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Affymetrix Latin Square Experiment. One lot of 14 arrays were used for the study using spikes along with the background-- enriched RNA from DR153 (Ecoli) strain. - PowerPoint PPT Presentation
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Model-based Saturation Handling
Xuemin Fang, Cheng Li
and Wing Hung Wong
Computational Biology Lab
Harvard School Of Public Health
GeneLogic workshop, 11/19/01
Affymetrix Latin Square Experiment
• One lot of 14 arrays were used for the study using spikes along with the background-- enriched RNA from DR153 (Ecoli) strain.
• Twenty assay spikes were labeled transcripts generated from the deletion area of DR153 chromosome, while their background RNA was isolated from DR153, subsequently enriched and direct-labeled.
• The twenty assay spikes were grouped into 14 sets and its concentration (nM) prepared in the mix according to the Latin-square scheme.
Latin Square Scheme
Mix b075
9_c-
galE
b077
2_c-
ybhC
b077
3_c-
ybhB
b078
2_w-
moa
B
b078
6_w-
w076
2 (yb
hL)
b079
1_w-
w076
7(yb
hQ)
b080
9_c-
glnQ
b081
0_c-
glnP
b081
2_c-
dps
b081
1_c-
glnH
b081
4_w-
ompX
b081
9_c-
w079
5 (yb
iS)
b082
6_c-
moe
B
b083
8_c-
w081
4 (yli
J)
b083
9_w-
dacC
b085
1_w-
mda
A
b085
3_w-
w082
9 (yb
jN)
b086
1_c-
artM
b086
2_c-
artQ
1 1024 512 256 128 64 32 32 16 16 8 4 4 2 1 0.5 0.5 0.25 0.25 02 512 256 128 64 32 16 16 8 8 4 2 2 1 0.5 0.25 0.25 0 0 10243 256 128 64 32 16 8 8 4 4 2 1 1 0.5 0.25 0 0 1024 1024 5124 128 64 32 16 8 4 4 2 2 1 0.5 0.5 0.25 0 1024 1024 512 512 2565 64 32 16 8 4 2 2 1 1 0.5 0.25 0.25 0 1024 512 512 256 256 1286 32 16 8 4 2 1 1 0.5 0.5 0.25 0 0 1024 512 256 256 128 128 647 16 8 4 2 1 0.5 0.5 0.25 0.25 0 1024 1024 512 256 128 128 64 64 328 8 4 2 1 0.5 0.25 0.25 0 0 1024 512 512 256 128 64 64 32 32 169 4 2 1 0.5 0.25 0 0 1024 1024 512 256 256 128 64 32 32 16 16 8
10 2 1 0.5 0.25 0 1024 1024 512 512 256 128 128 64 32 16 16 8 8 411 1 0.5 0.25 0 1024 512 512 256 256 128 64 64 32 16 8 8 4 4 212 0.5 0.25 0 1024 512 256 256 128 128 64 32 32 16 8 4 4 2 2 113 0.25 0 1024 512 256 128 128 64 64 32 16 16 8 4 2 2 1 1 0.514 0 1024 512 256 128 64 64 32 32 16 8 8 4 2 1 1 0.5 0.5 0.25
Model for one probe set
• Full model
• Reduced model
ijjiijij MMPM
ijjijijij
ijjijij
PM
MM
Scanning Saturation
Probe 1-15: PM and MM data overlaid.
Probe 1-30: PMand MM data concatenated
Probe 1-30: Red fitted curveoverlaid.
Saturation
0 10000 20000 30000 40000
05
00
00
10
00
00
15
00
00
20
00
00
25
00
00
cel$MEAN
Histogram of PM value
Quantiles of Standard Normal
ce
l$M
EA
N
-4 -2 0 2 4
01
00
00
20
00
03
00
00
40
00
0
QQ-norm Plot of PM value
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
x00825.01[x00825.01[, 3] > limit, 3]
10000 20000 30000 400000
50
01
00
01
50
02
00
02
50
0
x00825.02[x00825.02[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
x00825.03[x00825.03[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
30
00
x00825.04[x00825.04[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
x00825.05[x00825.05[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
30
00
x00825.06[x00825.06[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
x00825.07[x00825.07[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
x00825.08[x00825.08[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
x00825.09[x00825.09[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
x00825.10[x00825.10[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
x00825.11[x00825.11[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
x00825.12[x00825.12[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
x00825.13[x00825.13[, 3] > limit, 3]
10000 20000 30000 40000
05
00
10
00
15
00
20
00
25
00
x00825.14[x00825.14[, 3] > limit, 3]
Histograms of cel intensities of the 14 arraysHistograms of cel intensities of the 14 arrays
Handle Saturation
x
y
0 20000 40000 60000
0.0
0.0
00
02
0.0
00
04
0.0
00
06
0.0
00
08
0.0
00
10
X ~ Normal(mean, sd^2)
Impute E(X | X > observed value)
mean
Observed value(saturation limit)
Conditional Expectation
)m
1
inf )(
)(
inf )(
infinf )|()|(
?)|( s what',Given )2(~
m dxxxf
mxPm dxxxf
dxmxxxfmXXE
mXXEmXNX
Conditional Expectation (cont’d)
)1
)2)|(
when
))1(2)|(
when
2
2
2
2
(
(
m
me
mXXE
m
me
mXXE
m
m
m
After imputing saturated data points
Probe 1-15: PM and MM data overlaid.
