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

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

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