A computational approach and software package RNAexploreR for grouping RNA molecules of human genes by exon features
The study on the exon combinatoric rules of human genes during the process of splicing is of great interest for the diagnosis and treatment of cancer. A certain part of the research is aimed at developing reliable prediction models for global exon combinatorics during the formation of mature RNA. Th...
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| Format: | Article |
| Language: | Russian |
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National Academy of Sciences of Belarus, the United Institute of Informatics Problems
2019-12-01
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| Series: | Informatika |
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| Online Access: | https://inf.grid.by/jour/article/view/878 |
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| author | M. M. Yatskou V. V. Skakun V. V. Grinev |
| author_facet | M. M. Yatskou V. V. Skakun V. V. Grinev |
| author_sort | M. M. Yatskou |
| collection | DOAJ |
| description | The study on the exon combinatoric rules of human genes during the process of splicing is of great interest for the diagnosis and treatment of cancer. A certain part of the research is aimed at developing reliable prediction models for global exon combinatorics during the formation of mature RNA. The primary task is to develop standards or uniform systematic statistical approaches to the analysis and interpretation of possible exon sequences of genes.A computational approach is proposed to group alternative splicing events in primary messenger RNA of human genes with the aim of determining the gene correspondence or molecule class. The method consists of reducing the dimension of the exon feature space and combining closely located exons into a limited number of classes, replacing the exon pathways of RNA generation with sequences of corresponding exon class labels, calculating the distances between RNA transcripts by some measure of similarity, and associating closely spaced RNA objects into clusters. The performance evaluation of developed algorithms has been done using the examples of RNA molecules of selected nonhomologous human genes and human hybrid oncogene RUNX1/RUNX1T1. The mean accuracy of the assignment of the transcript to given gene is about 99,5 % for the considered nonhomologous pairs of genes.A software package and web application RNAexploreR, integrating the implemented algorithms for the analysis of alternative splicing of human gene RNA products, have been developed. The proposed algorithms and software can be used to study the organization and functioning of both aberrant and normal human genes. |
| format | Article |
| id | doaj-art-3174c42e32e843ada7df6e6a419d2395 |
| institution | DOAJ |
| issn | 1816-0301 |
| language | Russian |
| publishDate | 2019-12-01 |
| publisher | National Academy of Sciences of Belarus, the United Institute of Informatics Problems |
| record_format | Article |
| series | Informatika |
| spelling | doaj-art-3174c42e32e843ada7df6e6a419d23952025-08-20T03:02:37ZrusNational Academy of Sciences of Belarus, the United Institute of Informatics ProblemsInformatika1816-03012019-12-01164724847A computational approach and software package RNAexploreR for grouping RNA molecules of human genes by exon featuresM. M. Yatskou0V. V. Skakun1V. V. Grinev2Belarusian State UniversityBelarusian State UniversityBelarusian State UniversityThe study on the exon combinatoric rules of human genes during the process of splicing is of great interest for the diagnosis and treatment of cancer. A certain part of the research is aimed at developing reliable prediction models for global exon combinatorics during the formation of mature RNA. The primary task is to develop standards or uniform systematic statistical approaches to the analysis and interpretation of possible exon sequences of genes.A computational approach is proposed to group alternative splicing events in primary messenger RNA of human genes with the aim of determining the gene correspondence or molecule class. The method consists of reducing the dimension of the exon feature space and combining closely located exons into a limited number of classes, replacing the exon pathways of RNA generation with sequences of corresponding exon class labels, calculating the distances between RNA transcripts by some measure of similarity, and associating closely spaced RNA objects into clusters. The performance evaluation of developed algorithms has been done using the examples of RNA molecules of selected nonhomologous human genes and human hybrid oncogene RUNX1/RUNX1T1. The mean accuracy of the assignment of the transcript to given gene is about 99,5 % for the considered nonhomologous pairs of genes.A software package and web application RNAexploreR, integrating the implemented algorithms for the analysis of alternative splicing of human gene RNA products, have been developed. The proposed algorithms and software can be used to study the organization and functioning of both aberrant and normal human genes.https://inf.grid.by/jour/article/view/878human geneshybrid oncogene runx1/runx1t1alternative splicingexon featuresdata miningprincipal component analysiscluster analysis |
| spellingShingle | M. M. Yatskou V. V. Skakun V. V. Grinev A computational approach and software package RNAexploreR for grouping RNA molecules of human genes by exon features Informatika human genes hybrid oncogene runx1/runx1t1 alternative splicing exon features data mining principal component analysis cluster analysis |
| title | A computational approach and software package RNAexploreR for grouping RNA molecules of human genes by exon features |
| title_full | A computational approach and software package RNAexploreR for grouping RNA molecules of human genes by exon features |
| title_fullStr | A computational approach and software package RNAexploreR for grouping RNA molecules of human genes by exon features |
| title_full_unstemmed | A computational approach and software package RNAexploreR for grouping RNA molecules of human genes by exon features |
| title_short | A computational approach and software package RNAexploreR for grouping RNA molecules of human genes by exon features |
| title_sort | computational approach and software package rnaexplorer for grouping rna molecules of human genes by exon features |
| topic | human genes hybrid oncogene runx1/runx1t1 alternative splicing exon features data mining principal component analysis cluster analysis |
| url | https://inf.grid.by/jour/article/view/878 |
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