The turnover of both Hxt3 and Hxt7 is dependent on Rim15.

<p>BY4742 (WT) and <i>rim15</i>Δ expressing <i>MET25pro-HXT3-GFP</i> were cultured in glucose media minus methionine as described in the methods (time 0). Following a switch to ethanol media plus methionine, samples were collected at the indicated times and analyzed by (A) fluorescence microscopy, and (B) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control. BY4742 and <i>rim15</i>Δ expressing <i>CUP1pro-GFP-HXT7</i> were cultured in raffinose media plus CuSO₄ as described in the methods (time 0). After harvesting and washing, the cells were resuspended in raffinose media devoid of CuSO₄ and treated with rapamycin. Samples were collected at the indicated times and analyzed by (C) fluorescence microscopy, and (B) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control.</p

The combined deletion of <i>VID28</i> and <i>VID30</i> has an increased effect on Hxt3 turnover, which is maintained when the native promoter is exchanged for the <i>MET25</i> promoter.

<p>BY4742 (WT) and <i>vid28</i>Δ<i>vid30</i>Δ expressing <i>HXT3-GFP</i> from either the native promoter or the <i>MET25</i> promoter were cultured in glucose media (left) or glucose media minus methionine (right) as described in the methods (time 0). Following a switch to ethanol media (left) or ethanol media plus methionine (right), samples were collected at the indicated times and analyzed by (A) fluorescence microscopy, and (B) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control.</p

Components of the Vid30c are required for Hxt3 turnover.

<p>BY4742 (WT) and the indicated Vid30c mutants expressing <i>HXT3-GFP</i> were cultured in glucose media as described in the methods (time 0). Following a switch to ethanol media, samples were collected at the indicated times and analyzed by (A) fluorescence microscopy, and (B) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control.</p

The rapamycin-induced turnover of Hxt7 requires inactivation of Ras2.

<p>BY4742 expressing <i>CUP1pro-HXT7-GFP</i> was transformed with YCp50 and YCp50-<i>RAS2^VAL19</i>. Cells were cultured in raffinose media plus CuSO₄ as described in the methods (time 0). After harvesting and washing, the cells were resuspended in raffinose media and treated with rapamycin. Samples were collected at the indicated times and analyzed by (A) fluorescence microscopy, and (B) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control.</p

The turnover of Hxt3 is dependent on Rsp5 and Art8.

<p>(A and B) BY4742 (WT) and <i>rsp5-1</i>, and (C) BY4742 (WT), <i>art3</i>Δ, <i>art4</i>Δ, <i>art6</i>Δ and <i>art8</i>Δ expressing <i>HXT3-GFP</i> were cultured in glucose media as described in the methods (time 0). Following a switch to ethanol media, samples were collected at the indicated times and analyzed by (A) fluorescence microscopy, and (B and C) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control.</p

The function of Snf1 is not required for Hxt3 turnover.

<p>BY4742 (WT) and <i>snf1</i>Δ expressing <i>MET25pro-HXT3-GFP</i> were cultured in glucose media minus methionine as described in the methods (time 0). Following a switch to ethanol media plus methionine, samples were collected at the indicated times and analyzed by (A) fluorescence microscopy, and (B) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control.</p

Overexpression of <i>VID28</i> accelerates Hxt3 turnover.

<p>BY4742 (WT) and <i>PGK1pro-VID28</i> expressing <i>MET25pro-HXT3-GFP</i> were cultured in glucose media minus methionine as described in the methods (time 0). Following washing and a switch to ethanol media plus methionine, samples were collected at the indicated times and analyzed by (A) fluorescence microscopy, and (B) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control.</p

The turnover of Hxt3 requires inactivation of the Ras2/cAMP/PKA pathway.

<p>BY4742 expressing <i>MET25p-HXT3-GFP</i> was transformed with YCp50, YCp50-<i>RAS2</i> and YCp50-<i>RAS2^VAL19</i>. Cells were cultured in glucose media minus methionine as described in the methods (time 0). Following a switch to ethanol media plus methionine, samples were collected at the indicated times and analyzed by (A) fluorescence microscopy, and (B) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control. BY4743 (WT) and <i>bcy1</i>Δ/<i>bcy1</i>Δ strains expressing <i>HXT3-GFP</i> were cultured in glucose media as described in the methods (time 0). Following a switch to ethanol media, samples were collected at the indicated times and analyzed by (C) fluorescence microscopy, and (D) Western analysis with anti-GFP antibodies. Identical blots were also probed with anti-ADH antibody as a loading control.</p

Illustration of the Correlation Clustering using an example of the graph <i>G</i> with {+} and {-} edges colored in black and red respectively.

<p>In graph <i>G</i> the gray circles refer to nodes (e.g. gene names) and connecting lines to edges (E) with {+} and {-} values. Green and blue circles represent putative clusters.</p

Illustration of expression profile of <i>x</i> and <i>y</i> with following patterns: A) <i>x</i> and <i>y</i> have both high similarity based on absolute difference and <i>r</i>(<i>x</i>,<i>y</i>); B) <i>x</i> and <i>y</i> have low similarity based on absolute difference but high <i>r</i>(<i>x</i>,<i>y</i>); C) <i>x</i> and <i>y</i> have very low similarity based on absolute difference but high negative <i>r</i>(<i>x</i>,<i>y</i>).

<p>Illustration of expression profile of <i>x</i> and <i>y</i> with following patterns: A) <i>x</i> and <i>y</i> have both high similarity based on absolute difference and <i>r</i>(<i>x</i>,<i>y</i>); B) <i>x</i> and <i>y</i> have low similarity based on absolute difference but high <i>r</i>(<i>x</i>,<i>y</i>); C) <i>x</i> and <i>y</i> have very low similarity based on absolute difference but high negative <i>r</i>(<i>x</i>,<i>y</i>).</p