title: Toxicogenomic markers for corticosteroid treatment in beef cattle: integrated analysis of transcriptomic data.
abstract: In the present work, an integrated analysis was performed on DNA-microarray data of bovine muscle samples belonging to controls, animals treated with various growth promoters (GPs) and unknown commercial samples. The aim was identify a robust gene expression signature of corticosteroid treatment for the classification of commercial samples, despite the effects of biological variation and other confounding factors. DNA-Microarray data from 5 different batches of bovine skeletal muscle samples were analyzed (146 samples). After preprocessing, expression data from animals treated with corticosteroids and controls from the different batches (89 samples) were used to train a Support Vector Machines (SVMs) classifier. The optimal number of gene probes chosen by our classification framework was 73. The SVMs with linear kernel built on these 73 biomarker genes was predicted to perform on novel samples with a high classification accuracy (Matthew's correlation coefficient equal to 0.77) and an average percentage of false positive and false negative equal to 5% and 6%, respectively. Concluding, a relatively small set of genes was able to discriminate between controls and corticosteroid-treated animals, despite different breeds, animal ages, and combination of GPs. The results are extremely promising, suggesting that integrated analysis provides robust transcriptomic signatures for GP abuse.
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, Padova, Italy. Electronic address: sara.pegolo@unipd.it.
authors.forename: Sara
authors.initials: S
authors.lastname: Pegolo
authors.affiliation: Information Engineering Department, University of Padua, Via Gradenigo, 6/, 35131 Padova, Italy.
authors.forename: Barbara
authors.initials: B
authors.lastname: Di Camillo
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, Padova, Italy.
authors.forename: Clara
authors.initials: C
authors.lastname: Montesissa
authors.affiliation: Department of Animal Pathology, University of Turin, via L. da Vinci 44, 10095, Grugliasco, Italy.
authors.forename: Francesca Tiziana
authors.initials: FT
authors.lastname: Cannizzo
authors.affiliation: Department of Animal Pathology, University of Turin, via L. da Vinci 44, 10095, Grugliasco, Italy.
authors.forename: Bartolomeo
authors.initials: B
authors.lastname: Biolatti
authors.affiliation: Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, 35020 Legnaro, Padova, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Bargelloni
mesh_terms: D000284:Administration, Oral; D000305:Adrenal Cortex Hormones / Q000494:pharmacology*; D000818:Animals; D001947:Breeding; D002417:Cattle; D020869:Gene Expression Profiling / Q000379:methods*; D005819:Genetic Markers; D008297:Male; D008958:Models, Molecular; D018482:Muscle, Skeletal / Q000187:drug effects / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D060388:Support Vector Machine; D043922:Toxicogenetics / Q000379:methods*; D059467:Transcriptome
chemical_list: D000305:Adrenal Cortex Hormones; D005819:Genetic Markers
keywords: Biomarker; Bovine; DNA-microarray; Integrated analysis; Muscle