İntron Tutulmasının Belirlenmesi için Biyoinformatik Algoritmaların Ölçüm Metriklerinin Değerlendirilmesi

Intron retention (IR), one of the alternative types of splicing, occurs when an intron is inserted into the premRNA and remains in the final mRNA. It has been reported that IR is much more frequent in mammals than previously thought and has been determined to affect the transcripts of most genes. Misregulation of alternative splicing is also associated with cancers and abnormal expression or mutations in splicing factors contribute to tumor formation. Because these events are difficult to measure reliably, they constitute a class of alternative splicing that is often neglected. This study aims to examine the IRFinder, IRFinder-S, iREAD, and Whippet algorithms, which are widely used in determining intron retention in RNA-seq data, and to determine the operational differences between the algorithms. As a result of the evaluation, it was observed that IRFinder and IRFinder-S algorithms use IRratio as the metric of intron retention, iREAD uses a measurement metric based on Entropy score, and the Whippet algorithm determines the retained introns according to Percent Splice In (PSI) values. In differential gene expression measurements, IRFinder, IRFinder-s algorithms used DEseq2, IREAD used edgeR and whippet used Delta PSI values. In addition, IRFinder-S was found to be effective in long read sequences.