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.

The tissues and cells section in GeneAnalytics contains four powerful filters which enable you to focus on specific sub-sets of the results:

1. Tissue/system:

• The tissue/system results panel is available in the upper left part of the results screen, and also serves as a filter for the detailed results.
• Note, that in this panel, ‘Tissues’ are all organs, tissues and cell classes defined in LifeMap Discovery.
• Entities that are not categorized into a specific tissue or system (e.g., fibroblasts) are presented as “uncategorized” tissues/systems, which appear at the end of the tissues/systems list, with no score.

2. 'Expressed in’: is used to filter for specific entity types:

• Cells (in vivo and in vitro)
• Compartments (anatomical compartments)
• Organs and tissues
• High throughput comparisons (and large scale dataset samples)

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 specific annotations of the matched genes (see annotation details). ‘Specific’, ‘enriched’ and ‘selective’ annotations increase the gene score, while ‘abundant’ and’ housekeeping’ annotations decrease it.
• The total number of genes in the entity: there is a negative effect of a high total number of genes in the entity on the match score.
• The entity type: genes in large scale data set samples have lower scores when compared to genes in other entities. 

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. 

• You can view annotations for selective cell markers by clicking on the number of matched genes for a specific cell in the results table. Matched genes that serve as cellular markers are indicated by the following icon: .
• To view genes in your query that are annotated as abundant or housekeeping genes, go to the ‘Analyzed genes’ panel at the top of the results page, and click on  . Abundant genes are genes that appear in a large number of organs or tissues in LifeMap Discovery (for more information about LifeMap Discovery entities, click here). Housekeeping genes are genes contained within a list that was established by integrating information from several studies aimed to identify human housekeeping genes.
• The LifeMap Discovery database contains more gene annotations which are not yet presented to the user but are used for the GeneAnalytics calculations:
  • Specific gene: a gene that is specific to or is expressed in only a few organs or tissues.  
  • Enriched gene: a gene that is expressed in many entities of the same organ or tissue.

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.