Hebrew University of Jerusalem
Alexander Silberman Institute of Life Sciences
Databases and Software Online
- Stanford Microarray Database. Microarray data from various published
experiments is available, in addition to links, publications, and software.
is a public repository for microarray based gene expression data. (from
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).
SAGEmap - Expression data
from SAGE experiments at NCBI.
This database is searchable from GEO.
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.
Unigene - Expressed
sequence database from NCBI.
EST's are clustered to form one entry for each transcript.
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
- Online Mendelian Inheritance in Man. A useful database at NCBI for genetic
diseases in man.
The SAGE home page. Protocols, publications
and data from various experiments.
BioDiscovery home page. the makers
of Imagene (and the various Clontech products- Clontech has became a company
in the BD
Biosciences Businesses complex).
SpotFire gene expression analysis
Novartis Genomics research foundation. affymetrix chip expression
data for many human tissues.
Gene Ontology Consortium (GO).
gene clasification to molecular function, biological process
and cellular component, as well as databases and other information.
GO Tree Machine. Will cross
a list of genes with the GO database, generating a GO tree with or without
MILANO. A very cool tool (kachol
lavan) for automated literature searches (based on PubMed entries), including
alternative gene symbols and abstract search.
analysis software also gives out nice graphs, free two week trial version.
TMEV (TIGR Multiexperiment Viewer).
Completely FREE java based software to analyze and visualize chip data.
Rather slow on large files.
institute, great contribution to gene annotation. Enter your gene
name and get a comprehensive account of function, expression synonims etc.
Affymetrix home page.Where you go to find
annotations and use NetAffx.
GEO - The Gene Expression
Omnibus, is where you go if you want to find and analyze other people's
GenMAPP homepage. A tool that lets
you create pathways and use pathways others have drawn up, to visualize
microarray data. free download and use.
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.
comments are most welcome
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