Table 2

Prediction of environmental chemicals associated with prostate cancer samples (GSE6919).

Chemical Predicted

Hypergeometric P-value

Rank (percentile)

q-value

Relevant genes in set (number of references)

Citations


Estradiol

4 × 10-10

5 (99)

0

ESR2(37), PGR(34), MAPK1(14)

[37]


Raloxifene

1 × 10-9

6 (99)

0

ESR2(6), IGF1(5), BCL2(4)

[38]


Sodium arsenite

1 × 10-8

8 (99)

0

JUN(13), MAPK1(9), CCND1(8), FOS(6)

[30]


Doxorubicin

7 × 10-7

11 (99)

0

BCL2(23), MAPK1(14), TNF(10)

[39-42]


Cadmium

6 × 10-6

13 (99)

0

MT2A(14), MT1A(12), MT3(11), MT1(6)

[43]


Genistein

3 × 10-5

19 (99)

6 × 10-4

ESR2(22), PGR (10), MAPK1 (5)

[44-46]


Diethylstilbestrol

3 × 10-5

22 (98)

0.001

ESR2(8), FOS(8), HOXA10(4)

[47,48]


Fenretinide

3 × 10-4

40 (97)

0.004

BCL2(3), ELF3(2), LDHA(2)

[49]


Bisphenol A

6 × 10-4

47 (96)

0.01

PGR(8), ESR2(7), IL4RA(2)

[37]


Zinc

9 × 10-4

53 (96)

0.01

MT3(18), MT2A(13), MT1A(11)

[50-53]


Shown in the table are a subset of the highly ranked chemicals (p < 0.001) that were predicted to have association with prostate cancer gene expression and had evidence of association with the MeSH term "Prostatic Neoplasms" as in the CTD. The 1st column represents the chemical predicted and the 2nd and 3rd columns show the hypergeometric p-value and ranking. The 4th column shows q-value derived from random samples of genes. The 5th column shows the notable genes in the chemical-gene set that were differentially expressed. The 6th column contains references for the prostate cancer and chemical association found from the CTD.

Patel and Butte BMC Medical Genomics 2010 3:17   doi:10.1186/1755-8794-3-17

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