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Transcriptomics: Databases and Tools

Expression-based

 The Connectivity Map (cmap) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. It enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes. Supported by the Broad Institute, a research collaboration between MIT, Harvards and the Whitehead Institute.  You need to register for a free account to use this.

 The Gene Expression Omnibus: a public functional genomics data repository that helps users query and download experiments and curated gene expression profiles.  It also houses data analysis tools such as GEO2R for quantification of differential gene expression.

 Genvestigator biomedical is a "high performance search engine for gene expression. It elegantly integrates thousands of manually curated public microarray experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.)."  Genevestigator is free to try for 7 days but requires paid subscription after the 7 day trial period.

 The ArrayExpress Archive is a database of functional genomics experiments including gene expression. It includes a Gene Expression Atlas that contains a "subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments".

Transcriptomics tools

NCBI Splign:  A web tool used to align cDNA to genomic DNA (Splign was previously known as Spidey).

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