Table 1.
The Histone-Correlated and Histone-Anticorrelated TF Groups
| HA | I | HC | |||
|---|---|---|---|---|---|
| Azf1 | Abf2 | Abf1 | Hac1 | Reb1 | Tye7 |
| Cin5 | Cup9 | Ace2 | Hal9 | Rei1 | Uga3 |
| Eds1 | Dal80 | Adr1 | Hap1 | Rfx1 | Ume6 |
| Fkh1 | Fzf1 | Aft1 | Leu3 | Rgm1 | Urc2 |
| Fkh2 | Gat1 | Aft2 | Mbp1 | Rim101 | Usv1 |
| Hcm1 | Gln3 | Aro80 | Met31 | Rph1 | Xbp1 |
| Hmra2 | Gzf3 | Asg1 | Met32 | Rpn4 | Yap6 |
| Mot2 | Hsf1 | Bas1 | Mig1 | Rsc3 | Ybr239c |
| Nhp6a | Lys14 | Cat8 | Mig2 | Rsc30 | Yer130c |
| Nhp6b | Matapha2 | Cbf1 | Mig3 | Rsf2 | Yer184c |
| Pho2 | Mcm1 | Cep3 | Msn2 | Rtg3 | Ygr067c |
| Rox1 | Mga1 | Cha4 | Msn4 | Sip4 | Ykl222c |
| Sfl1 | Rgt1 | Crz1 | Ndt80 | Skn7 | Yll054c |
| Sfp1 | Srd1 | Cst6 | Nhp10 | Sok2 | Ylr278c |
| Smp1 | Stb4 | Dal82 | Nrg1 | Stb5 | Yml081w |
| Spt15 | Tea1 | Dot6 | Oaf1 | Stp2 | Ypr022c |
| Stb3 | Tos8 | Ecm22 | Pdr1 | Stp3 | Yrm1 |
| Ste12 | Upc2 | Ecm23 | Pdr8 | Stp4 | Yrr1 |
| Sum1 | Yap1 | Fhl1 | Phd1 | Sut2 | |
| Yap3 | Ynr063w | Gal4 | Pho4 | Swi4 | |
| Yox1 | Ypr013c | Gat3 | Put3 | Swi5 | |
| Ypr015c | Gat4 | Rap1 | Tbf1 | ||
| Ypr196w | Gcn4 | Rdr1 | Tbs1 | ||
| Gis1 | Rds1 | Tec1 | |||
| Gsm1 | Rds2 | Tod6 | |||
The yeast TFs with available PWMs (Badis et al., 2008; Zhu et al., 2009) were analyzed to determine whether their intrinsic binding preferences are positively or negatively correlated to the intrinsic binding preference of nucleosomal histones (Kaplan et al., 2009; Segal et al., 2006). The TFs with weak correlation or disagreement between PBM or nucleosome binding preference publications were classified into an intermediate class. The correlation coefficients of all PWMs can be found in Table S1.