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Table 5 Gene set enrichment analysis (GSEA) of classifiers on their original gene expression profiles (GEPs) for training

From: Discovery and validation of gene classifiers for endocrine-disrupting chemicals in zebrafish (danio rerio)

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

 
  1. 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.
  2. aSearched but no qualified classifier found for the condition. Its GSEA was conducted using classifiers for other unrelated chemical-tissues.
  3. bNo classifier search was conducted due to insufficient sample size for the condition. Its GSEA was conducted using classifiers for other unrelated chemical-tissues.