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

BMC Medical Genomics

Table 1 Chemical Prediction Results from the Verification Phase.

Actual Chemical Exposure (GEO accession)	Chemicals Predicted	Hypergeometric P-value	Rank (Percentile)	q-value	Relevant Genes Expressed
Vitamin D3 on H. sapiens muscle cells (GSE5145)	Calcitriol	1 × 10^-23	1 (100)	0	VDR (25), CYP24A1 (14)
TCDD on M. musculus (GSE10082)	TCDD	2 × 10^-15	3 (99)	0	CYP1A1 (59), CYP1B1 (15), AHRR(6), CYP1A2 (14)
Bisphenol A on H. sapiens Ishikawa cells (GSE17624)	Bisphenol A	1 × 10^-6	15 (99)	0	ESR1(31), ESR2(7), S100G (6)
Zinc sulfate on H. sapiens bronchial tissue (GSE2111)	Zinc sulfate	3 × 10^-3	15 (99)	0.04	SLC30A1 (3), MT1F(2), MT1G(2)
Estradiol on M. musculus thymus (GSE2889)	Estradiol	5 × 10^-3	17 (99)	0.08	C3(6), LPL (4), CTSB (2)
Estradiol on H. sapiens MCF7 cell line (GSE11352)	Estradiol	5 × 10^-3	19 (99)	0.08	ISG20 (2), MGP (2), SERPINA1 (2)

Each row represents a gene expression dataset and relevant prediction and ranking. The first column specifies the gene expression dataset, the 2^nd column the actual exposure applied to the samples for the gene expression set. The 3^rd and 4^th columns represent the hypergeometric p-value for chemical-gene set enrichment along with the rank of the chemical in the prediction list. The 5^th column shows the 5^th percentile of the ranking derived from 100 random samplings of genes from the gene expression dataset. The 6^th column show notable genes expressed in the chemical-gene set along with the number of references the chemical-gene relation in the CTD.

ISSN: 1755-8794