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The present Houston Vanguard sub-study examines a small group of subcutaneously IL-2 (…


Biology Articles » Immunobiology » CD8 apoptosis may be a predictor of T cell number normalization after immune reconstitution in HIV » Tables

Tables
- CD8 apoptosis may be a predictor of T cell number normalization after immune reconstitution in HIV

Table 1
Clinical, methylation and CGH data for prostate cancer tissues
Tumor No.
Stage
Gleason Score
Molecular Group
LINE-1 %hypo
No. hypem. genes
Chromosomal losses
Chromosomal gains
36
pT3bN0
7

1
4
-
3q21q26.2
38
pT2N0
7

4
4
-
-
50
pT3bN0
7
hypo
10
4
1q31
6p,7p,16p,17p, 18p,19, 20q13,21,22,Y
65
pT3bN0
7
both
9
4
Y
1p33p34.3, 2p21p23, 2q14.1q14.3, 2q33q36, 3p14.1p21.3, 3q25.1q26.3, 4q13.3q28, 5q22, 5q31.2q32, 6q16.1q22.1, 8q22.1q23, 10p11.2p13, 10q11.2q22.3, 12q13.2q24.31, 13q21.1q31, 14q21q32.2, 18q11.2q22, Xp21.3q27
83
pT3bN0
7
hypo
6
4
1q31, 2q33q37, 4q31, 13q21q31, 15q24,
4q12, 5q13, 17p, 18p, 19, Y
89
pT2bN0
3
hypo
5
2
9q33q34, X
2q11q24, 4q12q22, 6q22, 12p,18p, Y
93
pT3bN0
7

4
4
-
Yq
95
pT3bN1
10
hypo
7
4
Xq
18p, Y
99
pT2bN0
5

0
1
-
2q14q24,10q11q21
101
pT3aN0
8
none
0
3
1p36, 14q31q32, 17p, 22
-
105
pT3aN0
5

1
1
1p36,2,3,4
-
107
pT3aN0
7
none
3
4
18p, Y
4q24, 6q22, Xp11.2p11.4
117
pT3bN0
5

3
4
-
1q21q25,2q11q14,19q13
119
pT3bN1
9
none
1
3
7p15pter, 15q23qter, Y
10q21q22
121
pT2bN0
6
chrom8
1
4
1q32q41, 3p21, 4p15p16, 8p22p23, 9p23p24,10q25q26, 11q23q25, 12q24, 13q32q34, 14q24q32, 15q24q26, 17q24q25, Xp21p22
Yq
123
pT2aN0
5

1
1
9q21.2q21.3, 10q26, 16p, Y
2p14p16, 2q24.3q32.1, 6q14q16.1
125
pT2bN0
6

1
0
14q31
-
127
pT2bN0
7
none
2
2
7q36, Yq
2q22q32.3, 4q11q31.3, 13q14.1q21.1, 14q21q23, 15q21.1q23
133
pT2bN1
7
chrom8
0
4
22, Y
1q, 2q22q34, 3q11.1q26.1, 4q22q27, 5q21q31, 6q21q24, 8q11q23, 10q11q21.3, 12q21q22, 14q12q22, X
137
pT2bN0
8
chrom8
1
1
16, 17, 18p, 18q11.1q21.1, 19, 21q22, Y
3q23q26.3, 4q13.2q21.3, 5q, 7q13q31, 8p21pter, 8q24, 9p, 14q13qter
139
pT3bN1
9
chrom8
1
4
19q, Y
1q25q31, 2q11q33, 3, 4q, 5q13q23, 6q14q25, 7q21qter, 8q13q23, 11q14qter, 13q21q32, 14q11.1q21, 18q12, Xq21.3qter
141
pT2bN0
4
chrom8
0
2
16, 17, 18p, 19, 20, 22, Y
1q31q32.1, 2, 3q13.3qter, 4q11q31.1, 5q14qter, 6q, 7p12pter, 7q22q31.2, 8q12q21.2, 10q21.1q23.1, 11q14.3qter, 12q14qter, 13q14.1qter
145
pT4N1
7
hypo
11
3
Y
3q25q27,4q24q26,7q11q22,13q31q34,17p,18p
149
pT2bN0
6

2
2
Y
2p, 4p12, 4q24q26, 5q11q13, 7p12, 8q23q24, 9,11q22, 12q12q15, 14q24, 17, 19, 20q13,
151
pT3aN0
7

0
1
3p13p14
6p14, Xp21
153
pT3aN0
5

2
1

Xq11.2q13
155
pT3aN0
5

5
4
19p
3p25p26, Y
157
pT2aN0
8

2
0
-
1q21q31, 2q12q24, 3q, 4q12q21, 5q13q14, 6q14q16, 7q11, 8q12q22, 12q12q13, 18p, Y
161
pT2bN0
5

3
4
15q22q24, Xq22q25
-
163
pT3bN1
5
chrom8
2
2
16, 17p, 18p, 20, Y
1q25qter, 2p11p16, 2q32q34, 3q12, 3q21q27, 4q, 6q15q24, 8q12q21, 8q23q24, 12q13q21, 13q14q32, 14q12q21, 18q, Xq11.1q26
169
pT3aN0
7
chrom8
3
2
16, 17p, 18p, 19, Y
2, 3, 4q, 5q, 7p15pter, 8q22q24, 13q31qter, 14q24qter, 17q23, 18q21qter, Xq21.3q26
171
pT2bN0
5
hypo
8
4
10q26, 18p. -19, 22, Y
1p31, 2p12p13, 2q11q34, 4q22q26, 5q22, 6q11q23, 14q22q24, X
175
pT2bN0
8

