How are the tissues and cells results scored and ranked?

In the tissues & cells section, the matching algorithm relies on gene annotations of each gene in each entity available in LifeMap Discovery®. These annotations are derived from the scientific literature and/or on bioinformatics calculations executed on expression data in LifeMap Discovery.

Each gene can have one or more of the following annotations:

• Specific gene: a gene that is only expressed in a few tissues/organs
• Enriched gene: a gene that is expressed in many entities of the same tissue/organ
• Selective gene:  an established cell-specific marker or a gene suggested to be characteristic of the cell
• Expressed gene: a gene known to be expressed in the entity, but that is not defined as a selective cell marker
• Abundant gene: a gene that is expressed in a large number of organs and tissues
• Housekeeping gene:  a gene that appears in a list of housekeeping genes established by integrating information from several studies:
  • Eisenberg et al, 2013
  • Ramskold et al, 2009
  • She et al, 2009
  • Zhu et al, 2008
• A low confidence level gene: a gene for which expression evidence originates from the analysis of a large scale dataset but lacks strong supporting evidence (for example, appears in a small number of cells in a specific organ).

Each gene in each entity is scored, based on both the entity type and the combination of the above mentioned annotations of that particular gene in the specific entity.

The matching score is calculated at three levels: the entity, the tissue and the system. The calculation procedure is different between a single-gene query and larger queries:

All matched genes 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 entity (from highest to lowest).  In single-gene queries, in vivo entities will appear before in vitro entities with the same score.