Contents
What does Gene Ontology tell you?
The Gene Ontology allows users to describe a gene/gene product in detail, considering three main aspects: its molecular function, the biological process in which it participates, and its cellular location.
How do you represent a gene ontology?
Typically, gene ontology terms are represented as tree-maps that enclose all data into defined space. However, large datasets make this type of visualisation appear cluttered and busy, and often not informative as some labels are omitted due space limits, especially when published in two-dimensional (2D) figures.
How are gene annotations used in Gene Ontology?
GO annotations: the model of biology. Annotations are statements describing the functions of specific genes, using concepts in the Gene Ontology. The simplest and most common annotation links one gene to one function, e.g. FZD4 + Wnt signaling pathway. Each statement is based on a specified piece of evidence.
What is the mission of the Gene Ontology Consortium?
The mission of the GO Consortium is to develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life. The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes.
How to determine the specificity of a gene?
Tau varies from 0 to 1, where 0 means broadly expressed, and 1 is specific (used in e.g. [ 15–24 ]). Other methods have been proposed, such as the expression enrichment (EE) [ 25 ], to calculate for which tissue each gene is specific, for example, in the database TiGER [ 26 ].
How is the z score used to measure tissue specificity?
The z-score can be implemented in two ways: either only over-expressed genes are defined as tissue specific, or the absolute distance from the mean is used, so that under-expressed genes are also defined as tissue specific. Only the former method was used to be able to compare z-score with other methods.