11
4
13q14
-
183
pT3aN0
6

19
4
1p36,9q34
-
187
pT2bN0
8
chrom8
1
3
16, 17p, 18p, 19, 21, 22, Y
1, 2, 3q13qter, 4q, 5q14q33.1, 6q16q23, 7p, 7q22q33, 8q, 11q14.3qter, 12q14qter, 13q21qter, 14q24q31, 15q, Xq22qter
189
pT2bN0
7
none
0
4
3p25p26, 10q26, Xq22qter, Yq
-
191
pT2bN0
7

0
3
4q31, 5q31q35, 9q33, 12p12
-
205
pT3aN0
7

5
1
18p, 19, 22, Y
2q31q33, 6q22.3q23, 10q21q22, Xp11.1p11.4, Xq
209
pT3aN0
7
both
8
4
1p36, 8p, 16, 17, 18p, 19, 20, 22, Y
1q31q32.1, 2q11.1q34, 3, 4q21.1qter, 5q14q31, 6q11q23, 7q21q34, 8q, 9, 11q14q22, 12q15q24, 13q14qter, 18q
213
pT2aN0
7

8
4
8q24.2qter, 14q32, 16, 17, 18p, 22, Y
-
215
pT3aN0
7

9
4
19q13, 22q13,Y
3q24q26, 5q12, 8p12, 17, 18, Xp11p21, X21q24
217
pT2bN0
8

5
4
18p13, Y
2q33q35, 4q13q28,5q21q31,8q21,8q24,12q13, 12q21q23, Xq13q25
219
pT4N1
7
both
21
4
5q34qter, 8p22pter, 19, Yq
1p22p31.3, 4q21q22, 4q31.1, 5q13, 6q24q26, 7q, 8q21q24, 10q21, 11q14q22, 20q13, Xq13q22
225
pT3bN0
6

4
4
4q28, 8q24qter, Yq
-
227
pT2aN1
7

3
4
22q13
3q11q21
232
pT2bN1
7
both
13
4
8p22pter
-
245
pT3aN0
7

4
3
17p13, 18p
1p31
247
pT3bN1
7
chrom8
3
3
8p21pter, 9q21, 22, Y
Xq12
253
pT3aN1
7

1
4
1p36, 2q33q37, 6p21.3p25, 8p21, 14q31q32, Y
-
256
pT3bN0
7

1
4
2p2p21, 6q, 15q26,16p, 18,X
-
The numbers of the tumors used in the microarray analysis are in bold type, as are hypomethylation values considered significantly elevated (APC, GSTP1, RARB2, and RASSF1A. LINE-1 hypomethylation was determined by Southern blot analysis. Chromosomal dosage changes were determined by comparative genomic hybridization.
Table 2
Top 20 significant GO groups in interaction analysis, sorted according to the weight algorithm
Rank (weight)
GO ID
GO Term definition
Annotated number of genes
Significant number of genes
Expected number of genes
Rank (classic)
p-value (classic)
p-value (weight)
1
GO:0006955
immune response
1241
57
26.05
2
1.50E-08
3.30E-05
2
GO:0009607
response to biotic stimulus
1409
63
29.58
1
6.40E-09
5.30E-05
3
GO:0030865
cortical cytoskeleton organization and biogenesis
22
5
0.46
8
7.80E-05
7.80E-05
4
GO:0001766
lipid raft polarization
2
2
0.04
11
0.00044
0.00044
5
GO:0006956
complement activation
49
6
1.03
15
0.00054
0.00054
6
GO:0007155
cell adhesion
972
36
20.40
16
0.00067
0.00076
7
GO:0009967
positive regulation of signal transduction
176
11
3.69
22
0.00125
0.00125
8
GO:0009611
response to wounding
589
25
12.36
17
0.00070
0.00137
9
GO:0045995
regulation of embryonic development
12
3
0.25
24
0.00175
0.00175
10
GO:0042135
neurotransmitter catabolism
15
3
0.31
28
0.00346
0.00346
11
GO:0043122
regulation of I-kappaB kinase/NF-kappaB cascade
149
9
3.13
29
0.00425
0.00425
12
GO:0006952
defense response
1354
60
28.42
3
2.20E-08
0.00445
13
GO:0009190
cyclic nucleotide biosynthesis
33
4
0.69
33
0.00483
0.00483
14
GO:0050678
regulation of epithelial cell proliferation
17
3
0.36
34
0.00501
0.00501
15
GO:0008354
germ cell migration
7
2
0.15
39
0.00861
0.00861
16
GO:0009613
response to pest, pathogen or parasite
776
34
16.29
7
4.20E-05
0.01258
17
GO:0016064
humoral defense mechanism (sensu Vertebrata)
165
10
3.46
25
0.00258
0.01310
18
GO:0006024
glycosaminoglycan biosynthesis
24
3
0.50
46
0.01339
0.01339
19
GO:0050672
negative regulation of lymphocyte proliferation
9
2
0.19
47
0.01435
0.01435
20
GO:0008037
cell recognition
28
3
0.59
58
0.02038
0.02038

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