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This article will explain in detail what is the use of Gene Ontology database for you. The editor thinks it is very practical, so I share it with you as a reference. I hope you can get something after reading this article.

Gene Ontology, called Gene Ontology in Chinese, uses GO terms to describe the function of gene products and provides the relationship between different GO terms. The official website is as follows

Http://geneontology.org/

The gene functions defined by GO are divided into the following three categories:

Molecular function

Cellular component

Biological process

All GO term form a directed acyclic graph, as shown below.

Each GO is a node in the graph, and the connections between the GO represent the information of the edges in the graph. The arrows between different GO have direction and represent special meaning, so the network structure is called directed acyclic graph.

It should be noted that the relationship between GO is not a tree structure. First of all, the three nodes BP,CC and MF are independent and have no common parent node. Secondly, GO does not have a strict hierarchical relationship in the tree structure. All also have the concept of parent node and child node, but the hierarchical relationship is not obvious. A GO can have multiple parent nodes.

Each GO term is represented by a unique GO number, prefixed with GO, followed by six digits, such as GO:0015749. Because GO is based on existing biological knowledge, and these perceptions are constantly revised and improved, all cases in which some GO term will be deleted or merged with other GO Term.

The relationships between different GO term are varied. Here are only a few common relationships.

Is a

Part of

Hast part

Regulation

The schematic diagram of the is a relationship is as follows

Mitochondria is a kind of organelle, and the relationship between them is mitochondrial is an organelle.

The schematic diagram of the part of relationship is as follows

Mitochondria are the components of cytoplasm, and the relationship between them is mitochondrial part of cytoplasm.

The schematic diagram of the has part relationship is as follows

It is often used to describe the relationship between various complexes in cells.

Regulation indicates the regulatory relationship, as shown in the following diagram

As for the regulation relationship, there are two kinds of regulation: positive regulation and negative regulation.

All GO Terms information can be downloaded from the following link

Http://www.geneontology.org/page/download-ontology

Provide obo, owl and other formats, usually, the use of go-basic.obo files on it.

GO itself is a cross-species concept, and the official GO document covers all the functions of most species. But for species in a specific domain, its function only accounts for a part of the whole GO. At this time, the corresponding part can be extracted from the whole GO to form a subset, which is called GO Slim. The GO Slim of different domains is provided in the following link.

Http://www.geneontology.org/page/go-subset-guide

For specific species, the use of appropriate GO Slim can effectively reduce the workload of subsequent data mining.

GO annotation information for some species is also provided on the official website. The link is as follows.

Http://www.geneontology.org/page/download-go-annotations

In addition, it also provides the mapping relationship between GO and other databases, such as KEGG Pathway, RDP, COG, etc. The links are as follows

Http://www.geneontology.org/page/download-mappings

An example of the mapping between InterPro and GO is as follows

InterPro:IPR000003 Retinoid X receptor/HNF4 > GO:DNA binding; GO:0003677InterPro:IPR000003 Retinoid X receptor/HNF4 > GO:steroid hormone receptor activity; GO:0003707InterPro:IPR000003 Retinoid X receptor/HNF4 > GO:zinc ion binding; GO:0008270InterPro:IPR000003 Retinoid X receptor/HNF4 > GO:regulation of transcription, DNA-templated; GO:0006355InterPro:IPR000003 Retinoid X receptor/HNF4 > GO:nucleus This is the end of GO:0005634 's article on "what's the use of Gene Ontology database?". I hope the above content can be of some help to you, so that you can learn more knowledge. if you think the article is good, please share it for more people to see.

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