Probe 1-30: PMand MM data concatenated
Probe 1-30: Red fitted curveoverlaid.
b0579_c-galE
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0Gene 785
b0772_c-ybhC
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
Gene 798
b0773_c-ybhB
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
10
00
02
00
00
30
00
04
00
00
Gene 799
b0782_w-moaB
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
Gene 808
b0786_w-w0762
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 812
b0791_w-w0767
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
Gene 817
b0809_c-glnQ
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 835
b0810_c-glnP
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 836
b0812_c-dps
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
Gene 838
b0811_c-glnH
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
Gene 837
b0814_w-ompX
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 840
b0819_c-w0795
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 845
b0826_c-moeB
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 852
b0838_c-w0814
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 864
b0839_w-dacC
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 865
b0851_w-mdaA
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 877
b0853_w-w0829
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 879
b0861_c-artM
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 887
b0862_c-artQ
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
10
00
02
00
00
30
00
04
00
00
Gene 888
b0863_c-artI
PM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 889
PM only ModelPM only Model
MM only modelMM only model
b0579_c-galE
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 785
b0772_c-ybhC
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 798
b0773_c-ybhB
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 799
b0782_w-moaB
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
0
Gene 808
b0786_w-w0762
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 812
b0791_w-w0767
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 817
b0809_c-glnQ
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 835
b0810_c-glnP
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 836
b0812_c-dps
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
50
00
10
00
01
50
00
20
00
0
Gene 838
b0811_c-glnH
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 837
b0814_w-ompX
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 840
b0819_c-w0795
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 845
b0826_c-moeB
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 852
b0838_c-w0814
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 864
b0839_w-dacC
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 865
b0851_w-mdaA
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 877
b0853_w-w0829
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
50
00
10
00
01
50
00
Gene 879
b0861_c-artM
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 887
b0862_c-artQ
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
50
00
10
00
02
00
00
Gene 888
b0863_c-artI
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 889
Reduced modelReduced model
b0579_c-galE
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 785
b0772_c-ybhC
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 798
b0773_c-ybhB
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 799
b0782_w-moaB
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
0
Gene 808
b0786_w-w0762
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 812
b0791_w-w0767
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 817
b0809_c-glnQ
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 835
b0810_c-glnP
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 836
b0812_c-dps
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 838
b0811_c-glnH
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 837
b0814_w-ompX
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 840
b0819_c-w0795
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 845
b0826_c-moeB
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 852
b0838_c-w0814
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 864
b0839_w-dacC
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 865
b0851_w-mdaA
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 877
b0853_w-w0829
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
06
00
01
00
00
Gene 879
b0861_c-artM
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 887
b0862_c-artQ
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 888
b0863_c-artI
MM
on
ly M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 889
b0579_c-galE
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0Gene 785
b0772_c-ybhC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 798
b0773_c-ybhB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 799
b0782_w-moaB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 808
b0786_w-w0762
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 812
b0791_w-w0767
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 817
b0809_c-glnQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 835
b0810_c-glnP
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 836
b0812_c-dps
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 838
b0811_c-glnH
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 837
b0814_w-ompX
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 840
b0819_c-w0795
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 845
b0826_c-moeB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 852
b0838_c-w0814
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 864
b0839_w-dacC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 865
b0851_w-mdaA
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 877
b0853_w-w0829
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 879
b0861_c-artM
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 887
b0862_c-artQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 888
b0863_c-artI
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 889
Reduced(black) vs AD(orange) square rootReduced(black) vs AD(orange) square root
Full model without imputationFull model without imputation
b0579_c-galE
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 785
b0772_c-ybhC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 798
b0773_c-ybhB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
50
00
10
00
01
50
00
20
00
0
