Gene-level Integrated Metric of negative Selection (GIMS)Sampson et al, PLoS One 2013
If a gene entered in the search bar above has a GIMS and Podocyte score, it will light up red in the table. Also utilize table by clicking on discrete data points to return the gene name or selecting particular regions to zoom in or out.About Download Find Genes By Podocyte and GIMS Score
Interactive table of 11,310 genes with both a GIMS and Podocyte score.
Please type in a maximum podocyte score quantile and a maximum GIMS score and then click "Find Genes."
Negative selection is the process by which deleterious variants that cause disease or reduce fitness are reduced or eliminated over generations. It is widely known that common protein-altering (or non-synonymous) variants are depleted as compared to synonymous variants. Because rare, protein-altering variants within functionally important genes are more likely to cause deleterious effects, they are under stronger negative selection than average genes.
We hypothesized that genes playing key roles in NS and glomerular diseases are under stronger negative selection compared to an average gene. Thus, we used publically available comparative genomics and population genetics resources to create a genome-wide, Gene-level Integrated Metric of negative Selection (GIMS) for each human gene (Sampson et al. PLoS One. 2013). We also created a Transcript-level Integrated Metric of negative Selection (TIMS) to characterize the strength of negative selection on an isoform level to provide an additional level of specificity beyond the GIMS score.
GIMS Score: Genes with a lower GIMS score (as a quantile) are associated with a higher degree of negative selection. For example, WT1, with a GIMS score of 0.05, is in the top 5th percentile of all genes in the genome in terms of negative selection.
TIMS Score: Transcript-specific metric of negative selection for selected gene. Lower TIMS score indicates stronger negative selection upon that transcript.
Podocyte Score: Genes with a lower podocyte score (as a quantile) are associated with higher probability of being podocyte-enriched. For example, a gene with a Podocyte score of 0.1 would be in the top 10th percentile of all measured genes in terms of podocyte specificity. Data adapted from Ju et al. Genome Research, 2013.
Questions or comments? Email: mgsamps at med.umich.edu
Sampson lab website: http://kidneyomics.org