H* © Orly Alter 2005 *L
H* All Rights Reserved *L
H* Intersect Cell Cycle Expression Dataset and Its Cell Cycle- and Development-Binding Projections *L
arrays = 18;
partialgenenames = Intersection@genenames1, partialgenenames2, partialgenenames3D;
partialgenes = Dimensions@partialgenenamesD@@1DD
list = Flatten@TakeColumns@partialgenenames, 81<DD;
868
counter = Table@Flatten@Position@list, genenames1@@a, 1DDDD,
8a, 1, Dimensions@genenames1D@@1DD<D;
counter = ReplaceAll@counter, 8< -> 8Null<D;
partial = AppendRows@counter, matrix1D;
partial = Sort@partial, OrderedQ@8#1, #2<D &D;
partialmatrix1 = TakeRows@
TakeColumns@partial, 82, arrays + 1<D,
81, partialgenes<D;
counter = Table@Flatten@Position@list, partialgenenames2@@a, 1DDDD,
8a, 1, Dimensions@partialgenenames2D@@1DD<D;
counter = ReplaceAll@counter, 8< -> 8Null<D;
partial = AppendRows@counter, partialmatrix2D;
partial = Sort@partial, OrderedQ@8#1, #2<D &D;
matrix2 = TakeRows@
TakeColumns@partial, 82, arrays + 1<D,
81, partialgenes<D;
counter = Table@Flatten@Position@list, partialgenenames3@@a, 1DDDD,
8a, 1, Dimensions@partialgenenames3D@@1DD<D;
counter = ReplaceAll@counter, 8< -> 8Null<D;
partial = AppendRows@counter, partialmatrix3D;
partial = Sort@partial, OrderedQ@8#1, #2<D &D;
matrix3 = TakeRows@
TakeColumns@partial, 82, arrays + 1<D,
81, partialgenes<D;
H* Calculate HOEVD of Expression Dataset and Its Projections Onto Binding Datasets *L
H* Append Expression Dataset and Its Projections Onto Binding Datasets *L
tensor = AppendRows@
partialmatrix1,
matrix2,
matrix3D;
arraynames = AppendRows@arraynames1, arraynames1, arraynames1D;
8genes, arrays< = Dimensions@tensorD
8868, 54<
H* Calculate SVD *L
8eigenarrays, eigenexpressions, eigengenes< = SingularValues@tensorD;
eigengenes@@1DD = -eigengenes@@1DD;
eigenarrays@@1DD = -eigenarrays@@1DD;
eigengenes@@2DD = -eigengenes@@2DD;
eigenarrays@@2DD = -eigenarrays@@2DD;
eigenarrays = Transpose@eigenarraysD;
fractions = eigenexpressions ^ 2 ê
Sum@eigenexpressions@@aDD^ 2,
8a, 1, Dimensions@eigenexpressionsD@@1DD<D;
entropy = -N@Sum@fractions@@aDD * Log@fractions@@aDDD,
8a, 1, Dimensions@eigenexpressionsD@@1DD<D ê
Log@Dimensions@eigenexpressionsD@@1DDDD;
entropy = N@Round@100 * entropyD ê 100D
0.6
H* Create Fractions Bar Charts Displays *L
fractions@@3DD
0.0870328
HOEVD.nb
p. 2
limit = 0.1;
alsolimit = fractions@@3DD;
Clear@gridx, framex, framey, sizesD;
gridx = Table@a, 8a, 0, limit, N@limit ê 5D<D;
framex = gridx;
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@framex@@aDD
DDD, 8a, 1, 6<DD;
Do@
Do@framex@@aDD = StringJoin@ToString@framex@@aDDD, " "D,
8b, 1, 5 - sizes@@aDD<D,
8a, 1, 6<D;
framex = Table@8gridx@@aDD, framex@@aDD<, 8a, 1, 6<D;
gridx = Table@8gridx@@aDD, RGBColor@0, 0, 0D<, 8a, 1, 6<D;
framey = Table@8a + 1, 12 - a<, 8a, 0, 12 - 3<D;
table = Table@fractions@@aDD,
8a, 12, 3, -1<D;
g = BarChart@table,
BarOrientation -> Horizontal,
PlotRange -> 880, alsolimit * 1.0001<, 80.5, 12 - 2 + 0.5<<,
AspectRatio -> 1,
Axes -> False,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8gridx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 1.<, 80, 0<, 80, 1<D;
g1 = Show@g,
AspectRatio -> 1.25,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 3
fractions@@1DD
0.396389
limit = 0.4;
alsolimit = fractions@@1DD;
gridx = Table@a, 8a, 0, limit, N@limit ê 5D<D;
framex = gridx;
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@framex@@aDD
DDD, 8a, 1, 6<DD;
Do@
Do@framex@@aDD = StringJoin@ToString@framex@@aDDD, " "D,
8b, 1, size - sizes@@aDD<D,
8a, 1, 6<D;
framex = Table@8gridx@@aDD, framex@@aDD<, 8a, 1, 6<D;
gridx = Table@8gridx@@aDD, RGBColor@0, 0, 0D<, 8a, 1, 6<D;
framey = Table@8a + 1, Dimensions@eigenexpressionsD@@1DD - a<,
8a, 0, Dimensions@eigenexpressionsD@@1DD - 1<D;
labelx = ColumnForm@
8"HbL Eigenexpression Fraction", StringJoin@"d = ", ToString@entropyDD, " "<,
CenterD;
g = BarChart@
Table@fractions@@Dimensions@eigenexpressionsD@@1DD - aDD,
8a, 0, Dimensions@eigenexpressionsD@@1DD - 1<D,
BarOrientation -> Horizontal,
PlotRange -> 880, limit * 1.0001<, 80.5, Dimensions@eigenexpressionsD@@1DD + 0.5<<,
AspectRatio -> 1,
Axes -> False,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, None, labelx, None<,
GridLines -> 8gridx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 2.9<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 2<, 80, 0<, 80, 1<D;
g2 = Show@8g,
Graphics@8RGBColor@1, 1, 0.8D, [email protected], 1.5<, 8alsolimit, 35<D<D,
Graphics@[email protected], 1.5<, 8alsolimit, 35<, g1D<D<,
AspectRatio -> 1.35,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 4
H* Create Eigengenes 2 D Red & Green Raster Display *L
contrast = 50;
displaying = Table@
If@contrast * eigengenes@@i, jDD > 0,
If@contrast * eigengenes@@i, jDD < 1, 8contrast * eigengenes@@i, jDD, 0<, 81, 0<D,
If@contrast * eigengenes@@i, jDD > -1, 80, -contrast * eigengenes@@i, jDD<, 80, 1<DD,
8i, 1, Dimensions@eigenexpressionsD@@1DD<, 8j, 1, arrays<D;
framex = Table@8a - 0.5, arraynames@@1, aDD<, 8a, 1, arrays<D;
framey = Table@8a + 1 - 0.5, Dimensions@eigenexpressionsD@@1DD - a<,
8a, 0, Dimensions@eigenexpressionsD@@1DD - 1<D;
labely = "Eigengenes";
labelx = ColumnForm@8"HaL Arrays", " ", " "<, CenterD;
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, Dimensions@eigenexpressionsD@@1DD, 1, -1<, 8j, 1, arrays<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, labely, labelx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 3, c<, 80, 0<, 80, 1<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 3<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 2.7<, 80, 0<, 80, 1<D;
g1 = Show@g,
AspectRatio -> 1.05 * 39 ê 54,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 5
Eigengenes
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
0.08
0.06
0.04
0.02
0.4
0.32
0.24
0.16
0.08
HaL Arrays
0
0
0_min
7_min
14 _min
21 _min
28 _min
35 _min
42 _min
49 _min
56 _min
63 _min
70 _min
77 _min
84 _min
91 _min
98 _min
105_min
112_min
119_min
0_min
7_min
14 _min
21 _min
28 _min
35 _min
42 _min
49 _min
56 _min
63 _min
70 _min
77 _min
84 _min
91 _min
98 _min
105_min
112_min
119_min
0_min
7_min
14 _min
21 _min
28 _min
35 _min
42 _min
49 _min
56 _min
63 _min
70 _min
77 _min
84 _min
91 _min
98 _min
105_min
112_min
119_min
H* Display Eigengenes and Fractions *L
Show@GraphicsArray@8g1, g2<D,
GraphicsSpacing -> -0.275D;
HbL Eigenexpression Fraction
d = 0.6
3
4
5
6
7
8
9
10
11
12
HOEVD.nb
p. 6
H* Create Selected Eigengenes Graph Display *L
eigengenes2 = Chop@TrigFit@Drop@Drop@eigengenes@@2DD, 819, arrays<D, 81<D, 2, 8x - 1, arrays ê 3 - 1<D, 0.1D
eigengenes3 = Chop@TrigFit@Drop@Drop@eigengenes@@3DD, 819, arrays<D, 81<D, 2, 8x - 1, arrays ê 3 - 1<D, 0.1D
4
0.307764 SinA ÅÅÅÅÅÅÅ p H-1 + xLE
17
4
0.29524 CosA ÅÅÅÅÅÅÅ p H-1 + xLE
17
eigengenes2 = Sqrt@2 ê 17.D * Sin@4 * Pi * Hx - 1L ê 17D;
eigengenes3 = Sqrt@2 ê 17.D * Cos@4 * Pi * Hx - 1L ê 17D;
labelx = ColumnForm@8"HcL Arrays"<, CenterD;
labely = ColumnForm@8" ", "Expression Level"<, CenterD;
framex = Table@8a - 1, arraynames@@1, aDD<, 8a, 1, arrays<D;
framey = 8-1, -0.5, 0, 0.5, 1<;
coordinates = Table@8a - 1, eigengenes@@1, aDD<, 8a, 1, arrays<D;
points = Table@Point@coordinates@@aDDD, 8a, 1, arrays<D;
line = Line@coordinatesD;
g = Show@
8Graphics@8RGBColor@1, 0, 0D, [email protected], points<D,
Graphics@8RGBColor@1, 0, 0D, line<D<,
Frame -> True,
FrameLabel -> 8None, labely, labelx, None<,
GridLines -> 88817.5, RGBColor@0, 0, 0D<, 835.5, RGBColor@0, 0, 0D<<, 880, RGBColor@0, 0, 0D<<<,
FrameTicks -> 8None, framey, framex, None<,
PlotRange -> 8-0.55, 1.05<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 3.5, c<, 80, 0<, 80, 1<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.35<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.175<, 80, 0<, 80, 1<D;
p1 = Show@g,
AspectRatio -> 1.05 ê 2.25,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 7
graph = Plot@eigengenes2,
8x, 0, arrays - arrays ê 3 - 1<,
PlotStyle -> 8RGBColor@0, 0, 1D, [email protected], 0.02<D<,
DisplayFunction -> IdentityD;
labelx = ColumnForm@8"HcL Arrays"<, CenterD;
labely = ColumnForm@8" ", "Expression Level"<, CenterD;
framex = Table@8a - 1, arraynames@@1, aDD<, 8a, 1, arrays<D;
