## 3 Results
### Search for Common Attributes Affecting the Expression of Selected Genes  
To further explore the phenomena occurring within budding yeast cell populations during prolonged continuous culture and the importance of the proteins encoded by genes identified in our transcriptome analysis under these conditions, we looked for the common regulatory systems controlling them. With the help of the Yeastract+ web tool and database [20] ([[http://www.yeastract.com](http://www.yeastract.com)]([http://www.yeastract.com](http://www.yeastract.com))) we performed a search for transcription factors (TFs) regulating the expression of the genes on our list. The results of this analysis are shown in Table 1 and Table S2. The detailed strategy of this search is described in the Materials and Methods section. In brief, we were interested in TFs that regulate many genes in our gene sets, that regulate them preferentially, and for which the result of Yeastract+ analysis was statistically significant. The resulting lists contained 11 TFs for upregulated genes and 25 TFs for downregulated genes. The functions of these TFs, shown in the Description column, generally correlate well with the functions of genes on our lists. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline  & & \multicolumn{6}{c}{**Transcriptional Factors for Up-Regulated Genes**} \\ \hline
**TF** & **Fraction** & \(p\)**-Value** & **Gene Count** & **Over-representation** & **Rank** & **Description** \\ \hline \multirow{4}{*}{Adr1p} & \multirow{4}{*}{0.07} & \multirow{4}{*}{0} & \multirow{4}{*}{54} & \multirow{4}{*}{2.96} & \multirow{4}{*}{11.1} & Carbon source-responsive zinc-finger transcription factor; required for transcription of the glucose-repressed gene ADH2, of peroxisonal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization \\ \cline{1-1} \cline{5-5}  & & & & & & Protein similar to heat shock transcription factor; multicopy suppressor of pseudohyphal growth defects of ammonium permease mutants \\ \hline \multirow{4}{*}{Fzf1p} & \multirow{4}{*}{0.09} & \multirow{4}{*}{0} & \multirow{4}{*}{18} & \multirow{4}{*}{4.31} & Transcription factor involved in sulfite metabolism; sole identified regulatory target is SSU1; overexpression suppresses sulfite-sensitivity of many unrelated mutants due to hyperactivation of SSU1 \\ \cline{1-1} \cline{5-5}  & & & & & & GATA zinc finger protein; negatively regulates nitrogen catabolic gene expression by competing with GaitIP for GATA site binding; function requires a repressive carbon source; dimerizes with Dal80p and binds to Tor1p \\ \hline \multirow{4}{*}{Dal81p} & \multirow{4}{*}{0.06} & \multirow{4}{*}{0.0001} & \multirow{4}{*}{24} & \multirow{4}{*}{3.12} & \multirow{4}{*}{4.8} & Positive regulator of genes in multiple nitrogen degradation pathways \\ \cline{1-1} \cline{5-5}  & & & & & & Zinc cluster transcriptional activator; necessary for derepression of a variety of genes under non-fermentative growth conditions, active after diauxic shift, binds carbon source responsive elements \\ \hline \multirow{4}{*}{Dal80p} & \multirow{4}{*}{0.08} & \multirow{4}{*}{0.0003} & \multirow{4}{*}{15} & \multirow{4}{*}{3.18} & Negative regulator of genes in multiple nitrogen degradation pathways; expression is regulated by nitrogen levels and by Gln3p; member of the GATA-binding family, forms homodimers and heterodimers with GZ\(\beta\)p \\ \cline{1-1} \cline{5-5}  & & & & & & Negative regulator of genes in multiple nitrogen degradation pathways; expression is regulated by nitrogen levels and by Gln3p; member of the GATA-binding family, forms homodimers and heterodimers with GZ\(\beta\)p \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Transcriptional factors (TFs) are most strongly involved in the regulation of genes selected in transcriptome analysis. The list was generated with the help of the Yeastract+ online database [20] ([[http://www.yeastract.com](http://www.yeastract.com)]([http://www.yeastract.com](http://www.yeastract.com))).