Disease Analysis


The disease matching score is based on the following parameters:

  1. The number of genes in your query that match to a specific disease normalized by the total number of genes specifically associated with the disease.
  2. The quality and type of the gene-disease relation. These relations are based on MalaCards sources and include the following relation types:
        • Differentially expressed (DE) genes (DE Sprite) 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 200 downregulated genes, derived from high throughput experiments extracted from the Gene Expression omnibus (GEO) or from the literature. The differentially expressed genes are calculated by an algorithm which filters out genes which their expression is highly variable among the samples. Then, differentially expressed genes are identified using the e-bayesian method; a gene is defined as differentially expressed if it is up-regulated or down-regulated by more than 2-folds in the diseased tissue in comparison to the matched normal tissue, and the p-value is equal to 0.05 or lower.
        • Genetic associations to diseases (Genetic Association Sprite) 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 genetic association table in a descending order of their score.
        • The “GeneCards-inferred” (Gene Cards Inferred Sprite (1)) 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 may sometimes be unclear. For example, the gene can be indicated as ‘unaffected’ in the disease. Similarly, if a gene is related to a disease 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 has 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 scored is used as the final gene score. The disease score is based on the final scores of all the matched genes.

Disease Categories Filter

This panel filters results in accordance with the Malacards disease categorization. The Malacards algorithm categorizes each disease into 0-4 anatomical and 0-5 global disease categories based on:

  1. Existing and widely used categorization systems such as ICD10 and Orphanet.
  2.  Identification of category-specific keywords contained in disease names and annotations.

Use this filter to focus the results.

The numbers indicate the number of hits per disease category. These numbers are modified upon use of the additional category filter.

Note that not all the diseases are categorized. 

Genetic Associations Table

Association categoryGenetic associationSource
Causative mutation Pathogenic ClinVar
Likely Pathogenic ClinVar
Molecular basis known OMIM
Causative germline mutation Orphanet
Causative somatic mutation Orphanet
Causative mutation Uniprot
Risk factor Confers sensitivity ClinVar
Risk factor ClinVar
Genetic association OMIM
Susceptibility factor OMIM
Modifying Germline mutation Orphanet
Role in phenotype Orphanet
Modifying Somatic mutation Orphanet               
Resistance factor Protective ClinVar
Resistance factor OMIM
Genetic tests Genetic tests GeneTest
Drug response Drug response ClinVar
Structural gene variation Structural variation OMIM
Gene fusion Orphanet
Unconfirmed association Unconfirmed association OMIM
Candidate gene tested Orphanet
Genetic linkage OMIM

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