How are the disease results scored?
The disease matching score is determined using the following parameters:
- The number of genes in your query that match a specific disease normalized by the total number of genes specifically associated with the disease.
- The quality and type of the gene-disease relation. These relations are determined from MalaCards sources and include the following relation types:
- Differentially expressed (DE) genes are genes that were found to be significantly up- or downregulated in the diseased tissues in comparison to identical tissues obtained from unaffected subjects. The disease card contains up to 200 up- and /or 200 downregulated genes, calculated by a LifeMap Discovery algorithm, derived from high throughput experiments extracted from the Gene Expression omnibus (GEO) or from the literature. Each gene is tagged with a differential expression score determined by the fold-change in expression of the gene in the disease vs. the normal tissue.
- Genetic associations to diseases are determined from several MalaCards data sources. Since each data source has its own annotation terminology, we categorized all possible associations as shown in the table, in descending order of their score.
- The “GeneCards-inferred” relation indicates that the disease name appears in the gene page in GeneCards. Of note, the ‘GeneCards-inferred’ relation does not imply causality between the gene and the disease and the nature of this relation can sometimes be unclear. For example, the gene can be indicated as ‘unaffected’ in the disease. Similarly, if a gene-disease relation is based on a ‘publication’, it means that the gene and the disease were mentioned in the title and/or abstract of the same publication. There are two score levels for genes with GeneCards-inferred relations: a gene that appears in three or more different sections in GeneCards or a gene that has a higher score than a gene that appears in only one or two sections.
For each gene, the maximal score of all the above mentioned possible scores is used as the final gene score. The final disease score is based on the final scores of all the matched genes.
All matched diseases are presented in descending order of their score. If several matches have the same score, they are ordered by the ratio of matched to total number of genes in the disease (from highest to lowest).