Microarray and Gene Annotation Links

General

National Center for Biotechnology Information (NCBI):  A great starting place for gene and protein annotation, with links to many other sites. (Entrez, LocusLink, Unigene, Homologene, Nucleotide (genbank IDs and refseq IDs), etc...)

Ensembl:  Free, searchable site containing sequence, domain, gene family, disease, orthologs, transcription information and more for over 8 eukaryotic species. Also, there is Ensmart, which links accession, locuslink, ensembl IDs, GO IDs, sequences, Unigene IDs, etc. in single or batch format.

Swissprot and TREMBL:  Protein and nucleotide database, respectively, from European Bioinformatics Institute (EBI) give gene and protein IDs used in many other annotation programs

Functional / Pathway Analyses

David:  "Database for Annotation, visualization and Integrated Discovery" Very easy to use for annotating microarray and other genetic data online.  Also available as downloadable program, Ease. Accepts several different gene ID codes.

GenMAPP: Gene Microarray Pathway Profiler:  free downloadable program allowing the visualization of biological pathways and families of genes with your microarray data.  Contains KEGG pathways, GO categories, and other submitted pathways.  (human, mouse, rat, yeast, fruit fly, worm, and zebrafish data)  

Gene Ontology (GO): Database containing the molecular function, biological process, and cellular component of genes/proteins in a tree structure database.  Fatigo:  A user-friendly site for querying/data-mining GO.

KEGG: Kyoto Encyclopedia of Genes and Genomes: Contains current molecular pathway information in database for multiple species

Species Specific

Mouse Genome Informatics (MGI):  Contains all sorts of information for the laboratory mouse, including genetic maps, polymorphisms, gene families, tumor data, links to Gene Ontology, and much more.

RGD: Rat Genome Database

Flybase:  Database of the Drosophila Genome

Yeast Genome:  Saccharomyces Genome Database (SGD)

Transcription Binding Sites / Regulatory Regions

TRANSFAC: The transcription factor database  (free for non-profit organizations)

TRAFAC:  Web-based program to identify potential regulatory regions for well-annotated human-mouse orthologous pairs of genes, and  CisMols:  program that identifies predicted cis-clusters, (CisMols), in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

Clustering

EisenLab Clustering and TreeView:  Simple, commonly used clustering methods and a TreeView, a useful program for visualization of the clustering output.

Public Microarray Databases/ MIAME XML formatting

MIAMExpress:  A user-friendly online tool to format your microarray data for publication in MIAME (Minimum Information About a Microarray Experiment) compliant format.  

ArrayExpress: public repository for microarray data