Supplementary data Table 5 (doc 46K)

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Table 5A. Supplementary materials
Genomic regions showing significant alterations in signal intensities in samples of
metastatic- as compared to localized prostate cancer.
Chr.
Start*
End*
SNPs in
Region
Gain/loss
Region Size
(Mb)
p-value**
1
1
4
5
7
7
8
8
8
9
9
10
10
10
11
12
12
12
14
17
17
19
19
19
19
19
20
20
20
21
22
201.25
208.07
10.00
34.67
42.94
128.44
95.18
123.41
133.82
74.178
125.24
68.90
72.00
94.33
65.70
102.96
107.47
115.20
20.78
70.89
74.54
16.19
34.22
50.48
53.41
59.25
2.45
23.45
42.36
38.98
45.08
204.51
210.66
10.43
35.19
44.99
130.40
96.72
126.82
136.26
75.08
129.79
71.20
73.93
95.10
70.86
103.60
111.44
116.42
21.54
71.76
81.25
17.53
35.19
52.29
56.01
59.89
4.19
24.10
43.87
39.16
46.44
27
27
16
21
19
27
36
39
50
19
26
37
25
27
28
20
28
23
17
20
24
10
11
15
14
10
15
16
14
15
10
Gain
Gain
Loss
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
3.26
2.59
0.43
0.52
2.05
1.96
1.54
3.41
2.44
0.90
4.55
2.31
1.93
0.78
5.16
0.64
3.98
1.23
0.76
0.88
6.71
1.33
0.97
1.81
2.59
0.64
1.74
0.64
1.50
0.19
1.36
0.009
0.009
0.01
0.01
0.007
0.003
0.008
0.006
0.004
0.008
0.001
0.002
0.005
0.005
0.004
0.009
0.004
0.007
0.007
0.003
0.002
0.007
0.004
0.002
0.003
0.007
0.006
0.006
0.007
0.006
0.009
Listed are regions with consecutive SNPs each displaying a difference at 1% significance level in signal intensity
of the samples from localized compared to metastatic prostate cancer. Multiple regions at chromosomes 10 and
19 are not necessarily independent regions of altered DNA copy changes, but can be parts of larger regions. False
discovery rate of chromosomes with significant segments is less than 1/22=1.5%.
* The genomic positions were based on the May 2004 genome assembly (hg17) of the UCSC human genome
browser (http://genome.ucsc.edu/).
** Segments with p≤ 0.01 were reported
Table 5B Supplementary materials
Genomic regions showing significant alterations in signal intensities between samples of
metastatic prostate cancer with and without previous androgen deprivation.
Chr.
2
2
2
10
Start*
Region
End*
SNPs in
(Mb)
Gain/Loss
Region Size
p-value**
42.53
53.83
55.56
60.65
43.91
54.09
55.88
61.33
13
13
17
22
Gain
Gain
Gain
Gain
1.37
0.26
0.32
0.68
0.043
0.043
0.022
0.013
Listed are regions with consecutive SNPs each displaying significant difference (p<0.01) in signal intensity of the
samples from metastatic prostate cancer with and without antiandrogen therapy. Androgen deprivation therapy
was performed as orchiectomy. Multiple regions at chromosome 2 are not necessarily independent regions of
altered DNA copy changes, but can be parts of larger regions.
* The genomic positions was based on the May 2004 genome assembly (hg17) of the UCSC human genome
browser (http://genome.ucsc.edu/).
Table 5C Supplementary materials
Genomic regions showing significant alterations in signal intensities between samples of
Gleason score ≥ 8 as compared to Gleason score ≤7 prostate cancer.
Chr.
1
1
1
1
1
3
7
8
8
8
8
8
8
8
14
Start*
Region
143.19
196.95
198.23
204.63
209.45
156.70
127.94
70.26
80.29
94.96
98.00
100.79
109.020
122.20
32.70
End*
SNPs in
(Mb)
Gain/Loss
Region Size
p-value**
144.80
198.04
204.51
206.06
211.35
158.44
130.31
71.75
83.07
96.44
100.48
102.90
110.62
127.94
33.98
28
27
71
25
42
34
29
31
48
36
42
34
40
106
11
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
Gain
1.61
1.09
6.27
1.43
1.90
1.74
2.37
1.49
2.79
1.48
2.48
2.12
1.60
5.74
1.28
0.007
0.007
0.000
0.008
0.001
0.004
0.005
0.008
0.003
0.006
0.003
0.007
0.003
0.000
0.01
Listed are regions with consecutive SNPs each displaying significant difference (p<0.01) in signal intensity of the
samples from low differentiated compared to high differentiated prostate cancer. Multiple regions at
chromosomes 1 and 8 are not necessarily independent regions of altered DNA copy changes, but can be parts of
larger regions. FDR of chromosomes with significant segments is less than 1/5=20%.
* The genomic positions was based on the May 2004 genome assembly (hg17) of the UCSC human genome browser
(http://genome.ucsc.edu/).
** Segments with p≤ 0.01 were reported.
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