Skelton, A. | Search bioRxiv

bioRxiv2025

Distilling Direct Effects via Conditional Differential Gene Expression Analysis

Differential gene expression (DGE) analysis is foundational for interpreting RNA sequencing data, but it conflates direct biological effects with correlations propagated through gene co-expression. Across three RNA sequencing datasets (including a genome-scale perturb-seq experiment), we find that only a small fraction of differentially expressed genes have direct effects on the trait of interest, while the majority are undirected or passengers whose associations are mediated through other genes. To distinguish direct effect genes, we introduce conditional differential gene expression (CDGE) analysis, a framework that tests for conditional rather than marginal association between each gene and the trait of interest. Implemented via the GhostKnockoff procedure with lasso regression, CDGE delivers false discovery rate control, operates on summary statistics from existing DGE pipelines, and accommodates batch effects. The genes identified by CDGE mediate the effects of most other differentially expressed genes and show stronger enrichment for known protein-protein interactions and biological pathways than DGE-identified genes. These results suggest that the field has been systematically over-interpreting DGE outputs, and that distinguishing direct from mediated effects is essential for prioritizing genes for functional follow-up and therapeutic development.

bioinformatics↗

bioRxiv2024

Detection of tomato brown rugose fruit virus in environmental residues: the importance of contextualizing test results

Tomato brown rugose fruit virus (ToBRFV) is regulated as a quarantine pest in many countries worldwide. To assess whether ToBRFV is present in cultivations, plants or seed lots, testing is required. The interpretation of test results, however, can be challenging. Real-time RT-PCR results, even though considered "positive", may not always signify plant infection or indicate the presence of infectious virus, but could be due to the presence of viral residues in the environment. Here, case studies from the Netherlands, Belgium, and the United Kingdom address questions regarding the detection of ToBRFV in various settings, and the infectiousness of ToBRFV positive samples. These exploratory analyses demonstrate widespread detection of ToBRFV in diverse samples and environments. ToBRFV was detected inside and around greenhouses with no prior history of ToBRFV infection, on different materials and surfaces including those that were untouched by individuals, plants, or objects. This suggested the dispersal of viral residues through aerosols. ToBRFV or its residues were more often detected in areas with nearby tomato production yet were also found in a wider environment extending beyond infected crops. Given that ToBRFV originating from environmental contamination may or may not be infectious, adds complexity to decision-making in response to positive test results. Contextual information, such as the origin of the sample and the likelihood of residues from prior cultivations and/or the broader environment, is important for interpreting test results. A nuanced approach is crucial to correctly interpret ToBRFV test results, necessitating further research to support risk assessment.

microbiology↗