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:
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.
|Query size||Entity score||Tissue/system score|
|1 gene||=Gene score||The maximal gene score among all genes in the tissue/system.|
|>1 gene||A weighted sum of the scores of all genes matched to this entity, normalized to log of the maximal score that can be potentially achieved for the entity||A weighted sum of the scores of all genes matched to this tissue/system, normalized to log of the maximal score that can be potentially achieved for the tissue/system|
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.
The tissues and cells section in GeneAnalytics contains four powerful filters which enable you to focus on specific sub-sets of the results:
2. 'Expressed in’: is used to filter for specific entity types:
3. In vivo/In vitro filter
4. Prenatal/postnatal filter
The matching score is positively affected by higher numbers of matched genes, but is also significantly influenced by three additional parameters:
The organ/tissue column on the right side of the detailed result table indicates the organs, tissues, developmental paths and cell classes to which the matched entities belong.
The tissues in the tissue/system filter serve to filter the detailed result table, to only show the matches from the selected tissue(s). In addition, each tissue receives its own match score.
In the tissue/system filter, ‘tissues’ is a more general term that refers to all organs, tissues and cell classes defined in LifeMap Discovery.
To receive a list of all genes expressed in a specific tissue, organ or developmental path, including annotations for selective markers, specific genes and tissue-enriched genes, please contact us.