framey = 8-1, -0.5, 0, 0.5, 1<;
coordinates = Table@8a - 1, eigengenes@@2, aDD<, 8a, 1, arrays<D;
points = Table@Point@coordinates@@aDDD, 8a, 1, arrays<D;
line = Line@coordinatesD;
g = ShowA
9Graphics@8RGBColor@0, 0, 1D, [email protected], points<D,
Graphics@8RGBColor@0, 0, 1D, line<D,
graph,
2
4 pt
GraphicsA9RGBColor@0, 0, 1D, TextA"$%%%%%%
ÅÅÅÅ sinH ÅÅÅÅÅÅÅÅÅÅÅ L", 810.5, 0.9<E=E=,
T
T
Frame -> True,
FrameLabel -> 8None, labely, labelx, None<,
GridLines -> 88817.5, RGBColor@0, 0, 0D<, 835.5, RGBColor@0, 0, 0D<<, 880, RGBColor@0, 0, 0D<<<,
FrameTicks -> 8None, framey, framex, None<,
PlotRange -> 8-0.55, 1.05<,
DisplayFunction -> IdentityE;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 3.5, c<, 80, 0<, 80, 1<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.35<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.175<, 80, 0<, 80, 1<D;
p2 = Show@g,
AspectRatio -> 1.05 ê 2.25,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 8
graph = Plot@eigengenes3,
8x, 1, arrays - arrays ê 3 - 1<,
PlotStyle -> 8RGBColor@0, 0.5, 0D, [email protected], 0.02<D<,
DisplayFunction -> IdentityD;
labelx = ColumnForm@8"HcL Arrays"<, CenterD;
labely = ColumnForm@8" ", " "<, CenterD;
framex = Table@8a - 1, arraynames@@1, aDD<, 8a, 1, arrays<D;
framey = 8-1, -0.5, 0, 0.5, 1<;
coordinates = Table@8a - 1, eigengenes@@3, aDD<, 8a, 1, arrays<D;
points = Table@Point@coordinates@@aDDD, 8a, 1, arrays<D;
line = Line@coordinatesD;
g = ShowA
9Graphics@8RGBColor@0, 0.5, 0D, [email protected], points<D,
Graphics@8RGBColor@0, 0.5, 0D, line<D,
graph,
2
4 pt
GraphicsA9RGBColor@0, 0.5, 0D, TextA"$%%%%%%
ÅÅÅÅ cosH ÅÅÅÅÅÅÅÅÅÅÅ L", 810.5, 0.7<E=E=,
T
T
Frame -> True,
FrameLabel -> 8None, labely, labelx, None<,
GridLines -> 88817.5, RGBColor@0, 0, 0D<, 835.5, RGBColor@0, 0, 0D<<, 880, RGBColor@0, 0, 0D<<<,
FrameTicks -> 8None, framey, framex, None<,
PlotRange -> 8-0.55, 1.05<,
DisplayFunction -> IdentityE;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 3.5, c<, 80, 0<, 80, 1<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.35<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.175<, 80, 0<, 80, 1<D;
p3 = Show@g,
AspectRatio -> 1.05 ê 2.25,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 9
Expression Level
0_min
7_min
14_min
21_min
28_min
35_min
42_min
49_min
56_min
63_min
70_min
77_min
84_min
91_min
98_min
105_min
112_min
119_min
0_min
7_min
14_min
21_min
28_min
35_min
42_min
49_min
56_min
63_min
70_min
77_min
84_min
91_min
98_min
105_min
112_min
119_min
0_min
7_min
14_min
21_min
28_min
35_min
42_min
49_min
56_min
63_min
70_min
77_min
84_min
91_min
98_min
105_min
112_min
119_min
H* Display Selected Eigengenes *L
g3 = Show@8p3, p2, p1<,
DisplayFunction -> IdentityD;
Show@GraphicsArray@8g3<DD;
HcL Arrays
1
$ 2 cosH 4 pt L
T
T
$ 2 sinH 4 pt L
T
T
0.5
0
-0.5
H* Define Data *L
partialmatrix5 = tensor;
partialgenenames5 = partialgenenames;
arraynames5 = arraynames;
8genes5, arrays5< = Dimensions@partialmatrix5D
8868, 54<
HOEVD.nb
p. 10
H* Display Sorted Significant Eigenarrays *L
arraypatterns = Transpose@eigenarraysD;
H* Center Eigenarrays *L
average = Table@1, 8a, 1, genes<D;
average = N@average ê Sqrt@Dot@average, averageDDD;
arraypatterns = arraypatterns - N@Outer@Times, Dot@arraypatterns, averageD, averageDD;
H* Sort Eigenarrays *L
Do@
arraypatterns@@aDD = Sort@arraypatterns@@aDD, OrderedQ@88#2<, 8#1<<D &D,
8a, 1, 3<D
H* Create Sorted Eigenrrays Graph Display *L
p = Table@0, 8a, 1, 3<D;
color = 8
RGBColor@1, 0.5, 0D,
RGBColor@1, 0, 0D,
RGBColor@0, 0, 1D,
RGBColor@0, 0.5, 0D<;
labelx = "Expression Level";
labely = ColumnForm@
8"Number of Genes", " ", " ", " ", " ", " ", " ", " ", " "<,
CenterD;
framex = [email protected] * a, a<, 8a, 1, 3<D;
framey = 88-100, "100"<, 8-400, "400"<, 8-genes + 100, "768"<<;
Do@8
coordinates = Table@
If@arraypatterns@@n, aDD + 0.04 * n < -0.04, -0.04,
If@arraypatterns@@n, aDD + 0.04 * n > 0.2, 0.2,
arraypatterns@@n, aDD + 0.04 * nDD,
8a, 1, genes<D,
coordinates = Table@8coordinates@@aDD, -a + 1<, 8a, 1, genes<D,
line = Line@coordinatesD,
g = Show@
Graphics@8color@@Mod@n, 5D + 1DD, line<D,
Frame -> True,
FrameLabel -> 8None, labely, labelx, None<,
FrameTicks -> 8None, framey, framex, None<,
GridLines -> 8880.04 * n, RGBColor@0, 0, 0D<<, 88-100, RGBColor@0, 0, 0D<,
8-400, RGBColor@0, 0, 0D<, 8-genes + 100, RGBColor@0, 0, 0D<<<,
PlotRange -> 88-0.04, 0.2<, 832.5, -genes + 1 - 32.5<<,
DisplayFunction -> IdentityD,
g = FullGraphics@gD,
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b, c<, 80, 0<, 80, 1<D,
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 85<, 80, -1<, 81, 0<D,
p@@nDD = Show@g,
AspectRatio Ø 2 ê 1.2 ê GoldenRatio,
PlotRange -> All,
DisplayFunction Ø IdentityD
<, 8n, 1, 3<D;
HOEVD.nb
p. 11
H* Display Sorted Eigenarrays *L
Show@Table@p@@aDD, 8a, 1, 3<D,
DisplayFunction Ø $DisplayFunctionD;
Expression Level
1
2
3
Number of Genes
100
400
768
HOEVD.nb
p. 12
H* Estimate Significance of Association of Eigenarrays with the Cell Cycle *L
H* Use Cell Cycle Traditional or Microarray Classification of Yeast Genes *L
most = 100;
annotations = TakeColumns@partialgenenames5, 86<D;
stages = 8"MêG1", "G1", "S", "SêG2", "G2êM", "None"<;
numbers = Flatten@Table@8Count@Flatten@annotationsD, stages@@aDDD<, 8a, 1, Dimensions@stagesD@@1DD<DD
counter = Table@8a<, 8a, 1, 3<D;
probability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
parallelannotation = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
parallelprobability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
antiannotation = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
antiprobability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
838, 77, 13, 23, 40, 677<
Do@8
pattern = TakeColumns@Sort@
AppendRows@TakeColumns@eigenarrays, counter@@cDDD, annotationsD,
OrderedQ@88#2<, 8#1<<D &D, 82<D,
table = Table@8
stages@@aDD,
numbers@@aDD,
Count@Flatten@TakeRows@pattern, 81, most<DD, stages@@aDDD<,
8a, 1, Dimensions@stagesD@@1DD<D,
probability = Table@8
Sum@N@Binomial@table@@a, 2DD, bD * Binomial@genes - table@@a, 2DD, most - bD ê
Binomial@genes, mostDD, 8b, table@@a, 3DD, most<D,
stages@@aDD<,
8a, 1, Dimensions@stagesD@@1DD<D,
parallelannotation@@cDD = 8Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 2DD<,
parallelprobability@@cDD = 8ScientificForm@Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 1DD, 2D<,
table = Table@8
stages@@aDD,
numbers@@aDD,
Count@Flatten@TakeRows@pattern, 8genes - most + 1, genes<DD, stages@@aDDD<,
8a, 1, Dimensions@stagesD@@1DD<D,
probability = Table@8
Sum@N@Binomial@table@@a, 2DD, bD * Binomial@genes - table@@a, 2DD, most - bD ê
Binomial@genes, mostDD, 8b, table@@a, 3DD, most<D,
stages@@aDD<,
8a, 1, Dimensions@stagesD@@1DD<D,
antiannotation@@cDD = 8Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 2DD<,
antiprobability@@cDD = 8ScientificForm@Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 1DD, 2D<<,
8c, 1, Dimensions@counterD@@1DD<D
table1 = AppendRows@
counter,
parallelannotation,
parallelprobability,
antiannotation,
antiprobabilityD;
HOEVD.nb
p. 13
H* Estimate Significance of Association of Eigenarrays with the Pheromone Response *L
H* Use Pheromone Microarray Classification of Yeast Genes *L
most = 100;
annotations = TakeColumns@partialgenenames5, 87<D;
stages = 8"Up", "Down", "None"<;
numbers = Flatten@Table@8Count@Flatten@annotationsD, stages@@aDDD<, 8a, 1, Dimensions@stagesD@@1DD<DD
counter = Table@8a<, 8a, 1, 3<D;
probability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
parallelannotation = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
parallelprobability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
antiannotation = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
antiprobability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
837, 50, 781<
Do@8
pattern = TakeColumns@Sort@
AppendRows@TakeColumns@eigenarrays, counter@@cDDD, annotationsD,
OrderedQ@88#2<, 8#1<<D &D, 82<D,
table = Table@8
stages@@aDD,
numbers@@aDD,
Count@Flatten@TakeRows@pattern, 81, most<DD, stages@@aDDD<,
8a, 1, Dimensions@stagesD@@1DD<D,
probability = Table@8
Sum@N@Binomial@table@@a, 2DD, bD * Binomial@genes - table@@a, 2DD, most - bD ê
