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GO Enrichment Analysis

One of the main uses of the GO is to perform enrichment analysis on gene sets. For example, given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.

Authoritative Database Groups

Authoritative Database Groups Where two or more databases are submitting data on the same species the GO Consortium encourages the model whereby one database group collects all annotation data for that species, removes the redundant (duplicate) annotations, and then submits the total dataset to the central repository. This ensures that no redundant annotations will appear in the master dataset. The table below documents those species for which a single database group is responsible for collating and submitting annotations.

Authoritative Database Groups

Authoritative Database Groups Where two or more databases are submitting data on the same species the GO Consortium encourages the model whereby one database group collects all annotation data for that species, removes the redundant (duplicate) annotations, and then submits the total dataset to the central repository. This ensures that no redundant annotations will appear in the master dataset. The table below documents those species for which a single database group is responsible for collating and submitting annotations.

External Mapping File Format

Mappings of GO have been made to other many other classification systems; a full list is available on the Mappings to GO page. This page describes the format of these files.

Format Specification

The source of the external file is given in the line beginning !Uses: !Uses:http://www.tigr.org/docs/tigr-scripts/egad_scripts/role_reports.spl, 15 aug 2000.

The line syntax for mappings is:

external database:term identifier (id/name) > GO:GO term name ; GO:id

For example:

Temporal information in Annotation Extensions

Adding temporal information

Using biological process terms to enhance cellular component annotations

Cellular component annotations can be enhanced by specifying that localization is observed during a specific biological process, e.g. a cell cycle phase. These annotations are constructed by putting the exists_during relationship and the identifier from the biological process ontology in the annotation extension column.

Use cases

1. A gene product is localized to the nuclear periphery in S phase, G2, and mitosis (S. pombe Ulp1; PMID:11884512)

Spatial information in Annotation Extensions

Adding spatial information

Usefulness of capturing cell type or tissue type specific location of action

Investigative methods that work solely with a specific tissue or cell type (such as laser capture microdissection) are becoming more commonplace and allow for downstream genetic or proteomic analyses that are not contaminated by surrounding tissue. In addition the separation of subcelluar particles via cell fractionation techniques enables the study of the constituents of a particular cell part/organelle.

GO Editor Guides

These guides explain how to add to or alter the gene ontologies. They are intended for those members of the consortium whose job it is to make such modifications to the GO. However we make them available here for anyone who is interested to know how this work is carried out.

User Stories

The User Story Story

User stories are tags for GO documentation pages, that identify the pages most likely to be of interest to different types of users.

The different user stories are listed below. Clicking on a story will take you to the list of relevant GO documentation pages.

Evidence Code Decision Tree

The following flow chart illustrates the steps that a curator typically takes when deciding what evidence code should be applied to an annotation. Please see the evidence code guide for more information on each of the codes.

Preparing GO Annotations for Submission

This page documents the steps required to take when supplying Gene Ontology annotations to the GO Consortium (GOC). For general information on how to conduct GO annotations, please see the GO Annotation Policies Guide.