analysis

Topics including things like subsets (slimming) and enrichment analysis.

Can a single gene product be annotated with more than one GO term?

Yes!

It is possible and usually expected for a single gene / gene product to be associated with more than one GO term. The fact that you may have found that there are two or more different GO terms associated with a single gene / gene product in your results should not be a cause for concern.

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 can I programmatically get a list of GO terms associated with a gene identifier?

This very useful BIOSTARS thread clarifies "How Do I Do Simple GO Term Lookup Given A Gene (Or mRNA) Identifier?" You might find these responses useful when trying to simply create a list of GO terms associated with a given ID- and when you are not looking to conduct enrichment analyses - using a programatic approach. https://www.biostars.org/p/1226/

How can I do term enrichment analysis for a species that is not present in the list from AmiGO?

The Term Enrichment tool on the GO and AmiGO websites center only on data from the genomes available on the PANTHER Classification System Database (http://go.pantherdb.org). Details about how to use the tools available on AmiGO and how to interpret the results is available on our website at http://geneontology.org/page/go-enrichment-analysis.

How do I annotate a de novo assembled transcriptome against the GO database?

You can annotate the coding sequences in your transcripts using InterProScan. You can do this using WebServices or by downloading the tool and running it locally. Details can be found at: http://www.ebi.ac.uk/interpro/search/sequence-search/

This will predict GO terms based on domains detected using the mapping file here: http://geneontology.org/page/download-mappings

Does the Term Enrichment tool have a limit on the number genes in the input file?

Yes, there is a limit.

We're aware that our Term Enrichment tool on the homepage of the Gene Ontology Website cannot handle very large gene lists. The root of the problem is that at a certain number, the input (gene list) is too large for the form; however there is not an exact number at which it fails. One way to solve the problem, should you come across this situation, is to reduce the size of the input file by reducing the number of genes.

How do I use GO's Term Enrichment tool?

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.

What is the minimum information to include in a functional analysis paper?

Most journals require authors to submit high-throughput data to public repository as a pre-requisite for publication. As part of this process, the methods used to analyse data need to be reported in detail; this applies to both statistical and functional analysis. For papers describing enrichment analysis using GO, this means that the methods section should include the following information, to ensure the analysis is reproducible (an important criteria for reviewers' approval):
  1. What analysis tool was used and what version