Binomial@genes, mostDD, 8b, table@@a, 3DD, most<D,
stages@@aDD<,
8a, 1, Dimensions@stagesD@@1DD<D,
parallelannotation@@cDD = 8Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 2DD<,
parallelprobability@@cDD = 8ScientificForm@Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 1DD, 2D<,
table = Table@8
stages@@aDD,
numbers@@aDD,
Count@Flatten@TakeRows@pattern, 8genes - most + 1, genes<DD, stages@@aDDD<,
8a, 1, Dimensions@stagesD@@1DD<D,
probability = Table@8
Sum@N@Binomial@table@@a, 2DD, bD * Binomial@genes - table@@a, 2DD, most - bD ê
Binomial@genes, mostDD, 8b, table@@a, 3DD, most<D,
stages@@aDD<,
8a, 1, Dimensions@stagesD@@1DD<D,
antiannotation@@cDD = 8Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 2DD<,
antiprobability@@cDD = 8ScientificForm@Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 1DD, 2D<<,
8c, 1, Dimensions@counterD@@1DD<D
table2 = AppendRows@
counter,
parallelannotation,
parallelprobability,
antiannotation,
antiprobabilityD;
HOEVD.nb
p. 14
H* Display Significance of Association of Eigenarrays with the Cellular Programs *L
headerx = 88
ColumnForm@8" ", " ", " "<, LeftD,
ColumnForm@8" ", " ", "Classification"<, LeftD,
ColumnForm@8" ", " ", "Eigenarray"<, LeftD,
ColumnForm@8"Most Likely", "Parallel", "Association"<, LeftD,
ColumnForm@8"P-Value of", "Parallel", "Association"<, LeftD,
ColumnForm@8"Most Likely", "Antiparallel", "Association"<, LeftD,
ColumnForm@8"P-Value of", "Antiparallel", "Association"<, LeftD<,
8" ", " ", " ", " ", " ", " ", " "<<;
spacerx = 88" ", " ", " ", " ", " "<<;
headery = Table@" ", 8a, 1, 2 * Dimensions@counterD@@1DD + 1<, 8b, 1, 2<D;
headery@@1DD = 8"HaL", "Cell Cycle"<;
headery@@Dimensions@counterD@@1DD + 2DD = 8"HbL", "Pheromone Response"<;
association =
AppendColumns@headerx,
AppendRows@headery,
AppendColumns@table1, spacerx, table2DDD;
TableForm@association, TableSpacing Ø 81, 1<D
HaL
HbL
Classification
Eigenarray
Most Likely
Parallel
Association
Cell Cycle
1
MêG1
Pheromone Response
P-Value of
Parallel
Association
Most Likely
Antiparallel
Association
P-Value of
Antiparallel
Association
8. µ 10-7
G1
8.3 µ 10-20
G2êM
5.5 µ 10-18
-36
2
G1
1.4 µ 10
3
MêG1
3.1 µ 10-16
G1
4.8 µ 10-12
1
Up
5.3 µ 10-18
Down
5.5 µ 10-23
2
Down
8. µ 10-4
Down
2.7 µ 10-3
Down
1.6 µ 10-9
3
Up
1.8 µ 10
-3
HOEVD.nb
p. 15
H* Examine Data and Its Projections Genes µ Genes Correlations Tensor Matrices
*L
H* Read List of Cell Cycle-Regulated Genes *L
stream = "DesktopêNetwork_DecompositionêDataêCycle_Genes.txt";
genelist = Import@stream, "Table"D;
genelist = Drop@genelist, 1D;
partialgenes = Dimensions@Intersection@genelist, partialgenenames5DD@@1DD
Clear@streamD;
30
list = Flatten@TakeColumns@genelist, 81<DD;
counter = Table@Flatten@Position@list, partialgenenames5@@a, 1DDDD,
8a, 1, Dimensions@partialgenenames5D@@1DD<D;
counter = ReplaceAll@counter, 8< -> 8Null<D;
partial = AppendRows@counter, partialgenenames5, eigenarraysD;
partial = Sort@partial, OrderedQ@8#1, #2<D &D;
partialgenenames = TakeRows@
TakeColumns@partial, 82, 8<D,
81, partialgenes<D;
partialeigenarrays = TakeRows@
TakeColumns@partial, 89, Dimensions@eigenexpressionsD@@1DD + 8<D,
81, partialgenes<D;
H* Calculate Tensor Matrices *L
partialeigenarrays = Transpose@partialeigenarraysD;
tensormatrices = Table@0, 8a, 1, 3<, 8b, 1, 3<D;
Do@
Do@
tensormatrices@@a, bDD = Outer@Times, partialeigenarrays@@aDD, partialeigenarrays@@bDDD,
8a, 1, 3<D,
8b, 1, 3<D
tensormatrices = 8
tensormatrices@@1, 1DD,
tensormatrices@@2, 2DD,
tensormatrices@@3, 3DD,
-Htensormatrices@@1, 2DD + tensormatrices@@2, 1DDL,
Htensormatrices@@1, 3DD + tensormatrices@@3, 1DDL,
-Htensormatrices@@2, 3DD + tensormatrices@@3, 2DDL<;
partialeigenarrays = Transpose@partialeigenarraysD;
H* Keep Only Correlations Above Diagonals in Tensor Matrices *L
Do@
Do@
Do@
tensormatrices@@a, b, cDD = 0,
8c, 1, b<D,
8b, 1, Dimensions@tensormatrices@@1DDD@@1DD<D,
8a, 1, 6<D;
HOEVD.nb
p. 16
H* Flatten Tensor Matrices Into Tensor Vectors *L
tensorvectors = Table@0, 8partialgenes * Hpartialgenes - 1L ê 2<, 86<D;
Do@8
n = 0,
square = tensormatrices@@aDD,
Do@8
line = square@@bDD,
Do@8
n = n + 1,
tensorvectors@@n, aDD = line@@cDD
<, 8c, b + 1, partialgenes<D,
<, 8b, 1, partialgenes<D
<, 8a, 1, 6<D;
H* Create Genes µ Genes Annotation Matrices for Selected Genes *L
partialgenenames = Transpose@partialgenenamesD;
annotatematrices = Table@
Table@0, 8partialgenes<, 8partialgenes<D,
8a, 1, 7<D;
Do@
annotatematrices@@aDD = Outer@Times, partialgenenames@@aDD, partialgenenames@@aDDD,
8a, 1, 7<D
H* Keep Only Correlations Above Diagonals in Annotation Matrices *L
Do@
Do@
Do@
annotatematrices@@a, b, cDD = 0,
8c, 1, b<D,
8b, 1, partialgenes<D,
8a, 1, 7<D;
H* Flatten Annotation Matrices Into Annotation Vectors *L
annotatevectors = Table@0, 8partialgenes * Hpartialgenes - 1L ê 2<, 87<D;
Do@8
n = 0,
square = annotatematrices@@aDD,
Do@8
line = square@@bDD,
Do@8
n = n + 1,
annotatevectors@@n, aDD = line@@cDD
<, 8c, b + 1, partialgenes<D,
<, 8b, 1, partialgenes<D
<, 8a, 1, 7<D
partialgenenames = Transpose@partialgenenamesD;
HOEVD.nb
p. 17
H* Display Sorted Significant Tensor Matrices *L
arraypatterns = Transpose@tensorvectorsD;
genes = Dimensions@arraypatternsD@@2DD
435
H* Center Tensor Matrices *L
average = Table@1, 8a, 1, genes<D;
average = N@average ê Sqrt@Dot@average, averageDDD;
arraypatterns = arraypatterns - N@Outer@Times, Dot@arraypatterns, averageD, averageDD;
H* Sort Tensor Matrices *L
Do@
arraypatterns@@aDD = Sort@arraypatterns@@aDD, OrderedQ@88#2<, 8#1<<D &D,
8a, 1, 6<D
H* Create Sorted Tensor Matrices Graph Display *L
p = Table@0, 8a, 1, 6<D;
color = 8
RGBColor@1, 0.5, 0D,
RGBColor@1, 0, 0D,
RGBColor@0, 0, 1D,
RGBColor@0, 0.5, 0D<;
labelx = "Expression Correlation Level";
labely = ColumnForm@
8"Number of Gene Pairs", " ", " ", " ", " ", " ", " ", " ", " "<,
CenterD;
framex = 880.006, 1<, 80.012, 2<, 80.018, 3<, 80.024, 1 õ 2<, 80.03`, 1 õ 3<, 80.036, 2 õ 3<<;
framey = 88-50, "50"<, 8-250, "250"<, 8-genes + 50, "385"<<;
HOEVD.nb
p. 18
Do@8
coordinates = Table@
If@arraypatterns@@n, aDD + 0.006 * n < -0.012, -0.012,
If@arraypatterns@@n, aDD + 0.006 * n > 0.054, 0.054,
arraypatterns@@n, aDD + 0.006 * nDD,
8a, 1, genes<D,
coordinates = Table@8coordinates@@aDD, -a + 1<, 8a, 1, genes<D,
line = Line@coordinatesD,
g = Show@
Graphics@8color@@Mod@n, 4D + 1DD, line<D,
Frame -> True,
FrameLabel -> 8None, labely, labelx, None<,
FrameTicks -> 8None, framey, framex, None<,
GridLines -> 8880.006 * n, RGBColor@0, 0, 0D<<, 88-50, RGBColor@0, 0, 0D<,
8-250, RGBColor@0, 0, 0D<, 8-genes + 50, RGBColor@0, 0, 0D<<<,
PlotRange -> 88-0.012, 0.054<, 817.5, -genes + 1 - 17.5<<,
DisplayFunction -> IdentityD,
g = FullGraphics@gD,
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b, c<, 80, 0<, 80, 1<D,
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 42.5<, 80, -1<, 81, 0<D,
p@@nDD = Show@g,
AspectRatio Ø 1.5 ê 1.2 ê GoldenRatio,
PlotRange -> All,
DisplayFunction Ø IdentityD
<, 8n, 1, 6<D;
HOEVD.nb
p. 19
H* Display Sorted Tensor Matrices *L
Show@Table@p@@aDD, 8a, 1, 6<D,
DisplayFunction Ø $DisplayFunctionD;
Expression Correlation Level
1
2
3
1õ2
1õ3
2õ 3
Number of Gene Pairs
50
250
385
HOEVD.nb
p. 20
H* Estimate Significance of the Association of Tensor Matrices with the Cell Cycle *L
H* Use Cell Cycle Traditional or Microarray Classification of Yeast Genes *L
stages = 8"MêG1", "G1", "S", "SêG2", "G2êM"<;
stagematrix = Outer@Times, stages, stagesD;
stagevector =
Table@0, 8Dimensions@stagesD@@1DD * HDimensions@stagesD@@1DD + 1L ê 2<D;
n = 0;
Do@
Do@8
n = n + 1,
stagevector@@nDD = stagematrix@@a, bDD
<, 8b, 1, a<D,
8a, 1, Dimensions@stagesD@@1DD<D;
most = 50;
annotations = TakeColumns@annotatevectors, 86<D;
numbers = Flatten@Table@
8Count@Flatten@annotationsD, stagevector@@aDDD<,
8a, 1, Dimensions@stagevectorD@@1DD<DD
counter = Table@8a<, 8a, 1, 6<D;
probability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
parallelannotation = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
parallelprobability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
antiannotation = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
antiprobability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
