14 papers · ranked by Valyu relevance
Franziska Hoerbst, Gurpinder Singh Sidhu, Thelonious Omori, Melissa Tomkins + 1 more
Advances in sequencing technologies have revolutionised our ability to capture the complete RNA profile in tissue samples, allowing for comparative analyses of RNA levels between developmental processes, environmental responses, or treatments. However, quantifying changes in gene expression remains challenging, given…
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…
Haim Bar, Elizabeth D. Schifano
We propose an empirical Bayes approach using a three-component mixture model, the L_2_N model, that may be applied to detect both differential expression (mean) and variation. It consists of two log-normal components (L_2_) for the differentially expressed (dispersed) features (one component for under-expressed…
Xi Chen
Deep sequencing of bulk RNA enables the differential expression analysis at transcript level. We develop a Bayesian approach to directly identify differentially expressed transcripts from RNA-seq data, which features a novel joint model of the sample variability and the differential state of individual transcripts. For…
Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E.M. Furlong + 1 more
For most biological processes, organisms must respond to extrinsic cues, while maintaining essential gene expression programs. Although studied extensively in single cells, it is still unclear how variation is controlled in multicellular organisms. Here, we used a machine-learning approach to identify genomic features…
Guy Karlebach, Peter Hansen, Diogo F.T. Veiga, Robin Steinhaus + 4 more
The regulation of mRNA controls both overall gene expression as well as the distribution of mRNA isoforms encoded by the gene. Current algorithmic approaches focus on characterization of significant differential expression or alternative splicing events or isoform distribution without integrating both events. Here, we…
Ionas Erb, Thomas Quinn, David Lovell, Cedric Notredame
Gene expression data, such as those generated by next generation sequencing technologies (RNA-seq), are of an inherently relative nature: the total number of sequenced reads has no biological meaning. This issue is most often addressed with various normalization techniques which all face the same problem: once…
Mykhaylo M. Malakhov, Ben Dai, Xiaotong T. Shen, Wei Pan
Understanding how genetic variation affects gene expression is essential for a complete picture of the functional pathways that give rise to complex traits. Although numerous studies have established that many genes are differentially expressed in distinct human tissues and cell types, no tools exist for identifying…
Charlotte Soneson, Katarina L. Matthes, Malgorzata Nowicka, Charity W. Law + 1 more
Large-scale sequencing of cDNA (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 treatments or…
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…
Chloe J. Bennett, Rodolfo Aramayo
RNA sequencing (RNA-seq) is a commonly used method to identify changes in gene expression between two conditions. The analysis of RNA-seq output is complicated, with the possibility of getting different results from the same raw data. We developed and deployed four parallel pipelines to reanalyze an existing dataset of…
Nasser Bashkeel, Theodore J. Perkins, Mads Kærn, Jonathan M. Lee
Phenotypic variability of human populations is partly the result of gene polymorphism and differential gene expression. As such, understanding the molecular basis for diversity requires identifying genes with both high and low population expression variance and identifying the mechanisms underlying their expression…
Sumanta Ray, Snehalika Lall, Sanghamitra Bandyopadhyay
Differential coexpression has recently emerged as a new way to establish a fundamental difference in expression pattern among a group of genes between two populations. Earlier methods used some scoring techniques to detect changes in correlation patterns of a gene pair in two conditions. However, modeling differential…
Sk Md Mosaddek Hossain, Aanzil Akram Halsana, Lutfunnesa Khatun, Sumanta Ray + 1 more
Pancreatic Ductal Adenocarcinoma (PDAC) is the most lethal type of pancreatic cancer (PC), late detection of which leads to its therapeutic failure. This study aims to find out key regulatory genes and their impact on the progression of the disease helping the etiology of the disease which is still largely unknown. We…