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

BMC Medical Genomics

Table 3 Prediction of environmental chemicals associated with lung cancer samples (GSE10072).

Chemical Predicted	Hypergeometric P-value	Rank (percentile)	q-value	Relevant genes in set (number of references)	Citations
Doxorubicin	1 × 10^-6	16 (99)	4 × 10^-4	CASP3(60), ABCB1(28), BAX(26), BCL2 (23)	[54]
Sodium arsenite	8 × 10^-6	20 (98)	4 × 10^-4	JUN(13), NQ01(6), EGR1(6)	[55–57]
Vanadium pentoxide	1 × 10^-5	24 (98)	6 × 10^-4	HBEGF(3), CDK7(1), CDKN1B (1), CDKN1C(1)	[58]
Dimethylnitrosamine	6 × 10^-5	27 (98)	7 × 10^-4	TGFB1(23), TIMP1(15), PCNA(6)	[31]
Indomethacin	2 × 10^-4	34 (97)	0.002	BIRC5(3), CDKN1B(2), MMP9(2)	[59–61]
2-Acetylaminofluorene	3 × 10^-4	36 (97)	0.003	ABCB1(4), ABCG2(4), KRT19(2)	[62]
Asbestos, Serpentine	4 × 10^-4	39 (97)	0.004	IL6(2), MMP9(2), MMP12(2), PDGFB(2)	[63]

Shown in the table are a subset of the highly ranked chemicals (p < 0.001) that were predicted to have association with lung cancer gene expression (non-smokers) and had evidence of association with the MeSH term "Lung Neoplasms". Columns have similar definitions as Table 2.

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