01-introduction.Rmd

# Introduction {#chapter1}




## Terminology

### Gene sets and pathway

A gene set is an unordered collection of genes that are functional related. A pathway can be interpreted as a gene set by ignoring functional relationships among genes.

### Gene Ontology (GO)


[Gene Ontology](http://www.geneontology.org/) defines concepts/classes used to describe gene function, and relationships between these concepts. It classifies functions along three aspects:

+ MF: Molecular Function
  - molecular activities of gene products
+ CC: Cellular Component
  - where gene products are active
+ BP: Biological Process
  - pathways and larger processes made up of the activities of multiple gene products

GO terms are organized in a directed acyclic graph, where edge between the terms represent parent-child relationship.


### Kyoto Encyclopedia of Genes and Genomes (KEGG)

[KEGG](https://www.genome.jp/kegg/) is a collection of manually drawn pathway maps representing molecular interaction and reaction networks. These pathways cover a wide range of biochemical processes that can be divided in 7 broad categories: metabolism, genetic and environmental information processing, cellular processes, organismal systems, human diseases, and drug development^[<https://pathview.uncc.edu/data/khier.tsv>].

### Other gene sets

GO and KEGG are most frequently used for the functional analysis. They are typically the first choice because their long-standing curation and availability for a wide range of species.


Other gene sets including but not limited to Disease Ontology ([DO](http://disease-ontology.org/)), Disease Gene Network ([DisGeNET](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4397996/)), [wikiPathways](https://www.wikipathways.org), Molecular Signatures Database ([MSigDb](http://software.broadinstitute.org/gsea/msigdb)).