In Silico Validation of ncRNA-ncRNA Interaction Sites with ncRNAs Represented by k-mers Features

Malik Yousef, Walid Khaleifa, Tugba Onal-Suzek, Tugba Onal-Suzek

2019

Abstract

A recent catalogue of human transcriptome, namely CHESS database, assembled from RNA sequencing experiments as a part of the Genotype-Tissue Expression (GTEx) Project reported more non-coding RNA genes (21,856) than protein-coding (21,306), revealing an unexpectedly vast amount of transcriptional noise (Pertea et al, 2018). In this study, we introduce a workflow coded in KNIME that computationally distinguishes the ncRNA-ncRNA interaction sites with less reliable interaction sites containing less experimentally validated binding sites than the interaction sites with more experimental validation. Duplex structure and k-mer features of the ncRNA-ncRNA binding sites with experimental verification were used as input to the classification workflow. In our analysis, we observed that although duplex structure features had no positive effect on the success rate of the classification, using just the k-mer features, ~80% success could be achieved in categorization of the confidence of the ncRNA-ncRNA binding sites. Our result verified the classification performance of miRNA-mRNA targets using only k-mer features from our previous study (Yousef et al, 2018).

Paper Citation

in Harvard Style

Yousef M., Khaleifa W. and Onal-Suzek T. (2019). In Silico Validation of ncRNA-ncRNA Interaction Sites with ncRNAs Represented by k-mers Features. In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-353-7, SciTePress, pages 168-173. DOI: 10.5220/0007361801680173

in Bibtex Style

@conference{bioinformatics19,
author={Malik Yousef and Walid Khaleifa and Tugba Onal-Suzek},
title={In Silico Validation of ncRNA-ncRNA Interaction Sites with ncRNAs Represented by k-mers Features},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS},
year={2019},
pages={168-173},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007361801680173},
isbn={978-989-758-353-7},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS
TI - In Silico Validation of ncRNA-ncRNA Interaction Sites with ncRNAs Represented by k-mers Features
SN - 978-989-758-353-7
AU - Yousef M.
AU - Khaleifa W.
AU - Onal-Suzek T.
PY - 2019
SP - 168
EP - 173
DO - 10.5220/0007361801680173
PB - SciTePress