Ranked Choice Voting for Representative Transcripts with TRaCE

Olson, Andrew J, Ware, Doreen (July 2021) Ranked Choice Voting for Representative Transcripts with TRaCE. Bioinformatics. ISSN 1367-4803

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Abstract

Genome sequencing projects annotate protein-coding gene models with multiple transcripts, aiming to represent all of the available transcript evidence. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical transcript. To choose canonical transcripts, TRaCE (Transcript Ranking and Canonical Election) holds an ‘election’ in which a set of RNA-seq samples rank transcripts by annotation edit distance. These sample-specific votes are tallied along with other criteria such as protein length and InterPro domain coverage. The winner is selected as the canonical transcript, but the election proceeds through multiple rounds of voting to order all the transcripts by relevance. Based on the set of expression data provided, TRaCE can identify the most common isoforms from a broad expression atlas or prioritize alternative transcripts expressed in specific contexts.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
Investigative techniques and equipment
Investigative techniques and equipment > assays
bioinformatics > computational biology
Investigative techniques and equipment > assays > RNA-seq
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Ware lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 23 July 2021
Date Deposited: 28 Jul 2021 14:20
Last Modified: 25 Jan 2024 15:51
PMCID: PMC8696091
Related URLs:
URI: https://repository.cshl.edu/id/eprint/40304

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