Table 5

Gene set enrichment analysis (GSEA) of classifiers on their original gene expression profiles (GEPs) for training
Chemical Brain GEP (F-ratio) Brain classifiers enriched on brain GEP (FDR) Ovary GEP (F-ratio) Ovary classifiers enriched on ovary GEP (FDR)
Fadrozole (FAD) FAD-brain (3.41) No enrichment FAD-ovary (2.01)a PRO-ovary (0.005)
KET-ovary (0.006)
FLU-ovary (0.01)
17α-ethynyl estradiol (EE2) EE2-brain (5.96) EE2-brain (0.028) EE2-ovary (22.4)b KET-ovary (0.002)
PRO-ovary (0.004)
FLU-ovary (0.023)
Muscimol (MUS) MUS-brain (6.42) MUS-brain (0.0) MUS-ovary (42.62)b FIP-ovary (0.027)
KET-ovary (0.035)
PRO-ovary (0.052)
FLU-ovary (0.077)
Fipronil (FIP) FIP-brain (6.78) FIP-brain (0.002); MUS-brain (0.012) FIP-ovary (10.23) FIP-ovary (0.006);
PRO-ovary (0.0)
KET-ovary (0.0)
Flutamide (FLU) NA FLU-ovary (67.23) KET-ovary (0.002)
PRO-ovary (0.006)
FLU-ovary (0.007)
Ketoconazole (KET) KET-brain (9.17)

KET-brain (0.006);

MUS-brain (0.008)

KET-ovary (4.85) KET-ovary (0.0)
PRO-ovary (0.008)
FLU-ovary (0.18)
Prochloraz (PRO) PRO-brain (19.42) PRO-brain (0.0) PRO-ovary (14.48) PRO-ovary (0.0)
KET-ovary (0.009)
FLU-ovary (0.008)
17β-trenbolone (TRE) TRE-brain (22.94)b No enrichment TRE-ovary (3.28)a KET-ovary (0.1)
PRO-ovary (0.234);
FIP-ovary (0.236)
Trilostane (TRI) NA TRI-ovary (11.16)b PRO-ovary (0.121)
Vinclozolin (VIN) NA VIN-ovary (6.09) VIN-ovary (0.024);
KET-ovary (0.0)
PRO-ovary (0.107)
FLU-ovary (0.106)
F-ratio mean = 10.59 F-ratio mean = 18.44

Each classifier was formatted into a gene set, and multiple gene sets were grouped by their tissue of origin. GSEA was conducted by individual chemical-tissue conditions, at a threshold of FDR ≤ 0.25. Classifiers enriched on the top or bottom of a ranked gene list are separated by a semicolon. If two classifiers of the same condition are both significant, only the most significant one is listed. A GEP in bold indicates the availability of its corresponding classifier as a gene set. FDR, false discovery rate; F-ratio, maximum Fisher’s discriminant ratio; “NA“, a condition not included in the study.

aSearched but no qualified classifier found for the condition. Its GSEA was conducted using classifiers for other unrelated chemical-tissues.

bNo classifier search was conducted due to insufficient sample size for the condition. Its GSEA was conducted using classifiers for other unrelated chemical-tissues.

Wang et al.

Wang et al. BMC Genomics 2012 13:358   doi:10.1186/1471-2164-13-358

Open Data