Gene 799
b0782_w-moaB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
50
00
10
00
01
50
00
20
00
0
Gene 808
b0786_w-w0762
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 812
b0791_w-w0767
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 817
b0809_c-glnQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 835
b0810_c-glnP
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
50
00
10
00
01
50
00
20
00
0
Gene 836
b0812_c-dps
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 838
b0811_c-glnH
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 837
b0814_w-ompX
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 840
b0819_c-w0795
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 845
b0826_c-moeB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 852
b0838_c-w0814
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 864
b0839_w-dacC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 865
b0851_w-mdaA
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 877
b0853_w-w0829
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
20
00
60
00
10
00
01
40
00
Gene 879
b0861_c-artM
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
50
00
10
00
01
50
00
20
00
0
Gene 887
b0862_c-artQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
20
00
0
Gene 888
b0863_c-artI
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
00
00
15
00
02
00
00
Gene 889
Full model with imputationFull model with imputation
b0579_c-galE
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
00
10
00
00
15
00
00
Gene 785
b0772_c-ybhC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
30
00
05
00
00
Gene 798
b0773_c-ybhB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
00
15
00
00
25
00
00
Gene 799
b0782_w-moaB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
20
00
03
00
00
40
00
0
Gene 808
b0786_w-w0762
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
05
00
01
50
00
25
00
0
Gene 812
b0791_w-w0767
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
40
00
06
00
00
80
00
0
Gene 817
b0809_c-glnQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
30
00
05
00
00
Gene 835
b0810_c-glnP
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
40
00
06
00
00
Gene 836
b0812_c-dps
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
40
00
06
00
00
80
00
0
Gene 838
b0811_c-glnH
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
30
00
05
00
00
Gene 837
b0814_w-ompX
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
30
00
05
00
00
Gene 840
b0819_c-w0795
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
40
00
06
00
00
80
00
0
Gene 845
b0826_c-moeB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
30
00
05
00
00
Gene 852
b0838_c-w0814
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
60
00
01
00
00
0
Gene 864
b0839_w-dacC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
40
00
06
00
00
Gene 865
b0851_w-mdaA
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
60
00
01
00
00
0
Gene 877
b0853_w-w0829
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
40
00
06
00
00
80
00
0
Gene 879
b0861_c-artM
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
60
00
01
00
00
0
Gene 887
b0862_c-artQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
01
00
00
03
00
00
0
Gene 888
b0863_c-artI
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
00
00
60
00
01
00
00
0
Gene 889
Full w/o (black) vs full w/ (red) Transformed to same scaleFull w/o (black) vs full w/ (red) Transformed to same scale
b0579_c-galE
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 785
b0772_c-ybhC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 798
b0773_c-ybhB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 799
b0782_w-moaB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 808
b0786_w-w0762
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 812
b0791_w-w0767
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 817
b0809_c-glnQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 835
b0810_c-glnP
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 836
b0812_c-dps
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 838
b0811_c-glnH
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 837
b0814_w-ompX
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 840
b0819_c-w0795
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 845
b0826_c-moeB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 852
b0838_c-w0814
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 864
b0839_w-dacC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 865
b0851_w-mdaA
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 877
b0853_w-w0829
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 879
b0861_c-artM
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 887
b0862_c-artQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 888
b0863_c-artI
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 200 400 600 800 1000
02
04
06
08
01
00
Gene 889
Full w/o (black) vs full w/ (red) same scale square rootFull w/o (black) vs full w/ (red) same scale square root
b0579_c-galE
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0Gene 785
b0772_c-ybhC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 798
b0773_c-ybhB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 799
b0782_w-moaB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 808
b0786_w-w0762
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 812
b0791_w-w0767
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 817
b0809_c-glnQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 835
b0810_c-glnP
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 836
b0812_c-dps
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 838
b0811_c-glnH
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 837
b0814_w-ompX
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 840
b0819_c-w0795
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 845
b0826_c-moeB
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 852
b0838_c-w0814
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 864
b0839_w-dacC
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 865
b0851_w-mdaA
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 877
b0853_w-w0829
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 879
b0861_c-artM
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 887
b0862_c-artQ
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 888
b0863_c-artI
Li-
Wo
ng
Fu
ll M
od
el(
ME
I)
0 5 10 15 20 25 30
02
46
81
0
Gene 889
