Search · four archives
Search · four archives
19 papers · ranked by Valyu relevance
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 does not change. DTU analysis requires the quantification of individual isoforms from RNA-seq data, which has a high level…
Chinaza F. Nnam, Yiping Li, Minghui Zhang, Erick A. Mboya + 13 more
Clear cell renal cell carcinoma (ccRCC) is characterized by transcriptional reprogramming driven by hypoxia signaling, metabolic rewiring, and immune modulation. While gene-level analyses have defined key features of ccRCC biology, they do not capture isoform-level variation arising from alternative splicing.…
Courtney E. Gorman, Philip McGinnity, C. Darrin Hulsey
Background Accounting for isoforms is likely key to understanding muscle transcriptomic divergence. Muscles offer classic examples of tissues where changes in isoforms alter function and structure in response to stimuli like increased exercise or novel nutrient regimes. To determine how an essential micronutrient…
Rebecca E Lane, Eleanor Calcutt, Anandagopal Srinivasan, Vicki Gamble + 3 more
Long-read RNA sequencing enables isoform-resolved transcriptomics, but library preparation introduces systematic biases that shape biological interpretation. We benchmarked Oxford Nanopore’s two protocols—PCR-cDNA and direct RNA—using SKMM2 myeloma cells stimulated with interleukin-6 (IL-6) and ERCC synthetic…
Justin T. Roberts, Viktor M. Pastukh, Grant T. Daly, Adeyeye I. Haastrup + 3 more
Hypoxia is a fundamental pathophysiological stimulus that plays important roles in multiple cardiopulmonary diseases. During hypoxic stress, cells adapt by undergoing widespread transcriptional reprogramming. The conventional approach to investigating this response has largely involved RNA-seq analysis which typically…
Sulev Koks, Mari Muldmaa, Jack Price, Luke Whiley + 8 more
Parkinson’s disease (PD) is a complex neurodegenerative disorder with diverse molecular signatures that extend beyond the central nervous system. Peripheral blood serves as a minimally invasive source of transcriptomic biomarkers reflecting systemic inflammation, mitochondrial dysfunction, lysosomal impairment, and…
Eamon McAndrew, Anna Diamant, Georges Vassaux, Pascal Barbry + 1 more
Single-cell RNA sequencing and spatial transcriptomics have transformed our understanding of the transcriptional landscape by enabling high-resolution profiling of gene expression. Yet most experimental pipelines and their associated analysis frameworks collapse transcript diversity into gene-level counts, obscuring…
Chunxu Han, Jeroen Gilis, Elena Iriondo Delgado, Lieven Clement + 1 more
Alternative splicing enables a single gene to produce a variety of mRNA transcripts, significantly enhancing protein diversity in higher eukaryotes. Isoform switching refers to the differential usage of transcripts of a gene and occurs pervasively across physiological and pathological conditions. IsoformSwitchAnalyzeR…
Samantha L. Sison, Federico Zampa, Eric R. Kofman, Su Yeun Choi + 20 more
The brain displays the richest repertoire of post-transcriptional mechanisms regulating mRNA translation1-11. Among these, alternative splicing has been shown to drive cell-type specificity and, when disrupted, is strongly linked to neurological disorders12-17. However, genome-wide measurements of mRNA translation with…
Zhihua Jiang, Michee van Rooyen, Jennifer J. Michal, Isyana Khaerunnisa + 4 more
Despite decades of genome sequencing and annotation, a fundamental paradox remains unresolved: how organisms with finite and relatively stable gene numbers generate extraordinary phenotypic diversity. In this review, we propose that regulated RNA variant diversity provides a critical level of resolution for…
Marjan Hosseini, Devin McConnell, Derek Aguiar, Christina Kendziorski
In the synthetic data, we computed differential expression for all combinations of fold change pairs (28 in total) and focused on BSEEJ, StringTie, rMATS, and LeafCutter, due to the relatively low performance of MAJIQ on our simulated data and the high computational cost for Cufflinks and rnaSPAdes (see Supplementary…
Saloni Bhatia, Matt A Field, Lionel Hebbard, Ulf Schmitz
Alternative splicing (AS) plays a key role in regulating gene expression, and its dysregulation is implicated in numerous human diseases, including cancer. While bulk RNA sequencing has advanced our understanding of AS, it cannot capture cellular heterogeneity or reliably reconstruct full-length isoforms, both of which…
Eleanor Elgood Hunt, Claudia Vivori, Richard Mitter, Jenie Hannah Johnkingsly Jebaraj + 8 more
Transcription start site (TSS) selection diversifies the transcriptome and proteome, yet how alternative TSSs regulate development remains unclear. We show that the chromatin regulator ASH2L undergoes developmentally regulated alternative TSS switching in differentiating mouse cells, generating distinct mRNA and…
Arka Jain, Umesh Sharma
Public pooled single-cell perturbation atlases are valuable resources for studying transcription factor (TF) function, but downstream re-analysis can be limited by incomplete deposited metadata and missing internal controls. Here we re-analyze the human TF Atlas dataset (GSE216481), a MORF-based pooled overexpression…
Adams, Manuel, Amigó, José M. + 2 more
The concept of transcripts was introduced in 2009 as a means to characterize various aspects of the functional relationship between time series of interacting systems. Based on this concept that utilizes algebraic relations between ordinal patterns derived from time series, estimators for the strength, direction, and…
Mostafa Rezapour
Differential gene expression (DGE) analysis is foundational to transcriptomic research, yet tool selection can substantially influence results. This study presents a comprehensive comparison of two widely used DGE tools, edgeR and DESeq2, using real and semi-simulated bulk RNA-Seq datasets spanning viral, bacterial…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Authors not listed
While the method of manual inspection reliably produces correct results at the introductory level, it can often appear untidy and unintuitive and lacks teachable depth. This paper presents a novel alternative approach designed to achieve the same outcomes as manual inspection but with enhanced clarity. It serves as…
Ashka Shah, Rick Stevens
Next-generation sequencing technologies, including RNA-sequencing, provide genome-wide measurements of gene expression and enable broad explorations of biomarkers and mechanisms underlying disease and treatment response. Bioinformatics tools for processing this data, such as differential expression analysis, are…