821, 98, 91, 14, 28, 1, 21, 42, 6, 3, 28, 56, 8, 12, 6<
Do@8
pattern = TakeColumns@Sort@
AppendRows@TakeColumns@tensorvectors, counter@@cDDD, annotationsD,
OrderedQ@88#2<, 8#1<<D &D, 82<D,
table = Table@8
stagevector@@aDD,
numbers@@aDD,
Count@Flatten@TakeRows@pattern, 81, most<DD, stagevector@@aDDD<,
8a, 1, Dimensions@stagevectorD@@1DD<D,
probability = Table@8
Sum@N@Binomial@table@@a, 2DD, bD * Binomial@genes - table@@a, 2DD, most - bD ê
Binomial@genes, mostDD, 8b, table@@a, 3DD, most<D,
stagevector@@aDD<,
8a, 1, Dimensions@stagevectorD@@1DD<D,
parallelannotation@@cDD = 8Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 2DD<,
parallelprobability@@cDD = 8ScientificForm@Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 1DD, 2D<,
table = Table@8
stagevector@@aDD,
numbers@@aDD,
Count@Flatten@TakeRows@pattern, 8genes - most + 1, genes<DD, stagevector@@aDDD<,
8a, 1, Dimensions@stagevectorD@@1DD<D,
probability = Table@8
Sum@N@Binomial@table@@a, 2DD, bD * Binomial@genes - table@@a, 2DD, most - bD ê
Binomial@genes, mostDD, 8b, table@@a, 3DD, most<D,
stagevector@@aDD<,
8a, 1, Dimensions@stagevectorD@@1DD<D,
antiannotation@@cDD = 8Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 2DD<,
antiprobability@@cDD = 8ScientificForm@Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 1DD, 2D<<,
8c, 1, Dimensions@counterD@@1DD<D
HOEVD.nb
p. 21
table1 = AppendRows@
881<, 82<, 83<, 81 õ 2<, 81 õ 3<, 82 õ 3<< ,
parallelannotation,
parallelprobability,
antiannotation,
antiprobabilityD;
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
table1 = ReplaceAll@table1,
"MêG1"2 -> "MêG1 MêG1"D;
"G1" "MêG1" -> "G1
MêG1"D;
"G1"2 -> "G1
G1"D;
"MêG1" "S" -> "MêG1 S"D;
"G1" "S" -> "G1
S"D;
"S"2 -> "S
S"D;
"MêG1" "SêG2" -> "MêG1 SêG2"D;
"G1" "SêG2" -> "G1
SêG2"D;
"S" "SêG2" -> "S
SêG2"D;
"SêG2"2 -> "SêG2 SêG2"D;
"G2êM" "MêG1" -> "G2êM MêG1"D;
"G1" "G2êM" -> "G1
G2êM"D;
"G2êM" "S" -> "G2êM S"D;
"G2êM" "SêG2" -> "G2êM SêG2"D;
"G2êM"2 -> "G2êM G2êM"D;
HOEVD.nb
p. 22
H* Estimate Significance of the Association of Tensor Matrices with the Pheromone Response *L
H* Use Pheromone Microarray Classification of Yeast Genes *L
stages = 8"Up", "Down", "None"<;
stagematrix = Outer@Times, stages, stagesD;
stagevector =
Table@0, 8Dimensions@stagesD@@1DD * HDimensions@stagesD@@1DD + 1L ê 2<D;
n = 0;
Do@
Do@8
n = n + 1,
stagevector@@nDD = stagematrix@@a, bDD
<, 8b, 1, a<D,
8a, 1, Dimensions@stagesD@@1DD<D;
most = 50;
annotations = TakeColumns@annotatevectors, 87<D;
numbers = Flatten@Table@
8Count@Flatten@annotationsD, stagevector@@aDDD<,
8a, 1, Dimensions@stagevectorD@@1DD<DD
counter = Table@8a<, 8a, 1, 6<D;
probability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
parallelannotation = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
parallelprobability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
antiannotation = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
antiprobability = Table@80<, 8a, 1, Dimensions@counterD@@1DD<D;
828, 88, 55, 88, 121, 55<
Do@8
pattern = TakeColumns@Sort@
AppendRows@TakeColumns@tensorvectors, counter@@cDDD, annotationsD,
OrderedQ@88#2<, 8#1<<D &D, 82<D,
table = Table@8
stagevector@@aDD,
numbers@@aDD,
Count@Flatten@TakeRows@pattern, 81, most<DD, stagevector@@aDDD<,
8a, 1, Dimensions@stagevectorD@@1DD<D,
probability = Table@8
Sum@N@Binomial@table@@a, 2DD, bD * Binomial@genes - table@@a, 2DD, most - bD ê
Binomial@genes, mostDD, 8b, table@@a, 3DD, most<D,
stagevector@@aDD<,
8a, 1, Dimensions@stagevectorD@@1DD<D,
parallelannotation@@cDD = 8Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 2DD<,
parallelprobability@@cDD = 8ScientificForm@Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 1DD, 2D<,
table = Table@8
stagevector@@aDD,
numbers@@aDD,
Count@Flatten@TakeRows@pattern, 8genes - most + 1, genes<DD, stagevector@@aDDD<,
8a, 1, Dimensions@stagevectorD@@1DD<D,
probability = Table@8
Sum@N@Binomial@table@@a, 2DD, bD * Binomial@genes - table@@a, 2DD, most - bD ê
Binomial@genes, mostDD, 8b, table@@a, 3DD, most<D,
stagevector@@aDD<,
8a, 1, Dimensions@stagevectorD@@1DD<D,
antiannotation@@cDD = 8Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 2DD<,
antiprobability@@cDD = 8ScientificForm@Sort@probability, OrderedQ@88#1<, 8#2<<D &D@@1, 1DD, 2D<<,
8c, 1, Dimensions@counterD@@1DD<D
HOEVD.nb
p. 23
table2 = AppendRows@
881<, 82<, 83<, 81 õ 2<, 81 õ 3<, 82 õ 3<< ,
parallelannotation,
parallelprobability,
antiannotation,
antiprobabilityD;
table2 = ReplaceAll@table2,
table2 = ReplaceAll@table2,
table2 = ReplaceAll@table2,
table2 = ReplaceAll@table2,
table2 = ReplaceAll@table2,
table2 = ReplaceAll@table2,
"Up"2 -> "Up
Up"D;
"Down" "Up" -> "Down Up"D;
"Down"2 -> "Down Down"D;
"None" "Up" -> "None Up"D;
"Down" "None" -> "Down None"D;
"None"2 -> "None None"D;
HOEVD.nb
p. 24
H* Display Significance of Association of Tensor Matrices with the Cellular Programs *L
headerx = 88
ColumnForm@8" ", " ", " "<, LeftD,
ColumnForm@8" ", " ", "Classification"<, LeftD,
ColumnForm@8" ", " ", "Subnetwork"<, LeftD,
ColumnForm@8"Most Likely", "Parallel", "Association"<, LeftD,
ColumnForm@8"P-Value of", "Parallel", "Association"<, LeftD,
ColumnForm@8"Most Likely", "Antiparallel", "Association"<, LeftD,
ColumnForm@8"P-Value of", "Antiparallel", "Association"<, LeftD<,
8" ", " ", " ", " ", " ", " ", " "<<;
spacerx = 88" ", " ", " ", " ", " "<<;
headery = Table@" ", 8a, 1, 7<, 8b, 1, 2<D;
headery@@1DD = 8"HaL", "Cell Cycle"<;
headery@@5DD = 8"HbL", "Pheromone Response"<;
association =
AppendColumns@headerx,
AppendRows@headery,
AppendColumns@TakeRows@table1, 3D, spacerx, TakeRows@table2, 3DDDD;
TableForm@association, TableSpacing Ø 81, 1<D
headerx = 88" ", " ", " ", " ", " ", " ", " "<,
8" ", " ", "Coupling ",
"
", "
", "
", "
"<,
8" ", " ", " ", " ", " ", " ", " "<<;
headery = ReplaceAll@headery, "HaL" -> "HcL"D;
headery = ReplaceAll@headery, "HbL" -> "HdL"D;
association =
AppendColumns@headerx,
AppendRows@headery,
AppendColumns@TakeRows@table1, 84, 6<D, spacerx, TakeRows@table2, 84, 6<DDDD;
TableForm@association, TableSpacing Ø 81, 1<D
HaL
HbL
Classification
Subnetwork
Most Likely
Parallel
Association
Cell Cycle
1
MêG1
Pheromone Response
MêG1
P-Value of
Parallel
Association
Most Likely
Antiparallel
Association
P-Value of
Antiparallel
Association
2.2 µ 10-5
MêG1
S
3.1 µ 10-5
G1
G2êM
2.4 µ 10-8
-7
2
G1
G1
1.8 µ 10
3
G1
S
1.4 µ 10-6
MêG1
S
1.2 µ 10-7
1
Down
Down
7.5 µ 10-16
Down
Up
2. µ 10-27
-2
Down
Up
2.6 µ 10-2
Up
2.1 µ 10-6
2
Down
None
1.6 µ 10
3
Down
Down
1.4 µ 10-2
Down
1õ2
G1
G1
1.8 µ 10-5
G1
MêG1
6.2 µ 10-9
1õ3
G1
S
1.4 µ 10-6
MêG1
S
1.2 µ 10-7
-5
G1
G2êM
1.6 µ 10-7
Coupling
HcL
HdL
Cell Cycle
Pheromone Response
2õ3
G1
S
1.1 µ 10
1õ2
Down
Down
2.3 µ 10-10
Down
Up
2.7 µ 10-10
-7
Down
Up
3.6 µ 10-14
Down
Up
3.9 µ 10-5
1õ3
Down
Down
1.1 µ 10
2õ3
Down
Down
1.6 µ 10-8
HOEVD.nb
p. 25
H* Display Data and Its Projections Genes µ Genes Correlations Tensor Matrices
*L
H* Read List of Cell Cycle-Regulated Genes *L
stream = "DesktopêNetwork_DecompositionêDataêCycle_Genes.txt";
genelist = Import@stream, "Table"D;
genelist = Drop@genelist, 1D;
partialgenes = Dimensions@Intersection@genelist, partialgenenames5DD@@1DD
Clear@streamD;
30
list = Flatten@TakeColumns@genelist, 81<DD;
counter = Table@Flatten@Position@list, partialgenenames5@@a, 1DDDD,
8a, 1, Dimensions@partialgenenames5D@@1DD<D;
counter = ReplaceAll@counter, 8< -> 8Null<D;
partial = AppendRows@counter, partialgenenames5, eigenarrays, tensorD;
partial = Sort@partial, OrderedQ@8#1, #2<D &D;
partialgenenames = TakeRows@
TakeColumns@partial, 82, 8<D,
81, partialgenes<D;
partialeigenarrays = TakeRows@
TakeColumns@partial, 89, Dimensions@eigenexpressionsD@@1DD + 8<D,
81, partialgenes<D;
partialtensor = TakeRows@
TakeColumns@partial, 8Dimensions@eigenexpressionsD@@1DD + 8,
Dimensions@eigenexpressionsD@@1DD + arrays + 7<D,
81, partialgenes<D;
H* Calculate Tensor Matrices *L
partialeigenarrays = Transpose@partialeigenarraysD;
tensormatrices = Table@0, 8a, 1, 3<, 8b, 1, 3<D;
Do@
Do@
tensormatrices@@a, bDD = Outer@Times, partialeigenarrays@@aDD, partialeigenarrays@@bDDD,
8a, 1, 3<D,
8b, 1, 3<D
tensormatrices = 8
tensormatrices@@1, 1DD,
