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Statistical Bioinformatics
Genomic Annotation Resources
Databases
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
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.
Networks
Larger scale pathway and network analysis