Evaluation of single-cell gel electrophoresis data: Combination of variance analysis with sum of ranking differences
Само за регистроване кориснике
2014
Аутори
Heberger, KarolyKolarević, Stoimir
Kracun-Kolarević, Margareta
Sunjog, Karolina
Gačić, Zoran
Kljajic, Zoran
Mitric, Milena
Vukovic-Gacic, Branka
Чланак у часопису (Објављена верзија)
Метаподаци
Приказ свих података о документуАпстракт
Specimens of the mussel Mytilus galloprovincialis were collected from five sites in the Boka Kotorska Bay (Adriatic Sea, Montenegro) during the period summer 2011-autumn 2012. Three types of tissue, haemolymph, digestive gland were used for assessment of DNA damage. Images of randomly selected cells were analyzed with a fluorescence microscope and image analysis by the Comet Assay IV Image-analysis system. Three parameters, viz, tail length, tail intensity and Olive tail moment were analyzed on 4200 nuclei per cell type. We observed variations in the level of DNA damage in mussels collected at different sites, as well as seasonal variations in response. Sum of ranking differences (SRD) was implemented to compare use of different types of cell and different measure of comet tail per nucleus. Numerical scales were transferred into ranks, range scaling between 0 and 1; standardization and normalization were carried out. SRD selected the best (and worst) combinations: tail moment is the be...st for all data treatment and for all organs; second best is tail length, and intensity ranks third (except for digestive gland). The differences were significant at the 5% level. Whereas gills and haemolymph cells do not differ significantly, cells of the digestive gland are much more suitable to estimate genotoxicity. Variance analysis decomposed the effect of different factors on the SRD values. This unique combination has provided not only the relative importance of factors, but also an overall evaluation: the best evaluation method, the best data pre-treatment, etc., were chosen even for partially contradictory data. The rank transformation is superior to any other way of scaling, which is proven by ordering the SRD values by SRD again, and by cross validation.
Кључне речи:
Ranking / Mussels / Fluorescence / Ecogenotoxicity / Comet assay / Analysis of varianceИзвор:
Mutation Research-Genetic Toxicology and Environmental Mutagenesis, 2014, 771, 15-22Издавач:
- Elsevier, Amsterdam
Финансирање / пројекти:
- Ministry of Science of Montenegro
- OTKA (Hungarian Scientific - Research Foundation)Orszagos Tudomanyos Kutatasi Alapprogramok (OTKA) [K112547]
DOI: 10.1016/j.mrgentox.2014.04.028
ISSN: 1383-5718
PubMed: 25308437
WoS: 000341471100003
Scopus: 2-s2.0-84904387700
Институција/група
Institut za multidisciplinarna istraživanjaTY - JOUR AU - Heberger, Karoly AU - Kolarević, Stoimir AU - Kracun-Kolarević, Margareta AU - Sunjog, Karolina AU - Gačić, Zoran AU - Kljajic, Zoran AU - Mitric, Milena AU - Vukovic-Gacic, Branka PY - 2014 UR - http://rimsi.imsi.bg.ac.rs/handle/123456789/819 AB - Specimens of the mussel Mytilus galloprovincialis were collected from five sites in the Boka Kotorska Bay (Adriatic Sea, Montenegro) during the period summer 2011-autumn 2012. Three types of tissue, haemolymph, digestive gland were used for assessment of DNA damage. Images of randomly selected cells were analyzed with a fluorescence microscope and image analysis by the Comet Assay IV Image-analysis system. Three parameters, viz, tail length, tail intensity and Olive tail moment were analyzed on 4200 nuclei per cell type. We observed variations in the level of DNA damage in mussels collected at different sites, as well as seasonal variations in response. Sum of ranking differences (SRD) was implemented to compare use of different types of cell and different measure of comet tail per nucleus. Numerical scales were transferred into ranks, range scaling between 0 and 1; standardization and normalization were carried out. SRD selected the best (and worst) combinations: tail moment is the best for all data treatment and for all organs; second best is tail length, and intensity ranks third (except for digestive gland). The differences were significant at the 5% level. Whereas gills and haemolymph cells do not differ significantly, cells of the