tensormatrices@@2, 2DD,
tensormatrices@@3, 3DD,
-Htensormatrices@@1, 2DD + tensormatrices@@2, 1DDL,
Htensormatrices@@1, 3DD + tensormatrices@@3, 1DDL,
-Htensormatrices@@2, 3DD + tensormatrices@@3, 2DDL<;
partialeigenarrays = Transpose@partialeigenarraysD;
H* Keep Only Correlations Above Diagonals in Tensor Matrices *L
Do@
Do@
Do@
tensormatrices@@a, b, cDD = 0,
8c, 1, b<D,
8b, 1, Dimensions@tensormatrices@@1DDD@@1DD<D,
8a, 1, 6<D;
HOEVD.nb
p. 26
H* Set Correlations Cutoffs *L
cutoffs = Table@Sort@Flatten@Abs@tensormatrices@@aDDDD, OrderedQ@8#2, #1<D &D@@100DD,
8a, 1, 6<D;
Do@
tensormatrices@@aDD = Chop@tensormatrices@@aDD, cutoffs@@aDDD,
8a, 1, 6<D
H* Select Cell Cycle-Regulated Genes With Correlations Above Cutoffs *L
int = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@4DDD,
Position@Sign@tensormatrices@@5DDD,
Position@Sign@tensormatrices@@6DDD,
Table@0,
Table@0,
Table@0,
Table@0,
Table@0,
Table@0,
8a,
8a,
8a,
8a,
8a,
8a,
1,
1,
1,
1,
1,
1,
partialgenes<DD,
partialgenes<DD,
partialgenes<DD,
partialgenes<DD,
partialgenes<DD,
partialgenes<DDD;
Do@8
partialtensor = Drop@partialtensor, 8Flatten@intD@@aDD<D,
partialeigenarrays = Drop@partialeigenarrays, 8Flatten@intD@@aDD<D,
partialgenenames = Drop@partialgenenames, 8Flatten@intD@@aDD<D<,
8a, Dimensions@intD@@1DD, 1, -1<D
partialgenes = Dimensions@partialgenenamesD@@1DD
26
H* Calculate Tensor Matrices For Selected Genes *L
partialeigenarrays = Transpose@partialeigenarraysD;
tensormatrices = Table@0, 8a, 1, 3<, 8b, 1, 3<D;
Do@
Do@
tensormatrices@@a, bDD = Outer@Times, partialeigenarrays@@aDD, partialeigenarrays@@bDDD,
8a, 1, 3<D,
8b, 1, 3<D
tensormatrices = 8
tensormatrices@@1, 1DD,
tensormatrices@@2, 2DD,
tensormatrices@@3, 3DD,
-Htensormatrices@@1, 2DD + tensormatrices@@2, 1DDL,
Htensormatrices@@1, 3DD + tensormatrices@@3, 1DDL,
-Htensormatrices@@2, 3DD + tensormatrices@@3, 2DDL<;
partialeigenarrays = Transpose@partialeigenarraysD;
HOEVD.nb
p. 27
H* Create Network Tensor Decomposition 2 D Red & Green Raster Display *L
H* Create Genes µ Genes Correlations 2 D Red & Green Raster Display *L
framex = Table@8a - 0.5, partialgenenames@@a, 2DD<, 8a, 1, partialgenes<D;
framey = Table@8a + 1 - 0.5, partialgenes - a<, 8a, 0, partialgenes - 1<D;
labelx = "Genes";
labely = ColumnForm@8StyleForm@"8", FontSize Ø 200D, "Genes"<, CenterD;
labely = "Genes";
p = Table@0, 8a, 1, 11<D;
contrast = 1;
labelz = ColumnForm@
8" ", " ", " ", " ", " ", " ", StyleForm@",", FontSize Ø 40, FontWeight -> BoldD<,
LeftD;
Do@8
correlation = Dot@
TakeColumns@partialtensor, 818 * Ha - 1L + 1, 18 * a<D,
Transpose@TakeColumns@partialtensor, 818 * Ha - 1L + 1, 18 * a<DDD,
displaying = Table@
If@contrast * correlation@@i, jDD > 0,
If@contrast * correlation@@i, jDD < 1, 8contrast * correlation@@i, jDD, 0<, 81, 0<D,
If@contrast * correlation@@i, jDD > -1, 80, -contrast * correlation@@i, jDD<, 80, 1<DD,
8i, 1, partialgenes<, 8j, 1, partialgenes<D,
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, partialgenes, 1, -1<, 8j, 1, partialgenes<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, None, None, None<,
FrameLabel -> 8None, labely, labelx, labelz<,
DisplayFunction -> IdentityD,
g = FullGraphics@gD,
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 4, c<, 80, 0<, 80, 1<D,
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c<, 80, -1<, 81, 0<D,
p@@aDD = Show@g,
AspectRatio Ø 0.95,
PlotRange -> All,
DisplayFunction Ø IdentityD<,
8a, 1, 2<D
HOEVD.nb
p. 28
contrast = 5;
labelz = ColumnForm@8StyleForm@" ", FontSize Ø 40, FontWeight -> BoldD<, LeftD;
Do@8
correlation = Dot@
TakeColumns@partialtensor, 818 * Ha - 1L + 1, 18 * a<D,
Transpose@TakeColumns@partialtensor, 818 * Ha - 1L + 1, 18 * a<DDD,
displaying = Table@
If@contrast * correlation@@i, jDD > 0,
If@contrast * correlation@@i, jDD < 1, 8contrast * correlation@@i, jDD, 0<, 81, 0<D,
If@contrast * correlation@@i, jDD > -1, 80, -contrast * correlation@@i, jDD<, 80, 1<DD,
8i, 1, partialgenes<, 8j, 1, partialgenes<D,
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, partialgenes, 1, -1<, 8j, 1, partialgenes<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, None, None, None<,
FrameLabel -> 8None, labely, labelx, labelz<,
DisplayFunction -> IdentityD,
g = FullGraphics@gD,
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 4, c<, 80, 0<, 80, 1<D,
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c<, 80, -1<, 81, 0<D,
p@@aDD = Show@g,
AspectRatio Ø 0.95,
PlotRange -> All,
DisplayFunction Ø IdentityD<,
8a, 3, 3<D
HOEVD.nb
p. 29
H* Create Genes µ Genes Tensor Correlations 2 D Red & Green Raster Displays *L
contrast = 100;
labelz = ColumnForm@
8" ", " ", " ", " ", " ", " ", StyleForm@",", FontSize Ø 40, FontWeight -> BoldD<,
LeftD;
Do@8
correlation = tensormatrices@@a - 3DD,
displaying = Table@
If@contrast * correlation@@i, jDD > 0,
If@contrast * correlation@@i, jDD < 1, 8contrast * correlation@@i, jDD, 0<, 81, 0<D,
If@contrast * correlation@@i, jDD > -1, 80, -contrast * correlation@@i, jDD<, 80, 1<DD,
8i, 1, partialgenes<, 8j, 1, partialgenes<D,
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, partialgenes, 1, -1<, 8j, 1, partialgenes<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, None, None, None<,
FrameLabel -> 8None, labely, labelx, labelz<,
DisplayFunction -> IdentityD,
g = FullGraphics@gD,
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 4, c<, 80, 0<, 80, 1<D,
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c<, 80, -1<, 81, 0<D,
p@@aDD = Show@g,
AspectRatio Ø 0.95,
PlotRange -> All,
DisplayFunction Ø IdentityD<,
8a, 4, 5<D
HOEVD.nb
p. 30
contrast = 100;
labelz = ColumnForm@
8" ", " ", " ", " ", " ", " ", StyleForm@" ", FontSize Ø 40, FontWeight -> BoldD<,
LeftD;
Do@8
correlation = tensormatrices@@a - 3DD,
displaying = Table@
If@contrast * correlation@@i, jDD > 0,
If@contrast * correlation@@i, jDD < 1, 8contrast * correlation@@i, jDD, 0<, 81, 0<D,
If@contrast * correlation@@i, jDD > -1, 80, -contrast * correlation@@i, jDD<, 80, 1<DD,
8i, 1, partialgenes<, 8j, 1, partialgenes<D,
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, partialgenes, 1, -1<, 8j, 1, partialgenes<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, None, None, None<,
FrameLabel -> 8None, labely, labelx, labelz<,
DisplayFunction -> IdentityD,
g = FullGraphics@gD,
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 4, c<, 80, 0<, 80, 1<D,
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c<, 80, -1<, 81, 0<D,
p@@aDD = Show@g,
AspectRatio Ø 0.95,
PlotRange -> All,
DisplayFunction Ø IdentityD<,
8a, 6, 6<D
HOEVD.nb
p. 31
contrast = 100;
labelz = ColumnForm@
8" ", " ", " ", " ", " ", " ", StyleForm@",", FontSize Ø 40, FontWeight -> BoldD<,
LeftD;
Do@8
correlation = tensormatrices@@a - 3DD,
displaying = Table@
If@contrast * correlation@@i, jDD > 0,
If@contrast * correlation@@i, jDD < 1, 8contrast * correlation@@i, jDD, 0<, 81, 0<D,
If@contrast * correlation@@i, jDD > -1, 80, -contrast * correlation@@i, jDD<, 80, 1<DD,
8i, 1, partialgenes<, 8j, 1, partialgenes<D,
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, partialgenes, 1, -1<, 8j, 1, partialgenes<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, None, None, None<,
FrameLabel -> 8None, labely, labelx, labelz<,
DisplayFunction -> IdentityD,
g = FullGraphics@gD,
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 4, c<, 80, 0<, 80, 1<D,
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c<, 80, -1<, 81, 0<D,
p@@aDD = Show@g,
AspectRatio Ø 0.95,
PlotRange -> All,
DisplayFunction Ø IdentityD<,
8a, 7, 8<D
HOEVD.nb
p. 32
contrast = 100;
labelz = ColumnForm@
8" ", " ", " ", " ", " ", " ", StyleForm@" ", FontSize Ø 40, FontWeight -> BoldD<,
LeftD;
Do@8
correlation = tensormatrices@@a - 3DD,
displaying = Table@
If@contrast * correlation@@i, jDD > 0,
If@contrast * correlation@@i, jDD < 1, 8contrast * correlation@@i, jDD, 0<, 81, 0<D,
If@contrast * correlation@@i, jDD > -1, 80, -contrast * correlation@@i, jDD<, 80, 1<DD,
8i, 1, partialgenes<, 8j, 1, partialgenes<D,
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, partialgenes, 1, -1<, 8j, 1, partialgenes<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, None, None, None<,
