Predicting environmental chemical factors associated with disease-related gene expression data

BMC Medical Genomics

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 1^st column represents the chemical predicted and the 2^nd and 3^rd columns show the hypergeometric p-value and ranking. The 4^th column shows q-value derived from random samples of genes. The 5^th column shows the notable genes in the chemical-gene set that were differentially expressed. The 6^th column contains references for the prostate cancer and chemical association found from the CTD.

ISSN: 1755-8794