<p>Supplemental Table 2. ORFs displaying possible internal transcription factor binding.</p><p>Systematic Gene Size Bound Factors Evidence name name (amino acids) YBL044W 122 Tec1, Ste12, Sok2 2, 3, 4 YBR162C TOS1 455 Tec1, Ste12 2, 3, 4 YDR169C-A 49 Tec1, Ste12 1 YEL020W-A TIM9 87 Tec1, Ste12, Sok2 check this 2, 5 YEL035C UTR5 166 Sok2 2, 5 YER018C SPC25 221 Sok2 2, 3, 4 YGR035C 116 Sok2 2, 3, 5 YHL006C SHU1 150 Sok2 2, 3, 5 YHL015W-A 27 Tec1, Ste12, Sok2 1 YHL025W SNF6 332 Sok2 2, 3, 4, 5 YHR213W-A 77 Tec1, Ste12, Sok2 check this 1 YJL027C 138 Sok2 2 YLR412C-A 68 Tec1, Ste12 1 YNL015W PB12 75 Sok2 2, 3, 5 YOL019W-A 50 Tec1, Ste12, 1 YOR161C-C 48 Sok2 1 YPL067C 198 Sok2 2, 3</p><p>1 Detection of expression 1-3</p><p>2 Microarray expression (http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl)</p><p>3 Yeast Two-Hybrid interactions 4, 5</p><p>4 Affinity Precipitation interactions 6, 7</p><p>5 Other evidence in SGD (Mutant phenotypes, single gene studies etc)</p><p>References 1. Kessler, M. M. et al. Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13, 264-71 (2003). 2. Kumar, A. et al. An integrated approach for finding overlooked genes in yeast. Nat Biotechnol 20, 58-63 (2002). 3. Oshiro, G. et al. Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res 12, 1210-20 (2002). 4. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98, 4569-74 (2001). 5. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-7 (2000). 6. Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-7 (2002). 7. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-3 (2002).</p>