Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: We studied the characteristics of human miR-1 and miR-124 to create a miRNA target prediction program based on the common features of the interaction with their targets. The program yielded 78% sensitivity and 98% specificity for miR-1 target prediction and 77% sensitivity and 98% specificity for miR-124 target prediction. To test whether miRNA class grouping is necessary for miRNA target prediction, we used the features of the interaction of miR-1 and miR-124 to their targets to predict miR-16 and miR-15a targets. We also investigated the effect of growth and skeletal problems in meat-type chickens, and conservation genetics of the Houbara. PARTICIPANTS: Samuel E. Aggrey (PD) planned the miRNA work and supervised the work; Bram Sebastian, PhD student executed the programing; Amal Korrida PhD student undertook the conversation genetics work. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
MicroRNAs (miRNAs) are small non-coding RNAs which regulate gene expressions by targeting the mRNAs especially in the 3'UTR regions. The identification of miRNAs has been done by biological experiment and computational prediction. The computational prediction approach has been done by two major methods, comparative and non-comparative. Comparative method is dependent on the conservation of the miRNA sequences and secondary structure. Non-comparative method in the other hand does not rely on conservation. We hypothesized that each miRNA class has its own unique set of features therefore, grouping miRNA by classes before using them as training data will improve sensitivity and specificity. The average sensitivity was 88.62% for Mir-Explore which rely on within miRNA class alignment, and 70.82% for mir-Abela which relies on global alignment. Compared with global alignment, grouping miRNA by classes yield a better sensitivity with very high specificity for pre-miRNA prediction even when a simple positional based secondary and primary structure alignment are used. We studied the characteristics of human miR-1 and miR-124 to create a miRNA target prediction program based on the common features of the interaction with their targets. The program yielded 78% sensitivity and 98% specificity for miR-1 target prediction and 77% sensitivity and 98% specificity for miR-124 target prediction. To test whether miRNA class grouping is necessary for miRNA target prediction, we used the features of the interaction of miR-1 and miR-124 to their targets to predict miR-16 and miR-15a targets. We obtained 28% sensitivity and 98% specificity for both miR-16 and miR-15a. This indicates that the features of miR-1 and miR-124 target interaction are different than miR-16 and miR-15a and that miR-16 and miR-15a have their own target interaction characteristics. Hence grouping miRNA by classes significantly improves sensitivity and specificity of miRNA target prediction. We also tested the efficacy of two previously developed programs, miRanda and miTarget to predict miR-16 and miR-15a targets. These programs were developed based on generalized features of miRNA and target interactions. Sensitivity of miRanda was 23% for mir-15a and 0% for mir-16, while miTarget had 14% sensitivity for mir-15a and 16% for mir-16. Specificity for miRanda is 99% for miR-15a and 98% for miR-16.
Publications
- Samuel, D., S. Trabelsi, A. B. Karnuah, N. B. Anthony, and S. E. Aggrey, 2012. The use of dielectric spectroscopy as a tool for predicting meat quality in poultry. Int. J. Poultry. Sci. 11: 551-555.
- Sebastian, B., and S. E. Aggrey, 2013. miR-Explore: Predicting microRNA precursors by class grouping and secondary structure position alignment. Bioinformatics and Biology Insights 7:133-142;
- Korrida, A., S. N. Nahashon, A. Amin-Alami, S. Jadallah, and S. E. Aggrey, 2012. Modeling absolute and allometric growth in Houbara Bustard (Clamydotis undulata undulata) in captivity. Atlas J. Biol. 2: 110-115.;
- Shim, M.Y., A. B. Karnuah, N. B. Anthony, and S.E. Aggrey, 2012. The effect of broiler chicken growth rate on valgus, varus, and tibial dyschondroplasia. Poultry Sci. 91: 62-65.;
- Korrida,A., S. Jadallah, F. Chbel, A. Amin-Alami, M. Ahra, and S. E. Aggrey, 2012. Patterns of genetic diversity and population structure of the threatened Houbara and Macqueen's bustard as revealed by microsatellite markers. Genetics and Molecular Research 11: 3207-3221.;
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