Functional annotation methods

After we get either the list of significant genes or gene-expression fold change, we would like to understand what these genes mean biologically. Functional annotation allows to make sense from the set of genes. Sets of genes characterize biological processes much better than single genes.

Gene ontology

The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. The ontology covers three domains:

  • Biological Processes - operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units

  • Molecular Functions - the elemental activities of a gene product at the molecular level, such as binding or catalysis

  • Cellular Components - the parts of a cell or its extracellular environment

gene ontology
gene ontology
hexose biosynthesis
hexose biosynthesis

Methods

Usually 2 methods are considered [1-2]. Later topology-based method [3] was added

Functional annotation
Functional annotation

Note regarding ORA:

ORA
ORA

Online tools

  • Enrichr - ORA on many gene sets

  • David - a comprehensive set of functional annotation tools to help understand the biological meaning behind large gene lists

  • Reactome - Reactome is a free, open-source, curated and peer-reviewed pathway database

  • WikiPathways is an open science platform for biological pathways contributed, updated, and used by the research community

To Be Continued (let’s do it together) !

Prev Home Prev

By Petr Nazarov