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Identification of Chimeric RNAs Using RNA-Seq Reads and Protein–Protein Interactions of Translated Chimeras

  • Milana Frenkel-MorgensternEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2079)

Abstract

Chimeric RNA moieties typically consist of exons from two genes expressed from different genomic locations and produced by chromosomal translocations, trans-splicing or transcription errors. Recent advances in next-generation sequencing procedures have opened new horizons for identification of novel chimeric transcripts in various diseases in a personalized manner. Here we describe the detailed computational procedures to identify chimeric transcripts using RNA-seq reads. Moreover, we elaborate on the domain–domain co-occurrence method to detect alterations in chimeric protein–protein interaction (ChiPPI) networks produced by chimeric RNA that are translated to chimeric proteins.

Key words

RNA-seq reads Next-generation sequencing technology Domain–domain co-occurrence Chimeric mRNA Chimeric protein–protein interactions (ChiPPI) 

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Authors and Affiliations

  1. 1.Azrieli Faculty of MedicineBar-Ilan UniversitySafedIsrael

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