ISOFORMIC: A WORKFLOW FOR TRANSCRIPT LEVEL RNA-SEQ INTERPRETATION

Izabela Mamede; Lucio Rezende Queiroz; Julia Teixeira Rodrigues; Thomaz Luscher Dias; Nayara Evelin de Toledo; Glória Regina Franco

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Submission

Paper Title

ISOFORMIC: A WORKFLOW FOR TRANSCRIPT LEVEL RNA-SEQ INTERPRETATION

Authors

Izabela Mamede
Lucio Rezende Queiroz
Julia Teixeira Rodrigues
Thomaz Luscher Dias
Nayara Evelin de Toledo
Glória Regina Franco

Modality

Software demonstration

Subject area

RNA and transcriptomics

Publishing Date

21/11/2024

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting-2024/830839-isoformic--a-workflow-for-transcript-level-rna-seq-interpretation

ISBN

978-65-272-0843-3

Keywords

isoforms, transcriptome, alternative splicing

Summary

Transcriptome analysis is one of the most used methods in current biological sciences. However, this analysis is routinely performed at the gene level, which can be misleading, since over 90% of all mammalian genes produce transcripts that undergo alternative splicing or present different start and end transcription sites. These processes will produce multiple transcripts from the same gene template, which can be productive, generating different isoforms of the same protein, or unproductive, which are not able to undergo canonical translation. For humans, the current transcriptome annotation amounts to over 200,000 transcripts, with over 70% of them being products of atypical splicing and differential transcription initiation or termination. Software for calling the splicing site events which are executed on short-read transcriptomic data are known to have poor performance, requiring extremely deep sequencing and outputting transcripts that do not correspond to the annotated ones nor to each other`s results. Nevertheless, RNA sequencing experiments are routinely analyzed only at the gene level. Nevertheless, short-read sequencing technology is still the default for most bioinformatics analyses. Today there is no pipeline for short-read transcript level analysis that is customizable, usable for any type of transcripts, and results in ready-to-use plots and biological information from the data. Here, we present Isoformic, a pipeline for the biological interpretation of transcript level results from short-read sequencing data, which is publicly available on GitHub (https://github.com/luciorq/isoformic). The package allows you to input your differential expression data (gene and transcript) and your reference transcriptome, and from that, you can extract the transcript types, find genes whose transcripts are differentially expressed but the genes are not, plot the relative counts and Foldchange of those transcripts between conditions, visualize the difference in intron and exon composition between the same transcripts of a given gene, and functionally enrich the transcripts, separating them by transcript type and plot the results. Isoformic combines different types of visualization, creates functions to easily explore the transcript differential expression and to extract biologically relevant information from them. The pipeline was tested on human datasets of pregnant women with Preeclampsia (PE) and controls, on human cells infected with Sars-Cov-2 and control, on human lung cells with pulmonary hypertension and on neurons from mice with and without anxiety. In all these cases it was able to detect differential transcript presence and usage, showing the importance of transcript variability in eukaryote gene expression. The package allows for the extraction of biologically relevant information, detection of transcript variability, and identification of isoforms with significant implications in different biological phenotypes in any differential expression comparisons which uses well annotated transcriptomes as reference. In summary, while traditional transcriptome analysis often overlooks the complexity of alternative splicing and transcription events, Isoformic provides a solution for transcript-level analysis of short-read sequencing data. By offering versatile functionalities and compatibility with well-annotated transcriptomes, Isoformic enhances our ability to uncover transcript diversity and its biological implications.

Title of the Event: 20º Congresso Brasileiro de Bioinformática: X-Meeting 2024
City of the Event: Salvador
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

MAMEDE, Izabela et al.. ISOFORMIC: A WORKFLOW FOR TRANSCRIPT LEVEL RNA-SEQ INTERPRETATION.. In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/830839-ISOFORMIC--A-WORKFLOW-FOR-TRANSCRIPT-LEVEL-RNA-SEQ-INTERPRETATION. Access in: 19/06/2025