digestive gland are much more suitable to estimate genotoxicity. Variance analysis decomposed the effect of different factors on the SRD values. This unique combination has provided not only the relative importance of factors, but also an overall evaluation: the best evaluation method, the best data pre-treatment, etc., were chosen even for partially contradictory data. The rank transformation is superior to any other way of scaling, which is proven by ordering the SRD values by SRD again, and by cross validation. PB - Elsevier, Amsterdam T2 - Mutation Research-Genetic Toxicology and Environmental Mutagenesis T1 - Evaluation of single-cell gel electrophoresis data: Combination of variance analysis with sum of ranking differences EP - 22 SP - 15 VL - 771 DO - 10.1016/j.mrgentox.2014.04.028 ER -
@article{ author = "Heberger, Karoly and Kolarević, Stoimir and Kracun-Kolarević, Margareta and Sunjog, Karolina and Gačić, Zoran and Kljajic, Zoran and Mitric, Milena and Vukovic-Gacic, Branka", year = "2014", abstract = "Specimens of the mussel Mytilus galloprovincialis were collected from five sites in the Boka Kotorska Bay (Adriatic Sea, Montenegro) during the period summer 2011-autumn 2012. Three types of tissue, haemolymph, digestive gland were used for assessment of DNA damage. Images of randomly selected cells were analyzed with a fluorescence microscope and image analysis by the Comet Assay IV Image-analysis system. Three parameters, viz, tail length, tail intensity and Olive tail moment were analyzed on 4200 nuclei per cell type. We observed variations in the level of DNA damage in mussels collected at different sites, as well as seasonal variations in response. Sum of ranking differences (SRD) was implemented to compare use of different types of cell and different measure of comet tail per nucleus. Numerical scales were transferred into ranks, range scaling between 0 and 1; standardization and normalization were carried out. SRD selected the best (and worst) combinations: tail moment is the best for all data treatment and for all organs; second best is tail length, and intensity ranks third (except for digestive gland). The differences were significant at the 5% level. Whereas gills and haemolymph cells do not differ significantly, cells of the digestive gland are much more suitable to estimate genotoxicity. Variance analysis decomposed the effect of different factors on the SRD values. This unique combination has provided not only the relative importance of factors, but also an overall evaluation: the best evaluation method, the best data pre-treatment, etc., were chosen even for partially contradictory data. The rank transformation is superior to any other way of scaling, which is proven by ordering the SRD values by SRD again, and by cross validation.", publisher = "Elsevier, Amsterdam", journal = "Mutation Research-Genetic Toxicology and Environmental Mutagenesis", title = "Evaluation of single-cell gel electrophoresis data: Combination of variance analysis with sum of ranking differences", pages = "22-15", volume = "771", doi = "10.1016/j.mrgentox.2014.04.028" }
Heberger, K., Kolarević, S., Kracun-Kolarević, M., Sunjog, K., Gačić, Z., Kljajic, Z., Mitric, M.,& Vukovic-Gacic, B.. (2014). Evaluation of single-cell gel electrophoresis data: Combination of variance analysis with sum of ranking differences. in Mutation Research-Genetic Toxicology and Environmental Mutagenesis Elsevier, Amsterdam., 771, 15-22. https://doi.org/10.1016/j.mrgentox.2014.04.028
Heberger K, Kolarević S, Kracun-Kolarević M, Sunjog K, Gačić Z, Kljajic Z, Mitric M, Vukovic-Gacic B. Evaluation of single-cell gel electrophoresis data: Combination of variance analysis with sum of ranking differences. in Mutation Research-Genetic Toxicology and Environmental Mutagenesis. 2014;771:15-22. doi:10.1016/j.mrgentox.2014.04.028 .
Heberger, Karoly, Kolarević, Stoimir, Kracun-Kolarević, Margareta, Sunjog, Karolina, Gačić, Zoran, Kljajic, Zoran, Mitric, Milena, Vukovic-Gacic, Branka, "Evaluation of single-cell gel electrophoresis data: Combination of variance analysis with sum of ranking differences" in Mutation Research-Genetic Toxicology and Environmental Mutagenesis, 771 (2014):15-22, https://doi.org/10.1016/j.mrgentox.2014.04.028 . .