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The Alexander Silberman Institute of Life Sciences

Useful Databases and Software Online

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  1. SMD - Stanford Microarray Database. Microarray data from various published experiments is available, in addition to links, publications, and software.
  2. ArrayExpress is a public repository for microarray based gene expression data. (from EBI)
  3. GEO - Gene Expression Omnibus at NCBI. Search gene expression data from microarrays, SAGE and more. Search by  sample (organism, condition etc.) or by platform (SAGE, specific array).
  4. SAGEmap - Expression data from SAGE experiments at NCBI. This database is searchable from GEO.
  5. TIGR - The Institute for Genomic Research: Genome projects containing genomic sequences from many organisms and also Gene Indices which contain transcribed sequences (EST's). There is also a microarray project and plenty of software available.
  6. Unigene - Expressed sequence database from NCBI. EST's are clustered to form one entry for each transcript.
  7. LocusLink - Sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites.
  8. OMIM - Online Mendelian Inheritance in Man. A useful database at NCBI for genetic diseases in man.
  9. The SAGE home page. Protocols, publications and data from various experiments.
  10. BioDiscovery home page. the makers of Imagene (and the various Clontech products- Clontech has became a company  in the  BD Biosciences Businesses complex).
  11. SpotFire gene expression analysis software.
  12. Novartis Genomics research foundation. affymetrix chip expression data for many human tissues.
  13. Gene Ontology Consortium (GO). gene clasification to molecular function, biological process and cellular component, as well as databases and other information.
  14. GO Tree Machine. Will cross a list of genes with the GO database, generating a GO tree with or without significance analysis.
  15. MILANO. A very cool tool (kachol lavan) for automated literature searches (based on PubMed entries), including alternative gene symbols and abstract search.
  16. GeneSpring analysis software also gives out nice graphs, free two week trial version.
  17. TMEV (TIGR Multiexperiment Viewer). Completely FREE java based software to analyze and visualize chip data. Rather slow on large files.
  18. Genecards. Weizmann institute,  great contribution to gene annotation. Enter your gene name and get a comprehensive account of function, expression synonims etc.
  19. Affymetrix home page.Where you go to find annotations and use NetAffx.
  20. GEO - The Gene Expression Omnibus, is where you go if you want to find and analyze other people's chip data.
  21. GenMAPP homepage. A tool that lets you create pathways and use pathways others have drawn up, to visualize microarray data. free download and use.
  22. DAVID - The Database for Annotation, Visualization and Integrated Discovery. Gives GO enrichment scores, and links to KEGG and BioCarta, etc. easy and straightforward to use. Recommended.

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