The ultimate goal of genetic association studies is to discover which genes and pathways have direct roles in risk of a disease or trait. Several methods now combine genetic association results with multiple kinds of evidence to generate lists of the genes that are most likely to mediate the genetic associations. The Knowledge Portals currently host results from three such methods that predict type 2 diabetes effector genes. The methods differ in the evidence types that they use as input and in the classifications or scores that they generate. The T2D Effector Prediction Summary is a first attempt at integrating the results of these disparate methods so that they can be compared.
To generate this table, the top 100 genes from each method were considered and each gene was assigned a numerical score from 1-5.
For the Curated T2D effector gene prediction method, scores were assigned as follows:
CAUSAL = 5
STRONG = 4
MODERATE = 3
POSSIBLE = 2
WEAK = 1
For the Effector Index and Integrated Classifier predictions, probability scores were divided into quintiles. Genes with scores in each quintile were assigned scores from 1 (lowest probability) to 5 (highest probability). The highest score for a gene across the three methods is displayed in the "top score" column of the table. Note that the Integrated Classifier method excluded from consideration some of the genes included in the Curated T2D effector gene predictions, since these were part of the training set for the method.
In the plot, each dot represents a gene, plotted by top score (y-axis) vs. chromosomal location (y-axis). Mouse over a dot to see the gene name, coordinates, and scores in each of the methods.
Immediately above the plot, you can enter criteria to filter both the plot and the table. Enter a gene name in the Gene box, or enter a score from 1-5 in one or more of the other boxes to filter by score.
In the table, click on the "Evidence" button to view detailed evidence for a gene.