**"Rapid Analysis of the DNA Binding Specificities of
Transcription Factors with DNA Microarrays"**

**Supplementary
Figure 1. DNA microarray bound by CBP-FLAG-Rpn4, and labeled with
Alexa 488-conjugated anti(FLAG) antibody.**

**Supplementary
Figure 2. PBM negative controls. (a)** rGST. **(b)** GST-His6
purified from yeast. **(c)** GST-His6-Cmd1.** (d) **No GST-tagged protein
in PBM binding reaction (“milk only”).

**Supplementary
Figure 3. Reproducibility of PBM experiments. (a) **SD/mean for
triplicate Mig1 PBMs. **(b) **Cumulative SD/mean for triplicate Mig1 PBMs.
**(c)** Scatter plot of the SD/mean values versus the mean signal intensity
for triplicate Mig1 PBMs. **(d) **SD/mean for triplicate SybrGreen I
stained microarrays.** (e) **Cumulative SD/mean for triplicate SybrGreen
I stained microarrays.** (f) **Scatter plot of the SD/mean values versus
the mean signal intensity for SybrGreen I stained microarrays. **(g) **SD/mean
for triplicate Abf1 PBMs. **(h) **Cumulative SD/mean for triplicate Abf1
PBMs. **(i)** Scatter plot of the SD/mean values versus the mean signal
intensity for triplicate Abf1 PBMs. **(j)** SD/mean for triplicate Rap1
PBMs.** (k) **Cumulative SD/mean for triplicate Rap1 PBMs. **(l)** Scatter
plot of the SD/mean values versus the mean signal intensity for triplicate
Rap1 PBMs.

**Supplementary
Figure 4. Effect of varying the p-value threshold for the PBM data
on Rap1, Abf1, and Mig1 on the number of spots called “bound”.**

**Supplementary
Figure 5. DNA binding site motifs for PBM data passing 0.01 and
0.05 p-value thresholds. **

**Supplementary
Figure 6. Venn diagrams comparing the PBM data for Rap1, Abf1, and
Mig1, respectively, with the ChIP-chip data for these same TFs at 0.01 and
0.05 p-value thresholds. **

**Figures from the main body of the manuscript:**