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Table 1 Statistically enriched annotation clusters for each stressor exposure in the Western fence lizard (Sceloporus occidentalis) where top clusters are categorically matched to functions and toxicological phenotypes

From: Multiple environmental stressors induce complex transcriptomic responses indicative of phenotypic outcomes in Western fence lizard

Exposure 1 (TNT x Diet)
Treatments Significant Annotation Clusters Cluster ID Enrichment Score Top Clusters - Enriched Function (Summary of Cluster Components) Categorical Match 1 - Enriched Function Summary Response Categorical Match 2 - Cluster to Toxicological Phenotype
 TNT 18 C1 2.14 proteolysis, peptidase activity, serine hydrolase activity Protein Catabolism ↓: ALB, GLOB, TP, & TS
  C2 1.74 carbohydrate biosynthesis processes Carbohydrate Storage ↓ Body Weight
  C3 1.55 lipid transport, lipid localization, lipoprotein metabolism, extracellular Lipid Metabolism ↓ Body Weight, ↑ Liver Wt.
  C4 1.42 glycolysis, carbohydrate catabolic process, glucose catabolic process Carbohydrate to Cellular Energy ↓ Body Weight; ↓ Feeding
  C5 1.26 hemostasis, blood coagulation, wound healing, endopeptidase activity RBC Retention & Wound Healing ↓: Hb, Hct, RBC & MCHC; ↑ spleen wt.
 Diet 2 C1 1.12 mitochondrion, mitochondrial envelope Cellular energy production ↓ Body Weight; ↓ Inguinal fat
  C2 0.51 calcium binding, cation binding, metal binding Cell signaling –
INI x Diet 0 – – –   
Exposure 2 (Malaria Infection x Diet)
 Malaria 9 C1 2.57 positive regulation of T cell, lymphocyte & leukocyte activation. Regulation of immune system process, regulation of programmed cell death Immune Response ↑: WBC, Lympho, Mono; ↓ H/L
  C2 1.42 zinc finger - RING-type, zinc finger C3HC4 RING-type Immune Response ↑: WBC, Lympho, Mono; ↓ H/L
  C3 1.10 zinc finger - C2H2, cation binding Immune Response ↑: WBC, Lympho, Mono; ↓ H/L
  C4 1.02 apoptosis, programmed cell death Immune Response ↑ WBCs
  C5 0.60 immunoglobulin-like, signal peptide Immune Response ↑ WBCs
 Diet 10 C1 1.14 cofactor binding, coenzyme binding, oxidation reduction Electron Iransport, Energy Production ↓ Feeding; ↓: WBC, Lympho, H/L
  C2 1.04 plasma lipoprotein particle, protein-lipid complex, extracellular space Lipid Metabolism ↓ Feeding; ↓: WBC, Lympho, H/L
  C3 0.86 endoplasmic reticulum membrane, endomembrane system Cellular & endomembrane transport –
  C4 0.80 mitochondrion, mitochondrial envelope Cellular energy production ↓ Feeding; ↓: WBC, Lympho, H/L
  C5 0.54 organelle lumen, membrane-enclosed lumen - Nested in Mitrochnodria Cellular energy production ↓ Feeding; ↓: WBC, Lympho, H/L
Malaria x Diet 1 C1 0.71 zinc ion binding, cation binding Immune Response Malaria: ↑ WBCs & Lympho; Diet: ↓ WBCs & Lympho
Exposure 3 (TNT x Malaria Infection)
 TNT 10 C1 1.54 ribonucleoprotein complex biogenesis, rRNA processing Ribosomal Function –
  C2 1.49 homeostatic process, membrane fraction PPAR Signaling, Lipid Metab. ↓ Body Weight, ↑ Liver Wt.
  C3 1.15 vesicle-mediated transport, endocytosis Intracellular transport, Immune Sys. ↑ WBCs
  C4 1.11 WD40 repeat, RNA processing, ribonucleoprotein complex Transcriptional Reg., Signal Trans. –
  C5 0.85 proteolysis, protein catabolic process, endopeptidase activity Protein Catabolism ↓ Body Weight
 Malaria 0 – – –   
 TNT x iviaiaria 0 – – –   
  1. The top clusters column provides representative biological processes, molecular functions, cellular components, canonical pathways and functional motifs within each enriched cluster (See Additional file 1: Tables S5 and S6 for full detail). The categorical matches to enriched function represent a summary response of the enriched annotation cluster. The categorical matches to toxicological phenotypes provide putative connections to toxicological observations summarized in Table 2 of McFarland et al. [1]
  2. Key for Toxicological Phenotype Symbols: ALB = Albumin, GLOB = Globulin, TP = Total Protein, TS = Total Solids, Hb = Hemoglobin Concentration, Hct = Hematocrit, RBC = Red Blood Cell Concentration, MCHC = Mean Corpuscular Hemoglobin Concentration, WBC = White Blood Cell Concentration, Lympho = Lymphocyte Concentration, Mono = Monocyte Concentration, H/L = Heterophyl / Lymphocyte Ratio
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BMC Genomics

ISSN: 1471-2164

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