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Selecting Genes Putatively Regulated By Msn4 Or Hap4
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Despite a significant
improvement when restricting the expression profiles to putative
targets, the reproducibility of individual gene expression levels
between the two replicate data sets in model #1 is still relatively
low. Among the 65 downstream genes in model #1, only 27 genes
experienced significant changes in the same directions in both SWI4
deletion data sets.
Thus, rather than validating individual interactions between
Msn4/Hap4 and these downstream genes, we instead validated the
overall pathways of Swi4-Sok2-(Msn4, Hap4). To reduce both false
positives and false negatives from the downstream hubs (Msn4, Hap4)
to their affected genes, we selected the genes which are known to be
directly regulated by one of these factors (obtained from the Proteome BioKnowledge Library and
ChIP-chip data (Lee et al.
2002); Table S4 includes the selected genes for the validation of
Msn4 and Hap4 pathways.
Table S4: Gene sets for external validation.
Msn4 subset
ALD3
ARA1
CTT1
YMR173W
DOT5
GLK1
GLO1
GRE3
GSY1
HOR2
HSP12
HSP26
HSP104
HXK1
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LAP4
PGM2
RAS2
SOD2
SOL4
SPS100
SSA4
TKL2
TPS1
TTR1
YDL124W
YKR011C
YMR315W
YNL200C
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Hap4 subset
ATP3
ATP7
ATP16
COX4
COX7
COX12
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COX13
QCR7
TUF1
QCR10
YLR294C
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