Search · four archives
Search · four archives
17 papers · ranked by Valyu relevance
Michael I. Love, Charlotte Soneson, Rob Patro
Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Here we present a simple workflow using a set of existing R/Bioconductor packages for analysis of DTU. We show how these packages can be used downstream of…
Jishu Xu, Michaela Hörner, Elena Buena Atienza, Kalaivani Manibarathi + 6 more
Long-read RNA sequencing has transformed transcriptome analysis by enabling comprehensive mapping of full-length transcripts, providing an unprecedented resolution of transcript diversity, alternative splicing, and transcript-specific regulation. In this study, we employed nanopore long-read RNA sequencing to profile…
Koen Van den Berge, Charlotte Soneson, Mark D. Robinson, Lieven Clement
'Lieven Clement'] RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene level. We propose stageR, a two-stage testing paradigm that leverages the increased power of…
Fiona Dick, Gonzalo S. Nido, Guido Werner Alves, Ole-Bjørn Tysnes + 4 more
'Gry Hilde Nilsen' 'Christian Dölle' 'Charalampos Tzoulis' 'Bruce A. Hamilton'] Studies of differential gene expression have identified several molecular signatures and pathways associated with Parkinson’s disease (PD). The role of isoform switches and differential transcript usage (DTU) remains, however, unexplored.…
Jingni He, Devika Ganesamoorthy, Jessie J.-Y. Chang, Jianshu Zhang + 7 more
'Sharon L. Trevor' 'Kristen S. Gibbons' 'Stephen J. McPherson' 'Jessica C. Kling' 'Luregn J. Schlapbach' 'Antje Blumenthal' 'Lachlan J. M. Coin' ''] Background RNA sequencing of whole blood has been increasingly employed to find transcriptomic signatures of disease states. These studies traditionally utilize short-read…
Chit Tong Lio, Tolga Düz, Markus Hoffmann, Lina-Liv Willruth + 3 more
RNA sequencing offers unique insights into transcriptome diversity, and a plethora of tools have been developed to analyze alternative splicing. One important task is to detect changes in the relative transcript abundance in differential transcript usage (DTU) analysis. The choice of the right analysis tool is…
Charlotte Soneson, Katarina L. Matthes, Malgorzata Nowicka, Charity W. Law + 1 more
'Charity W. Law' 'Mark D. Robinson'] Background RNA-seq has been a boon to the quantitative analysis of transcriptomes. A notable application is the detection of changes in transcript usage between experimental conditions. For example, discovery of pathological alternative splicing may allow the development of new…
Koen Van den Berge, Charlotte Soneson, Mark D. Robinson, Lieven Clement
Reductions in sequencing cost and innovations in expression quantification have prompted an emergence of RNA-seq studies with complex designs and data analysis at transcript resolution. These applications involve multiple hypotheses per gene, leading to challenging multiple testing problems. Conventional approaches…
Pedro L. Baldoni, Lizhong Chen, Mengbo Li, Yunshun Chen + 1 more
Differential transcript usage (DTU) refers to changes in the relative abundance of transcript isoforms of the same gene between experimental conditions, even when the total expression of the gene doesn’t change. DTU analysis requires the quantification of individual isoforms from RNA-seq data, which has a high level of…
Panagiotis Papastamoulis, Magnus Rattray
Next generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in the relative within gene…
Stephen W. Hartley, James C. Mullikin
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce JunctionSeq, a new method that builds on the statistical techniques used by the…
Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco + 12 more
'Héctor del Risco' 'Cristina Martí' 'Sonia Tarazona' 'Pedro Salguero' 'Raymond Scott' 'Alberto Lerma' 'Ana Alastrue-Agudo' 'Pablo Bonilla' 'Jeremy R. B. Newman' 'Shunichi Kosugi' 'Lauren M. McIntyre' 'Victoria Moreno-Manzano' 'Ana Conesa'] Recent advances in long-read sequencing solve inaccuracies in alternative…
Stefan Gerber, Gerhard Schratt, Pierre-Luc Germain
Background Despite the importance of alternative poly-adenylation and 3′ UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data. Results We present the diffUTR Bioconductor package which streamlines and improves upon differential exon usage…
Panagiotis Papastamoulis, Magnus Rattray
Summary. Recent advances in molecular biology allow the quantification of the transcriptome and scoring transcripts as differentially or equally expressed between two biological conditions. Although these two tasks are closely linked, the available inference methods treat them separately: a primary model is used to…
Marjan Hosseini, Devin McConnell, Derek Aguiar
Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer full-length transcripts from high-throughput sequencing data. However, this is a…
Balakrishnan Venkatesh, Ursula Hettwer, Birger Koopmann, Petr Karlovský
'Petr Karlovský'] Background: Gene expression studies on non-model organisms require open-end strategies for transcription profiling. Gel-based analysis of cDNA fragments allows to detect alterations in gene expression for genes which have neither been sequenced yet nor are available in cDNA libraries. Commonly used…
Arnaud Liehrmann, Etienne Delannoy, Alexandra Launay-Avon, Elodie Gilbault + 3 more
To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along…