Frequently Asked Questions

1. What is gene prioritisation and how can this tool be useful for me?
In attempts to determine the genetic causes of human disease, researchers are often left with a large selection of candidate genes. Linkage studies can point to a genomic region containing hundreds of genes, while the high-throughput sequencing approach will identify a multitude of non-synonymous, potentially pathogenic variants which are mostly benign. Systematic experimental verification of each such candidate gene is infeasible due to time and cost implications. A researcher will therefore have to decide which gene(s) is worth investigating further. This decision can be made by manually trawling through vast amounts of literature and/or public databases and selecting the likeliest candidates based on various factors. However, such approach is time consuming and prone to human biases and errors. Computational gene prioritisation presents itself as a solution to this problem, systematically analysing candidate genes based on various criteria and sorting the candidates from the most likely gene to be disease causative to the least in a fraction of the time it would take a researcher to perform such queries manually. Here, candidate genes are prioritised using baseline gene expression data for various normal tissues, working under a hypothesis that the expression patterns of a disease gene are different in tissues affected by the disease than in those that do not exhibit the disease phenotype.
2.How do I query?
4.I have input a list containing gene "X", but in the results "X" links to the wrong genomic region or shows incorrect IDs/functional annotations. Why?
5. What does "assign lower priority to ubiquitously expressed genes" option do?
6. If I query mouse tissues, should I input mouse genomic region/ genes?
7. How do you derive mouse-human homologs?
8. How is the expression data sourced?
9. What does "mouse weighting" slider do?
10. Can I prioritise genes from multiple genomic regions?
11. What does the number of genes returned slider do? How do I get the full results?
13. How well does the gene prioritisation tool predict disease genes?
14. I am studying a phenotype that presents itself mostly in tissue X, but it does not appear in the selection.
15. I have an RNA-Seq/Microarray dataset that may be of interest to you.