An integrated analysis tool reveals intrinsic biases in gene set enrichment
Thakur, N.; Pujol, N.; van Helden, J.; Waterston, R. H.; Hillier, L. W.; Tichit, L.; Ewbank, J. J.
Show abstract
Generating meaningful interpretations of gene lists remains a challenge for all large-scale studies. Many approaches exist, often based on evaluating gene enrichment among pre-determined gene classes. Here, we conceived and implemented yet another analysis tool (YAAT), specifically for data from the widely-used model organism C. elegans. YAAT extends standard enrichment analyses, using a combination of co-expression data and profiles of phylogenetic conservation, to identify groups of functionally-related genes. It additionally allows class clustering, providing inference of functional links between groups of genes. We give examples of the utility of YAAT for uncovering unsuspected links between genes and show how the approach can be used to prioritise genes for in-depth study. Our analyses revealed several limitations to the meaningful interpretation of gene lists, specifically related to data sources and the "universe" of gene lists used. We hope that YAAT will represent a model for integrated analysis that could be useful for large-scale exploration of biological function in other species.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons 96%
- The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-Caenorhabditis nematodes 95%
- BioLitMine: advanced mining of biomedical and biological literature about human genes and genes from major model organisms 94%
Similar papers in this journal
- FLYNC: A Machine Learning-Driven Framework for Discovering Long Non-Coding RNAs in Drosophila melanogaster 94%
- Decoding proteome functional information in model organisms using protein language models. 94%
- BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database 94%
Similar papers in this journal
Similar papers in this journal
- FunCoup 6: advancing functional association networks across species with directed links and improved user experience 94%
- paraCell: A novel software tool for the interactive analysis and visualization of standard and dual host-parasite single cell RNA-Seq data 94%
- DGINN, an automated and highly-flexible pipeline for the Detection of Genetic INNovations on protein-coding genes 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.