0.00 0.23,0.61 ORourke03 ZT WT 1MKCL 0.96,1.07 0.44,0.48 0.46,0.86 0.09,0.09 1.60,1.64 0.96,1.02 0.00,0.00 0.00,0.00 ORourke03 ZT WT 1Msorb 0.16,0.64 0.41,0.41 0.74,0.95 0.33,0.35 0.00,0.00 0.26,0.64 0.00,0.00 0.50,0.77 ORourke03 ZT WT alpha 0.00,0.00 0.58,0.81 1.40,1.29 0.67,0.80 0.00,0.00 0.69,1.10 1.40,1.54 0.00,0.00 ORourke03 ZT hog1 0.125MKCl 1.05,0.99 0.09,0.39 2.30,1.62 0.06,0.31 0.00,0.00 0.00,0.00 2.42,1.86 0.00,0.00 ORourke03 ZT hog1 0.5MKCl 0.70,0.94 0.89,0.95 0.14,0.62 0.53,0.49 1.16,1.40 0.68,0.93 0.00,0.00 0.47,0.81 ORourke03 ZT pbs2 0.5MKCl 1.52,1.36 0.00,0.00 0.46,0.92 0.30,0.46 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 ORourke03 ZT sho1 0.5MKCl 1.30,1.23 0.11,0.11 1.66,1.37 0.07,0.11 0.00,0.00 0.00,0.00 1.22,1.42 0.20,0.60 ORourke03 ZT ssk1 0.0625MKCl 0.00,0.00 2.12,1.49 0.00,0.00 0.37,0.67 0.00,0.00 2.30,1.98 0.00,0.00 0.89,1.16 ORourke03 ZT ssk1 0.125MKCl 1.78,1.31 0.03,0.27 4.20,2.30 0.22,0.43 1.88,1.70 0.00,0.00 4.20,2.41 0.00,0.00 ORourke03 ZT ssk1 0.5MKCl 0.93,1.12 0.05,0.06 1.10,1.23 0.01,0.01 0.00,0.00 0.00,0.00 1.39,1.62 0.11,0.50 ORourke03 ZT ssk1sho1 0.5MKCl 0.82,1.05 0.33,0.32 1.90,1.36 0.24,0.23 0.00,0.00 0.23,0.63 1.23,1.54 0.00,0.00 ORourke03 ZT ssk1ste11 0.0625MKCl 0.79,0.96 1.28,1.29 0.00,0.00 0.74,1.06 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 ORourke03 ZT ssk1ste11 0.125MKCl 0.00,0.00 2.05,1.44 0.00,0.00 0.99,0.91 0.00,0.00 1.20,1.34 0.00,0.00 0.70,1.02 ORourke03 ZT ssk1ste11 0.25MKCL 0.93,1.11 0.28,0.40 0.40,0.85 0.32,0.35 0.00,0.00 0.70,1.01 0.00,0.00 0.47,0.87 ORourke03 ZT ssk1ste11 0.5MKCl 0.83,0.88 1.10,1.22 0.54,0.78 0.12,0.13 0.00,0.00 0.66,0.95 0.70,1.11 0.00,0.00 ORourke03 ZT ssk1ste11 1MKCL 0.64,0.94 0.03,0.04 1.42,1.28 0.05,0.06 0.00,0.00 0.00,0.00 1.50,1.72 0.00,0.00 ORourke03 ZT ste11 0.0625MKCl 2.80,1.75 0.00,0.00 0.30,0.60 0.00,0.00 2.80,2.15 0.00,0.00 0.00,0.00 0.00,0.00 ORourke03 ZT ste11 0.125MKCl 0.00,0.00 0.16,0.16 1.72,1.46 0.39,0.40 0.00,0.00 0.32,0.78 1.46,1.61 0.28,0.67 ORourke03 ZT ste11 0.5MKCl 0.73,1.04 0.14,0.14 1.10,1.16 0.18,0.19 0.00,0.00 0.46,0.76 0.00,0.00 0.42,0.76 Lai05 WT Gal N2 R1 3.05,2.20 0.15,0.36 0.55,0.59 0.04,0.22 3.22,2.06 0.00,0.00 0.00,0.00 0.00,0.00 Lai05 WT Gal N2 R2 2.16,1.55 0.12,0.29 0.51,0.58 0.08,0.24 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 Lai05 WT Gal N2 R3 2.40,1.77 0.24,0.45 0.78,0.73 0.14,0.37 2.46,1.84 0.00,0.00 0.58,0.97 0.00,0.00 Lai05 WT Glu N2 R1 1.29,1.05 0.56,0.72 0.24,0.48 2.22,1.51 0.00,0.00 0.00,0.00 0.41,0.87 0.00,0.00 Lai05 WT Glu N2 R2 0.42,0.63 0.00,0.00 0.12,0.34 1.31,1.01 1.31,1.31 0.00,0.00 0.00,0.00 0.00,0.00 Lai05 WT Glu N2 R3 1.31,1.15 0.07,0.35 0.96,0.91 0.73,0.77 1.66,1.51 0.00,0.00 0.00,0.00 0.00,0.00 Lai05 msn2/4 Galactose R1 4.02,2.94 0.19,0.48 1.72,1.36 0.08,0.36 4.50,2.43 0.00,0.00 1.29,1.30 0.00,0.00 Lai05 msn2/4 Galactose R2 3.33,2.05 0.06,0.41 0.42,0.53 0.05,0.37 1.76,1.52 0.00,0.00 0.00,0.00 0.00,0.00 Lai05 msn2/4 Galactose R3 4.50,2.38 0.16,0.42 0.80,0.86 0.14,0.38 4.50,3.61 0.00,0.00 0.78,1.14 0.00,0.00 LaiMean05 WT Gal N2 R1 2.36,1.65 0.24,0.45 0.38,0.48 0.08,0.28 1.21,1.29 0.00,0.00 0.00,0.00 0.00,0.00 LaiMean05 WT Glu N2 R1 1.31,1.10 0.08,0.46 0.00,0.00 1.31,1.09 1.10,1.31 0.00,0.00 0.00,0.00 0.00,0.00 LaiMean05 msn2/4 Galactose R1 3.80,2.41 0.25,0.57 0.72,0.72 0.17,0.48 4.50,2.73 0.00,0.00 0.92,1.18 0.00,0.00 Zakrzewska05 0.67,0.67 0.00,0.00 2.30,1.82 0.00,0.00 0.31,0.82 0.00,0.00 1.62,1.38 0.00,0.00 Mercier05 18733 200GY 0.24,0.51 0.57,0.70 0.27,0.50 0.53,0.66 0.00,0.00 0.55,1.00 0.00,0.00 0.00,0.00 Mercier05 18734 200Gy 0.18,0.42 1.00,0.91 0.10,0.37 0.90,0.82 0.00,0.00 1.80,1.64 0.00,0.00 0.00,0.00 Mercier05 18735 200Gy 0.26,0.48 0.38,0.65 0.24,0.51 0.44,0.68 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 Mercier05 6053 200Gy 0.14,0.60 0.46,0.46 0.23,0.60 0.66,0.66 0.00,0.00 0.26,0.75 0.00,0.00 1.00,1.21 Mercier05 hdf1 LM79 200Gy 0.03,0.22 1.31,0.97 0.05,0.17 0.20,0.41 0.00,0.00 0.00,0.00 0.00,0.00 0.00,0.00 total over segments 4.00 0.11 4.00 0.17 4.00 0.25 4.00 0.00