List of BioInfoRx Knowledge Base Articles

Genomic Annotation Resources


Genomic Annotation Resources

Primary repositories of genomic sequence and functional information.

  • Affymetrix NETAFFX.
  • Ensembl. Joint project of EMBL - EBI and the Sanger Institute.
  • Hugo Nomenclature Committee. Naming of human genes.
  • NCBI
  • GO: Gene Ontology Consortium. Provides a controlled vocabulary for describing how gene products behave. Directed trees which progress from more general to more specific terms are provided for Molecular Function, Biological Process and Cellular Component.
  • GOA: Gene Ontology Annotation. A project of the European Bioinformatics Institute that aims to provide assignments of gene products to the GO vocabulary.
  • KEGG: Kyoto Encyclopedia of Genes and Genomes.
  • MGI: Mouse Genome Informatics. Includes the MouseCyc database of curated biochemical pathways data for the laboratory mouse. The Jackson Laboratory.
  • SRS: Sequence Retrieval System. EMBL, Heidelberg.
  • UCSC Genome Browser.
  • BioCarta. Includes the proteomic pathway project for human and mouse.
  • BioCyc. A collection of pathway/genome databases for many individual organisms.
  • MetaCyc. A database of non-redundant, experimentally elucidated metabolic cross-organism pathways.


Analysis of and connections between the databases.

  • AmiGO. Nice interface to the Gene Ontology databases. Gene Ontology Consortium.
  • Bioconductor. Includes a number of annotation orientated packages.
  • GOstat. A web based tool for analysing over-representation of GO categories in gene lists. Tim Beissbarth, Walter and Eliza Hall Institute.
  • Clone/Gene ID Converter.
  • Institute for Genomic Research's (Tigr) Program for Genomic Application. Follow the link to 'Analysis Tools'. Includes PGA-XRef and RESOURCERER.
  • MatchMiner is a set of tools that enables the user to translate between disparate ids for the same gene.
  • NIH DAVID Use DAVID online to search for enriched annotation terms including GO terms or KEGG pathways, or download EASE to undertake similar analyses on a Windows PC.
  • SOURCE. A unification tool which compiles data from different databases. Genetics Department, Stanford University.
  • BioGPS. Gene and protein annotation portal produced by the Genomics Institute of the Novartis Research Foundation.
  • NCGI UniGene DDD (Digital Differential Display).
  • Onto-Tools. Intelligent Systems and Bioinformatics Laboratory, Wayne State University.
  • ProbematchDB. Microarray Lab, Mental Health Research Institute, University of Michigan.

Literature Search

  • Fable. Find published articles relevant to particular genes or proteins.


Larger scale pathway and network analysis