FrameLabel -> 8None, labely, labelx, labelz<,
DisplayFunction -> IdentityD,
g = FullGraphics@gD,
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 4, c<, 80, 0<, 80, 1<D,
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c<, 80, -1<, 81, 0<D,
p@@aDD = Show@g,
AspectRatio Ø 0.95,
PlotRange -> All,
DisplayFunction Ø IdentityD<,
8a, 9, 9<D
HOEVD.nb
p. 33
H* Create Coefficients of Tensor Correlations 2 D Red & Green Raster Displays *L
core = 8
Flatten@Dot@Transpose@eigenarraysD, partialmatrix1, Transpose@partialmatrix1D, eigenarraysDD,
Flatten@Dot@Transpose@eigenarraysD, matrix2, Transpose@matrix2D, eigenarraysDD,
Flatten@Dot@Transpose@eigenarraysD, matrix3, Transpose@matrix3D, eigenarraysDD<;
contrast = 0.25;
coefficients = Table@0, 83<D;
Do@
coefficients@@aDD = 8
core@@aDD@@0 * 39 + 1DD,
core@@aDD@@1 * 39 + 2DD,
core@@aDD@@2 * 39 + 3DD<,
8a, 1, 3<D
coefficients = Transpose@coefficientsD;
displaying = Table@
If@contrast * coefficients@@i, jDD > 0,
If@contrast * coefficients@@i, jDD < 1, 8contrast * coefficients@@i, jDD, 0<, 81, 0<D,
If@contrast * coefficients@@i, jDD > -1, 80, -contrast * coefficients@@i, jDD<, 80, 1<DD,
8i, 1, 3<, 8j, 1, 3<D;
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, 3, 1, -1<, 8j, 1, 3<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, None, None, None<,
FrameLabel -> 8None, None, None, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 3, c<, 80, 0<, 80, 1<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 3<, 80, -1<, 81, 0<D;
p@@10DD = Show@g,
AspectRatio Ø 1.05,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 34
contrast = 0.25;
coefficients = Table@0, 83<D;
Do@
coefficients@@aDD = 8
-core@@aDD@@0 * 39 + 2DD,
core@@aDD@@0 * 39 + 3DD,
-core@@aDD@@1 * 39 + 3DD<,
8a, 1, 3<D
coefficients = Transpose@coefficientsD;
displaying = Table@
If@contrast * coefficients@@i, jDD > 0,
If@contrast * coefficients@@i, jDD < 1, 8contrast * coefficients@@i, jDD, 0<, 81, 0<D,
If@contrast * coefficients@@i, jDD > -1, 80, -contrast * coefficients@@i, jDD<, 80, 1<DD,
8i, 1, 3<, 8j, 1, 3<D;
g = Show@
Graphics@
RasterArray@
Table@
RGBColor@displaying@@i, j, 1DD, displaying@@i, j, 2DD, 0D,
8i, 3, 1, -1<, 8j, 1, 3<DDD,
AspectRatio -> 1,
Frame -> True,
FrameTicks -> 8None, None, None, None<,
FrameLabel -> 8None, None, None, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8b - 3, c<, 80, 0<, 80, 1<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 3<, 80, -1<, 81, 0<D;
p@@11DD = Show@g,
AspectRatio Ø 1.05,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 35
H* Display Network Decompsoition *L
approx = Show@Graphics@
Text@StyleForm@"º", FontSize Ø 40, FontWeight -> BoldD, 80, 0<D
D, DisplayFunction -> IdentityD;
plus = Show@Graphics@
Text@StyleForm@"+", FontSize Ø 40, FontWeight -> BoldD, 80, 0<D
D, DisplayFunction -> IdentityD;
right = Show@Graphics@
Text@StyleForm@"D", FontSize Ø 160D, 80, 0<D
D, DisplayFunction -> IdentityD;
left = Show@Graphics@
Text@StyleForm@"@", FontSize Ø 160D, 80, 0<D
D, DisplayFunction -> IdentityD;
labelx0 = Show@Graphics@
Text@StyleForm@"Networks"D, 80, 0<D
D, DisplayFunction -> IdentityD;
labelx1 = Show@Graphics@
Text@StyleForm@"Subnetworks"D, 80, 0<D
D, DisplayFunction -> IdentityD;
labely1 = Show@Graphics@
Text@StyleForm@"Subnetworks"D, 80, 0<, 80, 0<, 80, 1<D
D, DisplayFunction -> IdentityD;
labelx2 = Show@Graphics@
Text@StyleForm@"Couplings"D, 80, 0<D
D, DisplayFunction -> IdentityD;
labely2 = Show@Graphics@
Text@StyleForm@"Couplings"D, 80, 0<, 80, 0<, 80, 1<D
D, DisplayFunction -> IdentityD;
Show@8
Graphics@[email protected], 0<, 82.1, 1<, leftD<D,
Graphics@[email protected], 0<, 82.2, 1<, p@@7DDD<D,
Graphics@[email protected], 0<, 83.2, 1<, p@@8DDD<D,
Graphics@[email protected], 0<, 84.2, 1<, p@@9DDD<D,
Graphics@[email protected], 0<, 85.2, 1<, rightD<D,
Graphics@[email protected], 0.5<, 85.75, 0.975<, labelx0D<D,
Graphics@[email protected], 0.5<, 85, 1.15<, labelx2D<D,
Graphics@[email protected], 0<, 85, 1<, labely2D<D,
Graphics@[email protected], 0<, 85.5, 1<, leftD<D,
Graphics@[email protected], 0.3<, 85.7, 0.7<, p@@11DDD<D,
Graphics@[email protected], 0<, 86.3, 1<, rightD<D,
Graphics@[email protected], 0.75<, 82.1, 1.75<, leftD<D,
Graphics@[email protected], 0.75<, 82.2, 1.75<, p@@4DDD<D,
Graphics@[email protected], 0.75<, 83.2, 1.75<, p@@5DDD<D,
Graphics@[email protected], 0.75<, 84.2, 1.75<, p@@6DDD<D,
Graphics@[email protected], 0.75<, 85.2, 1.75<, rightD<D,
Graphics@[email protected], 1.25<, 85.75, 1.725<, labelx0D<D,
Graphics@[email protected], 1.25<, 85, 1.9<, labelx1D<D,
Graphics@[email protected], 0.75<, 85, 1.75<, labely1D<D,
Graphics@[email protected], 0.75<, 85.5, 1.75<, leftD<D,
Graphics@[email protected], 1.05<, 85.7, 1.45<, p@@10DDD<D,
Graphics@[email protected], 0.75<, 86.3, 1.75<, rightD<D,
Graphics@[email protected], 0.75<, 85.75, 1.75<, plusD<D,
Graphics@[email protected], 1.5<, 82.1, 2.5<, leftD<D,
Graphics@[email protected], 1.5<, 82.2, 2.5<, p@@1DDD<D,
Graphics@[email protected], 1.5<, 83.2, 2.5<, p@@2DDD<D,
Graphics@[email protected], 1.5<, 84.2, 2.5<, p@@3DDD<D,
Graphics@[email protected], 1.5<, 85.2, 2.5<, rightD<D,
Graphics@[email protected], 2<, 85, 2.65<, labelx0D<D,
Graphics@[email protected], 1.5<, 84.65, 2.5<, approxD<D
<, PlotRange -> AllD;
HOEVD.nb
p. 36
Genes
,
Subnetworks
Genes
Genes
,
,
Couplings
Genes
Genes
,
Genes
Genes
Genes
Genes
,
Networks
Subnetworks
Genes
Genes
Genes
Genes
Networks
Couplings
,
D
D@D
D@D
º
Genes
Genes
Genes
@
@
@
Networks
Genes
Genes
HOEVD.nb
p. 37
H* Create Coefficients of Tensor Correlations Bar Chart Display *L
core = 8
Flatten@Dot@Transpose@eigenarraysD, partialmatrix1, Transpose@partialmatrix1D, eigenarraysDD,
Flatten@Dot@Transpose@eigenarraysD, matrix2, Transpose@matrix2D, eigenarraysDD,
Flatten@Dot@Transpose@eigenarraysD, matrix3, Transpose@matrix3D, eigenarraysDD<;
coefficients = Table@0, 83<D;
Do@
coefficients@@aDD = 8
core@@aDD@@0 * 39 + 1DD,
core@@aDD@@1 * 39 + 2DD,
core@@aDD@@2 * 39 + 3DD<,
8a, 1, 3<D
coefficients = Chop@coefficients ê
Sum@eigenexpressions@@aDD ^ 2, 8a, 1, Dimensions@eigenexpressionsD@@1DD<DD;
labelx = ColumnForm@8" ", " ",
StyleForm@"1", FontSize Ø 24, FontColor -> RGBColor@1, 0, 0DD<, CenterD;
gridx = Table@a, 8a, -0.1, 0.4, 0.1<D;
framex = gridx;
framex@@2DD = "0";
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@framex@@aDD
DDD, 8a, 1, Dimensions@framexD@@1DD<DD;
Do@
Do@framex@@aDD = StringJoin@ToString@framex@@aDDD, " "D,
8b, 1, size - sizes@@aDD<D,
8a, 1, Dimensions@framexD@@1DD<D;
framex = Table@8gridx@@aDD, framex@@aDD<, 8a, 1, Dimensions@framexD@@1DD<D;
gridx = Table@8gridx@@aDD, RGBColor@0, 0, 0D<, 8a, 1, Dimensions@gridxD@@1DD<D;
framey = 881, "
3"<, 82, "
2"<, 83, "
1"<<;
g = BarChart@
Table@coefficients@@1DD@@Dimensions@coefficientsD@@1DD - aDD,
8a, 0, Dimensions@coefficientsD@@1DD - 1<D,
BarOrientation -> Horizontal,
PlotRange -> 880, 0.4 * 1.0001<, 80.5, 3 + 0.5<<,
AspectRatio -> 1,
Axes -> False,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, None, labelx, None<,
GridLines -> 8gridx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.75<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.35<, 80, 0<, 80, 1<D;
g1 = Show@g,
AspectRatio -> 1.5,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 38
labelx = ColumnForm@8"Networks", " ",
StyleForm@"2", FontSize Ø 24, FontColor -> RGBColor@0, 0, 1DD<, CenterD;
gridx = Table@a, 8a, 0, 0.008, 0.002<D;
framex = gridx;
framex@@1DD = "0";
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@framex@@aDD
DDD, 8a, 1, Dimensions@framexD@@1DD<DD;
Do@
Do@framex@@aDD = StringJoin@ToString@framex@@aDDD, " "D,
8b, 1, size - sizes@@aDD<D,
8a, 1, Dimensions@framexD@@1DD<D;
framex = Table@8gridx@@aDD, framex@@aDD<, 8a, 1, Dimensions@framexD@@1DD<D;
gridx = Table@8gridx@@aDD, RGBColor@0, 0, 0D<, 8a, 1, Dimensions@gridxD@@1DD<D;
framey = 881, "
"<, 82, "
"<, 83, "
"<<;
g = BarChart@
Table@coefficients@@2DD@@Dimensions@coefficientsD@@1DD - aDD,
8a, 0, Dimensions@coefficientsD@@1DD - 1<D,
BarOrientation -> Horizontal,
BarStyle Ø 8RGBColor@0, 0, 1D<,
PlotRange -> 880, 0.008 * 1.0001<, 80.5, 3 + 0.5<<,
AspectRatio -> 1,
Axes -> False,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, None, labelx, None<,
