Annotations can be imported during project setup. This topic describes how to import annotations after a project has already been set up.
•To download and import Gene Ontology (GO) annotations, select Data > Download Annotations. See the topic Gene Ontology Annotations for detailed information about this procedure.
•To import local annotations (e.g., dbNSFP, VCF, Affymetrix, NimbleGen, etc.), select File > Import Annotations. This command opens a file chooser from which you may select the desired file.
Imported annotation information can be accessed within the Gene Table and used for Advanced Filtering.
Annotation sources:
•dbNSFP (v. 4.1) is an integrated database of functional annotations for the human genome (Liu et al., 2011 and 2013). The file dbNSFPv4.1_gene.zip, which can be downloaded for free, as part of a .zip archive from the DNASTAR website, compiles data from multiple sources to provide highly distilled information at the gene level. The entire dbNSFP database can be downloaded from the Jpopgen website.
•VCF files are available for free download from various sources, including the 1000 Genomes Project and the NHLBI Exome Sequencing Project (ESP). Note, however, that files 10-50 GB and larger will cause significant slowdowns in the ArrayStar program and are not recommended.