Gene

• Ensembl ENSG00000139618
• Entrez Gene 675
• Unigene Hs.34012

RNA transcript

• GenBank BC026160.1
• RefSeq NM_000059
• Ensembl ENST00000380152

• There are many IDs
• Software tools recognize only a handful
• Humans better recognize gene names

• Avoid errors: map IDs correctly
  • Beware of 1-to-many mappings
• Gene name ambiguity – not a good ID
  • e.g. FLJ92943, LFS1, TRP53, p53
  • Better to use the standard gene symbol, not aliases: TP53
• Excel error-introduction
  • OCT4 is changed to October-4 (open file/paste as text)
• Problems reaching 100% cross-mapping
  • E.g. due to version issues
  • Use multiple sources to increase coverage

http://www.biomart.org/

https://bioconductor.org/packages/release/bioc/html/biomaRt.html

The getBM() function has three arguments that need to be introduced: filters, attributes and values.

• Filters define a restriction on the query. Tell BiomaRt what kind of IDs do you have, so it will look for it. The listFilters() function shows you all available filters in the selected dataset.
• Attributes define the values we are interested in to retrieve. Which IDs associated with your IDs you want to get. The listAttributes() function displays all available attributes in the selected dataset.
• Values is a vector of IDs you want to convert

• host is the database version. For gene ID conversion, use the latest database.

For genomic coordinates, use database that corresponds to genome assembly version you are interested in

Annotation data as R dataframes

R data package for annotating/converting Gene IDs

• annotables R package by Stephen Turner, https://github.com/stephenturner/annotables

http://www.gettinggeneticsdone.com/2015/11/annotables-convert-gene-ids.html