GridLines -> 8gridx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.75<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.35<, 80, 0<, 80, 1<D;
g2 = Show@g,
AspectRatio -> 1.5,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 39
labelx = ColumnForm@8" ", " ",
StyleForm@"3", FontSize Ø 24, FontColor -> RGBColor@0, 0.5, 0DD<, CenterD;
gridx = Table@a, 8a, -0.001, 0.004, 0.001<D;
framex = gridx;
framex@@2DD = "0";
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@framex@@aDD
DDD, 8a, 1, Dimensions@framexD@@1DD<DD;
Do@
Do@framex@@aDD = StringJoin@ToString@framex@@aDDD, " "D,
8b, 1, size - sizes@@aDD<D,
8a, 1, Dimensions@framexD@@1DD<D;
framex = Table@8gridx@@aDD, framex@@aDD<, 8a, 1, Dimensions@framexD@@1DD<D;
gridx = Table@8gridx@@aDD, RGBColor@0, 0, 0D<, 8a, 1, Dimensions@gridxD@@1DD<D;
framey = 881, "
"<, 82, "
"<, 83, "
"<<;
g = BarChart@
Table@coefficients@@3DD@@Dimensions@coefficientsD@@1DD - aDD,
8a, 0, Dimensions@coefficientsD@@1DD - 1<D,
BarOrientation -> Horizontal,
BarStyle Ø 8RGBColor@0, 0.5, 0D<,
PlotRange -> 880, 0.004 * 1.0001<, 80.5, 3 + 0.5<<,
AspectRatio -> 1,
Axes -> False,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, None, labelx, None<,
GridLines -> 8gridx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.75<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.35<, 80, 0<, 80, 1<D;
g3 = Show@g,
AspectRatio -> 1.5,
PlotRange -> All,
DisplayFunction Ø IdentityD;
coefficients = Table@0, 83<D;
Do@
coefficients@@aDD = 8
-core@@aDD@@0 * 39 + 2DD,
core@@aDD@@0 * 39 + 3DD,
-core@@aDD@@1 * 39 + 3DD<,
8a, 1, 3<D
coefficients = Chop@coefficients ê
Sum@eigenexpressions@@aDD ^ 2, 8a, 1, Dimensions@eigenexpressionsD@@1DD<DD;
size = 6;
HOEVD.nb
p. 40
labelx = ColumnForm@8" ", " ", " "<, CenterD;
gridx = Table@a, 8a, -0.004, 0, 0.001<D;
framex = gridx;
framex@@5DD = "0";
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@framex@@aDD
DDD, 8a, 1, Dimensions@framexD@@1DD<DD;
Do@
Do@framex@@aDD = StringJoin@ToString@framex@@aDDD, " "D,
8b, 1, size - sizes@@aDD<D,
8a, 1, Dimensions@framexD@@1DD<D;
framex = Table@8gridx@@aDD, framex@@aDD<, 8a, 1, Dimensions@framexD@@1DD<D;
gridx = Table@8gridx@@aDD, RGBColor@0, 0, 0D<, 8a, 1, Dimensions@gridxD@@1DD<D;
framey = 881, 2 õ 3<, 82, 1 õ 3<, 83, 1 õ 2<<;
g = BarChart@
Table@coefficients@@1DD@@Dimensions@coefficientsD@@1DD - aDD,
8a, 0, Dimensions@coefficientsD@@1DD - 1<D,
BarOrientation -> Horizontal,
PlotRange -> 88-0.004, 0.0000001<, 80.5, 3 + 0.5<<,
AspectRatio -> 1,
Axes -> False,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, None, labelx, None<,
GridLines -> 8gridx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.75<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.35<, 80, 0<, 80, 1<D;
g4 = Show@g,
AspectRatio -> 1.5,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 41
labelx = ColumnForm@8" ", " ", " "<, CenterD;
gridx = Table@a, 8a, 0, 0.004, 0.001<D;
framex = gridx;
framex@@1DD = "0";
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@framex@@aDD
DDD, 8a, 1, Dimensions@framexD@@1DD<DD;
Do@
Do@framex@@aDD = StringJoin@ToString@framex@@aDDD, " "D,
8b, 1, size - sizes@@aDD<D,
8a, 1, Dimensions@framexD@@1DD<D;
framex = Table@8gridx@@aDD, framex@@aDD<, 8a, 1, Dimensions@framexD@@1DD<D;
gridx = Table@8gridx@@aDD, RGBColor@0, 0, 0D<, 8a, 1, Dimensions@gridxD@@1DD<D;
framey = 881, "
"<, 82, "
"<, 83, "
"<<;
g = BarChart@
Table@coefficients@@2DD@@Dimensions@coefficientsD@@1DD - aDD,
8a, 0, Dimensions@coefficientsD@@1DD - 1<D,
BarOrientation -> Horizontal,
BarStyle Ø 8RGBColor@0, 0, 1D<,
PlotRange -> 880, 0.004 * 1.0001<, 80.5, 3 + 0.5<<,
AspectRatio -> 1,
Axes -> False,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, None, labelx, None<,
GridLines -> 8gridx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.75<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.35<, 80, 0<, 80, 1<D;
g5 = Show@g,
AspectRatio -> 1.5,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 42
labelx = ColumnForm@8" ", " ", " "<, CenterD;
gridx = Table@a, 8a, -0.002, 0.002, 0.001<D;
framex = gridx;
framex@@3DD = "0";
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@framex@@aDD
DDD, 8a, 1, Dimensions@framexD@@1DD<DD;
Do@
Do@framex@@aDD = StringJoin@ToString@framex@@aDDD, " "D,
8b, 1, size - sizes@@aDD<D,
8a, 1, Dimensions@framexD@@1DD<D;
framex = Table@8gridx@@aDD, framex@@aDD<, 8a, 1, Dimensions@framexD@@1DD<D;
gridx = Table@8gridx@@aDD, RGBColor@0, 0, 0D<, 8a, 1, Dimensions@gridxD@@1DD<D;
framey = 881, "
"<, 82, "
"<, 83, "
"<<;
g = BarChart@
Table@coefficients@@3DD@@Dimensions@coefficientsD@@1DD - aDD,
8a, 0, Dimensions@coefficientsD@@1DD - 1<D,
BarOrientation -> Horizontal,
BarStyle Ø 8RGBColor@0, 0.5, 0D<,
PlotRange -> 88-0.002, 0.002 * 1.0001<, 80.5, 3 + 0.5<<,
AspectRatio -> 1,
Axes -> False,
Frame -> True,
FrameTicks -> 8None, framey, framex, None<,
FrameLabel -> 8None, None, labelx, None<,
GridLines -> 8gridx, None<,
DisplayFunction -> IdentityD;
g = FullGraphics@gD;
g@@1, 2DD = g@@1, 2DD ê.
Text@labelx, 8b_, c_<, 80., -1.<D Ø
Text@labelx, 8b, c + 0.75<, 80, -1<, 81, 0<D;
g@@1, 2DD = g@@1, 2DD ê.
Text@a_, 8b_, c_<, 80., -1.<D Ø
Text@a, 8b, c + 0.35<, 80, 0<, 80, 1<D;
g6 = Show@g,
AspectRatio -> 1.5,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 43
H* Display Coefficients of Tensor Correlations Bar Chart *L
labely = "HaL Subnetworks
";
p1 = Show@GraphicsArray@88g1, g2, g3<<D,
Frame Ø True,
FrameStyle Ø 8RGBColor@1, 1, 1D<,
FrameLabel -> 8None, labely, None, None<,
GraphicsSpacing Ø -0.125,
DisplayFunction Ø IdentityD;
labely = "HbL Couplings
";
p2 = Show@GraphicsArray@88g4, g5, g6<<D,
Frame Ø True,
FrameStyle Ø 8RGBColor@1, 1, 1D<,
FrameLabel -> 8None, labely, None, None<,
GraphicsSpacing Ø -0.125,
DisplayFunction Ø IdentityD;
Show@GraphicsArray@88p1<, 8p2<<D,
GraphicsSpacing Ø -0.225D;
Networks
0.3
0.4
0
0.002
0.004
0.006
0.008
0
0.001
0.002
0.003
0.004
-0.001
0
0
0.001
0.002
0.003
0.004
-0.002
-0.001
0
0.001
0.002
3
0.2
0.1
2
-0.002
HaL Subnetworks
0
1
1
2
HbL Couplings
-0.003
-0.004
3
1õ2
1õ3
2õ3
HOEVD.nb
p. 44
H* Create Genes µ Genes Tensor Correlations Network Displays *L
H* Keep Only Correlations Above Diagonals in Tensor Matrices *L
Do@
Do@
Do@
tensormatrices@@a, b, cDD = 0,
8c, 1, b<D,
8b, 1, Dimensions@tensormatrices@@1DDD@@1DD<D,
8a, 1, 6<D;
H* Cutoff Correlations in Tensor Matrices *L
Do@
tensormatrices@@aDD = Chop@tensormatrices@@aDD, cutoffs@@aDDD,
8a, 1, 6<D
Do@
Do@
Do@
tensormatrices@@a, b, cDD = 0,
8c, 1, b<D,
8b, 1, Dimensions@tensormatrices@@1DDD@@1DD<D,
8a, 1, 6<D;
sizes = Flatten@
Table@
Dimensions@
Characters@
ToString@partialgenenames@@a, 2DD
DDD,
8a, 1, partialgenes<DD;
size = Sort@sizes, OrderedQ@8#2, #1<D &D@@1DD;
Do@
Do@partialgenenames@@a, 2DD = StringJoin@ToString@partialgenenames@@a, 2DDD, " "D,
8b, 1, size - sizes@@aDD<D,
8a, 1, partialgenes<D;
HOEVD.nb
p. 45
H* Define Display Parameters *L
Clear@x, y, zD;
R@theta_D = 88Cos@thetaD, Sin@thetaD<, 8-Sin@thetaD, Cos@thetaD<<;
polypoints@theta_, x_D = Flatten@Transpose@Dot@R@thetaD, Transpose@880, x<<DDDD;
redline@y_, z_D = Graphics@8RGBColor@1, 0, 0D,
Line@8polypoints@2 * y * Pi ê partialgenes, 1D, polypoints@2 * z * Pi ê partialgenes,
greenline@y_, z_D = Graphics@8RGBColor@0, 0.5, 0D,
Line@8polypoints@2 * y * Pi ê partialgenes, 1D, polypoints@2 * z * Pi ê partialgenes,
blueline@y_, z_D = Graphics@8RGBColor@0, 0, 1D,
Line@8polypoints@2 * y * Pi ê partialgenes, 1D, polypoints@2 * z * Pi ê partialgenes,
orangeline@y_, z_D = Graphics@8RGBColor@1, 0.5, 0D,
Line@8polypoints@2 * y * Pi ê partialgenes, 1D, polypoints@2 * z * Pi ê partialgenes,
1D<D<D;
1D<D<D;
1D<D<D;
1D<D<D;
color1@stage_D =
If@stage == "Up", RGBColor@0, 0, 0D,
If@stage == "Down", [email protected], 0.5, 0.5D, RGBColor@1, 1, 1DD
D;
color2@stage_D =
If@stage == "MêG1", RGBColor@1, 1, 0D,
If@stage == "G1", RGBColor@0, 0.5, 0D,
If@stage == "S", RGBColor@0, 0, 1D,
If@stage == "SêG2", RGBColor@1, 0, 0D,
If@stage == "G2êM", RGBColor@1, 0.5, 0D, RGBColor@1, 1, 1DD
DDDD;
circle1 = Table@
Graphics@8
color1@partialgenenames@@a, 7DDD,
Disk@80, 0<, 1.35,
8-2 * Ha + 0.5L * Pi ê partialgenes + Pi ê 2., -2 * Ha - 0.5L * Pi ê partialgenes + Pi ê 2.<D<D,
