Comparison of the P-value significance between Wild Type and ΔGLN3  ANOVA WT ΔGLN3 p < 0.05 38.42% 30.11% p < 0.01 24.67% 16.29% p < 0.001 13.90% 6.53% p < 0.0001 7.43% 2.04% B-H p < 0.05 26.76% Bonferroni p < 0.05 3.68% 0.42%

ΔGLN3 STEM Significance Profiles

ΔGLN3 Profile 45

ΔGLN3 Profile 9

ΔGLN3Profile 2

ΔGLN3Profile 22

ΔGLN3Profile 48

ΔGLN3Profile 31

Wild Type Clusters

Wild Type Profile 45

Wild Type Profile 22

Wild Type Profile 9

Wild Type Profile 28

Wild Type Profile 48

Wild Type Profile 0

Only DNA Binding Degree Distribution

GRNSight Only DNA Binding Degree Distribution

Binding AND Expression Distribution

GRNSight Binding AND Expression

Binding PLUS Expression Distribution

GRNSight Binding PLUS Expression

Compared Parameter Mappings for b=0 and b=1

ACE2 (b=0 on the left, b=1 right)

ASG1 (b=0 on the left, b=1 right)

CIN5 (b=0 on the left, b=1 right)

CYC8 (b=0 on the left, r=1 right)

FKH2 (b=0 on the left, r=1 right)

GCR2(b=0 on the left, r=1 right)

GLN3 (b=0 on the left, r=1 right)

HMO1(b=0 on the left, r=1 right)

INO4 (b=0 on the left, r=1 right)

MCM1 (b=0 on the left, r=1 right)

MIG1 (b=0 on the left, r=1 right)

MSN2(b=0 on the left, r=1 right)

MSN4(b=0 on the left, r=1 right)

PDR1(b=0 on the left, r=1 right)

RIF1(b=0 on the left, r=1 right)

SFP1(b=0 on the left, r=1 right)

SNF5(b=0 on the left, r=1 right)

SNF6(b=0 on the left, r=1 right)

STB5(b=0 on the left, r=1 right)

SWI5(b=0 on the left, r=1 right)

YHP1(b=0 on the left, r=1 right)

YLR278C(b=0 on the left, r=1 right)

YOX1(b=0 on the left, r=1 right)

ZAP1(b=0 on the left, r=1 right)

GRNsight Map for both Inputs

GRNsight Map for output b=0

GRNsight Map for b=1

Comparison of GRNsight outputs b=1 on the left, b=0 on the right

Bar Graph comparing fixed and estimated weights ControllerGeneA->TargetGeneB

Production Rates of Fixed vs. Estimated b By standard name