microRNAs (miRNAs) are short nucleotide sequences expressed by a genome that are involved in post transcriptional modulation of gene expression. Since miRNAs need to be co-expressed with their target mRNA to observe a...microRNAs (miRNAs) are short nucleotide sequences expressed by a genome that are involved in post transcriptional modulation of gene expression. Since miRNAs need to be co-expressed with their target mRNA to observe an effect and since miRNAs and target interactions can be cooperative, it is currently not possible to develop a comprehensive experimental atlas of miRNAs and their targets. To overcome this limitation, machine learning has been applied to miRNA detection. In general binary learning (two-class) approaches are applied to miRNA discovery. These learners consider both positive (miRNA) and negative (non-miRNA) examples during the training process. One-class classifiers, on the other hand, use only the information for the target class (miRNA). The one-class approach in machine learning is gradually receiving more attention particularly for solving problems where the negative class is not well defined. This is especially true for miRNAs where the positive class can be experimentally confirmed relatively easy, but where it is not currently possible to call any part of a genome a non-miRNA. To do that, it should be co-expressed with all other possible transcripts of the genome, which currently is a futile endeavor. For machine learning, miRNAs need to be transformed into a feature vector and some currently used features like minimum free energy vary widely in the case of plant miRNAs. In this study it was our aim to analyze different methods applying one-class approaches and the effectiveness of motif-based features for prediction of plant miRNA genes. We show that the application of these one-class classifiers is promising and useful for this kind of problem which relies only on sequence- based features such as k-mers and motifs comparing to the results from two-class classification. In some cases the results of one-class are, to our surprise, more accurate than results from two-class classifiers.展开更多
MicroRNAs (miRNAs) are short (~21 nt) nucleotide sequences that are either co-transcribed during the production of mRNA or are organized in intergenic regions transcribed by RNA polymerase II. In animals, Drosha, and ...MicroRNAs (miRNAs) are short (~21 nt) nucleotide sequences that are either co-transcribed during the production of mRNA or are organized in intergenic regions transcribed by RNA polymerase II. In animals, Drosha, and in plants DCL1 recognize pre-miRNAs which set themselves apart by their characteristic stem loop (hairpin) structure. This structure appears important for their recognition during the process of maturation leading to functioning mature miRNAs. A large body of research is available for computational pre-miRNA detection in animals, but less within the plant kingdom. For the prediction of pre-miRNAs, usually machine learning approaches are employed. Therefore, it is necessary to convert the pre-miRNAs into a set of features that can be calculated and many such features have been described. We here select a subset of the previously described features and add sequence motifs as new features. The resulting model which we called MotifmiRNAPred was tested on known pre-miRNAs listed in miRBase and its accuracy was compared to existing approaches in the field. With an accuracy of 99.95% for the generalized plant model, it distinguishes itself from previously published results which reach an average accuracy between 74% and 98%. We believe that our approach is useful for prediction of pre-miRNAs in plants without per species adjustment.展开更多
Computational biology plays a significant role in the discovery of new biomarkers, the analyses of disease states and the validation of potential biomarkers. Biomarkers are used to measure the progress of disease or t...Computational biology plays a significant role in the discovery of new biomarkers, the analyses of disease states and the validation of potential biomarkers. Biomarkers are used to measure the progress of disease or the physiological effects of therapeutic intervention in the treatment of disease. They are also used as early warning signs for various diseases such as cancer and inflammatory diseases. In this review, we outline recent progresses of computational biology application in research on biomarkers discovery. A brief discussion of some necessary preliminaries on machine learning techniques (e.g., clustering and support vector machines—SVM) which are commonly used in many applications to biomarkers discovery is given and followed by a description of biological background on biomarkers. We further examine the integration of computational biology approaches and biomarkers. Finally, we conclude with a discussion of key challenges for computational biology to biomarkers discovery.展开更多
文摘microRNAs (miRNAs) are short nucleotide sequences expressed by a genome that are involved in post transcriptional modulation of gene expression. Since miRNAs need to be co-expressed with their target mRNA to observe an effect and since miRNAs and target interactions can be cooperative, it is currently not possible to develop a comprehensive experimental atlas of miRNAs and their targets. To overcome this limitation, machine learning has been applied to miRNA detection. In general binary learning (two-class) approaches are applied to miRNA discovery. These learners consider both positive (miRNA) and negative (non-miRNA) examples during the training process. One-class classifiers, on the other hand, use only the information for the target class (miRNA). The one-class approach in machine learning is gradually receiving more attention particularly for solving problems where the negative class is not well defined. This is especially true for miRNAs where the positive class can be experimentally confirmed relatively easy, but where it is not currently possible to call any part of a genome a non-miRNA. To do that, it should be co-expressed with all other possible transcripts of the genome, which currently is a futile endeavor. For machine learning, miRNAs need to be transformed into a feature vector and some currently used features like minimum free energy vary widely in the case of plant miRNAs. In this study it was our aim to analyze different methods applying one-class approaches and the effectiveness of motif-based features for prediction of plant miRNA genes. We show that the application of these one-class classifiers is promising and useful for this kind of problem which relies only on sequence- based features such as k-mers and motifs comparing to the results from two-class classification. In some cases the results of one-class are, to our surprise, more accurate than results from two-class classifiers.
文摘MicroRNAs (miRNAs) are short (~21 nt) nucleotide sequences that are either co-transcribed during the production of mRNA or are organized in intergenic regions transcribed by RNA polymerase II. In animals, Drosha, and in plants DCL1 recognize pre-miRNAs which set themselves apart by their characteristic stem loop (hairpin) structure. This structure appears important for their recognition during the process of maturation leading to functioning mature miRNAs. A large body of research is available for computational pre-miRNA detection in animals, but less within the plant kingdom. For the prediction of pre-miRNAs, usually machine learning approaches are employed. Therefore, it is necessary to convert the pre-miRNAs into a set of features that can be calculated and many such features have been described. We here select a subset of the previously described features and add sequence motifs as new features. The resulting model which we called MotifmiRNAPred was tested on known pre-miRNAs listed in miRBase and its accuracy was compared to existing approaches in the field. With an accuracy of 99.95% for the generalized plant model, it distinguishes itself from previously published results which reach an average accuracy between 74% and 98%. We believe that our approach is useful for prediction of pre-miRNAs in plants without per species adjustment.
文摘Computational biology plays a significant role in the discovery of new biomarkers, the analyses of disease states and the validation of potential biomarkers. Biomarkers are used to measure the progress of disease or the physiological effects of therapeutic intervention in the treatment of disease. They are also used as early warning signs for various diseases such as cancer and inflammatory diseases. In this review, we outline recent progresses of computational biology application in research on biomarkers discovery. A brief discussion of some necessary preliminaries on machine learning techniques (e.g., clustering and support vector machines—SVM) which are commonly used in many applications to biomarkers discovery is given and followed by a description of biological background on biomarkers. We further examine the integration of computational biology approaches and biomarkers. Finally, we conclude with a discussion of key challenges for computational biology to biomarkers discovery.