8a, partialgenes, 1, -1<D;
circle2 = Table@
Graphics@8
color2@partialgenenames@@a, 6DDD,
Disk@80, 0<, 1.3,
8-2 * Ha + 0.5L * Pi ê partialgenes + Pi ê 2., -2 * Ha - 0.5L * Pi ê partialgenes + Pi ê 2.<D<D,
8a, partialgenes, 1, -1<D;
circle3 = Graphics@8RGBColor@1, 1, 1D, Disk@80, 0<, 1.25D<D;
circle4 = Table@
Graphics@8
RGBColor@0, 0, 0D,
Disk@polypoints@2 * a * Pi ê partialgenes, 1D, 0.02D<D, 8a, 1, partialgenes<D;
circle5 = Table@
Graphics@8
RGBColor@0, 0, 0D,
Text@partialgenenames@@a, 2DD, polypoints@2 * a * Pi ê partialgenes, 1.15D,
80, 0<, polypoints@2 * a * Pi ê partialgenes, 1.15DD<D,
8a, 1, partialgenes<D;
HOEVD.nb
p. 46
H* Display First Genes µ Genes Tensor Correlations Network *L
int1 = Position@Sign@tensormatrices@@1DDD, 1D;
int2 = Position@Sign@tensormatrices@@1DDD, -1D;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HaL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p1 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
H* Display Second Genes µ Genes Tensor Correlations Network *L
int1 = Position@Sign@tensormatrices@@2DDD, 1D;
int2 = Position@Sign@tensormatrices@@2DDD, -1D;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HbL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p2 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 47
H* Display Third Genes µ Genes Tensor Correlations Network *L
int1 = Position@Sign@tensormatrices@@3DDD, 1D;
int2 = Position@Sign@tensormatrices@@3DDD, -1D;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HcL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p3 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
H* Display Fourth Genes µ Genes Tensor Correlations Network *L
int1 = Position@Sign@tensormatrices@@4DDD, 1D;
int2 = Position@Sign@tensormatrices@@4DDD, -1D;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HdL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p4 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 48
H* Display Fifth Genes µ Genes Tensor Correlations Network *L
int1 = Position@Sign@tensormatrices@@5DDD, 1D;
int2 = Position@Sign@tensormatrices@@5DDD, -1D;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HeL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p5 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 49
H* Display Sixth Genes µ Genes Tensor Correlations Network *L
int1 = Position@Sign@tensormatrices@@6DDD, 1D;
int2 = Position@Sign@tensormatrices@@6DDD, -1D;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HfL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p6 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 50
H* Display Selected Genes µ Genes Tensor Correlations Networks *L
A3
RF
2
CDC20
CDC20
SPO12
SPO12
1
1
CIK
A3
RF
D5
4
RA
D5
1
CDC9
1
CDC9
1
RA
D5
1
SST2
N3
CL
SW
I4
CLB
2
CDC20
ASF1
CDC20
SPO12
CLB5
SPO12
CIK
1
1
CIK
CLN
2
A
RF
CLB
2
SW
I4
1
TIP
FK
S1
RA
D
RA
D
S
CH
1
54
RA
D5
1
CDC9
1
MFA2
M1
NU
SST2
MCD1
MFA2
SST2
M1
NU
MNN1
R5
HP
HTA1
HT
B1
HeL
1
2
S
GA
CW
P
N3
CL
FK
S1
R5
HP
MCD1
MNN1
HTA1
HT
B1
1
2
S
GA
CW
P
S
CH
MFA2
CIK
FK
S1
54
CLB
2
CLB5
CLN
2
A
RF
CLB
SW
I4
ASF1
1
N3
CL
SW
I4
1
TIP
HdL
RA
RA
CH
S1
D5
4
RA
D5
1
CDC9
1
SST2
N3
CL
S1
CH
HbL
FK
S1
M1
NU
HaL
MFA2
Show@GraphicsArray@88p1, p2, p3<, 8p4, p5, p6<<D,
GraphicsSpacing Ø 0D;
R5
HP
MCD1
MNN1
HTA1
HT
B1
1
P2
S
GA
CW
M1
NU
R5
HP
MCD1
MNN1
HTA1
HT
B1
1
P2
S
GA
CW
HOEVD.nb
p. 51
H* Compare Genes µ Genes Eigencorrelations Networks Using Logic *L
H* Display Parallel Intersection of Fourth AND First AND Second Networks *L
int1 = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@4DDD,
int2 = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@4DDD,
1D,
1D,
1DD;
-1D,
-1D,
-1DD;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HaL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p1 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 52
H* Display Antiparallel Intersection of Fourth AND @First AND SecondD Networks *L
int1 = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@4DDD,
int2 = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@4DDD,
1D,
1D,
-1DD;
-1D,
-1D,
1DD;
orangetable = Table@orangeline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
bluetable = Table@blueline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, orangetable, bluetable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HbL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p2 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
H* Display Parallel Intersection of Fifth AND First AND Third Networks *L
int1 = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@5DDD,
int2 = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@5DDD,
1D,
1D,
1DD;
-1D,
-1D,
-1DD;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HcL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p3 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 53
H* Display Antiparallel Intersection of Fifth AND @First AND ThirdD Networks *L
int1 = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@5DDD,
int2 = Intersection@
Position@Sign@tensormatrices@@1DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@5DDD,
1D,
1D,
-1DD;
-1D,
-1D,
1DD;
orangetable = Table@orangeline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
bluetable = Table@blueline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, orangetable, bluetable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HdL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p4 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 54
H* Display Parallel Intersection of Sixth AND Second AND Third Networks *L
int1 = Intersection@
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@6DDD,
int2 = Intersection@
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@6DDD,
1D,
1D,
1DD;
-1D,
-1D,
-1DD;
redtable = Table@redline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
greentable = Table@greenline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, redtable, greentable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HeL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p5 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
HOEVD.nb
p. 55
H* Display Antiparallel Intersection of Sixth AND @Second AND ThirdD Networks *L
int1 = Intersection@
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@6DDD,
int2 = Intersection@
Position@Sign@tensormatrices@@2DDD,
Position@Sign@tensormatrices@@3DDD,
Position@Sign@tensormatrices@@6DDD,
1D,
1D,
-1DD;
-1D,
-1D,
1DD;
orangetable = Table@orangeline@int1@@a, 1DD, int1@@a, 2DDD, 8a, 1, Dimensions@int1D@@1DD<D;
bluetable = Table@blueline@int2@@a, 1DD, int2@@a, 2DDD, 8a, 1, Dimensions@int2D@@1DD<D;
p = Show@
8circle1, circle2, circle3, circle4, circle5, orangetable, bluetable,
Graphics@8RGBColor@0, 0, 0D, Text@StyleForm@"HfL", FontSize Ø 24D, 8-1.1, 1.1<D<D<,
AspectRatio -> 1,
PlotRange -> 88-1.25, 1.25<, 8-1.25, 1.25<<,
Frame Ø False,
FrameTicks -> False,
FrameLabel -> 8None, None, None, None<,
GridLines -> 8None, None<,
DisplayFunction -> IdentityD;
p = FullGraphics@pD;
p@@1, 2DD = p@@1, 2DD ê.
Text@labely, 8b_, c_<, 81., 0.<D Ø
Text@labely, 8-1.18, 0<, 80, 0<, 80, 1<D;
p6 = Show@p,
AspectRatio -> 1.,
PlotRange -> All,
DisplayFunction Ø IdentityD;
H* Display Selected Intersections of Genes µ Genes Tensor Correlations Networks *L
Show@GraphicsArray@88p1, p2<, 8p3, p4<, 8p5<<D,
GraphicsSpacing Ø 0D;
HOEVD.nb
p. 56
RA
D5
MFA2
SST2
CDC9
1
N3
CL
4
RA
D5
1
S1
M1
NU
M1
NU
2
CLB
1
CIK
1
CIK
SW
I4
HOEVD.nb
R5
HP
MCD1
MNN1
HTA1
HT
B1
S1
P2
CLB
2
1
TIP
GA
CW
MCD1
A3
RF
CLB
2
FK
S1
MFA2
SST2
CDC9
1
N3
CL
4
RA
D5
1
S1
RA
D5
CDC9
1
SST2
MFA2
N3
CL
RA
D5
1
S1
D5
4
CH
RA
CH
R5
HP
CLN
2
MCD1
1
TIP
MNN1
SW
I4
A3
RF
HTA1
HT
B1
HdL
1
2
MNN1
R5
HP
HTA1
HT
B1
1
2
S
GA
CW
P
CH
RA
D
CDC9
1
SST2
MFA2
N3
CL
RA
D5
1
1
CDC9
1
SST2
MFA2
N3
CL
54
RA
D5
1
1
54
S
CH
RA
D
S
CH
HbL
S
GA
CW
P
R5
HP
MCD1
MNN1
HTA1
HT
B1
1
2
HeL
S
GA
CW
P
HcL
SW
I4
M1
NU
FK
S1
M1
NU
1
CIK
CLN
2
1
CIK
2
CLB
1
TIP
CLB
2
SW
I4
A3
RF
SW
I4
HaL
A3
RF
TI
CDC20
ASF1
CDC20
A
SPO12
CLB5
SPO12
C
CL
FK
S1
A3
RF
TI
CDC20
ASF1
CDC20
A
SPO12
CLB5
SPO12
C
CL
FK
S1
p. 57
CDC20
1
TIP
C
CDC20
ASF1
SPO12
CLB5
CIK
CLN
2
FK
S1
M1
NU
GA
CW
P
S1
2
R5
HP
MCD1
MNN1
HTA1
HT
B1
HOEVD.nb
p. 58
1