RNA-Seq Atlas - A reference database for gene expression profiling in normal tissue by next generation sequencing
RNA-Seq Atlas is a web-based repository of RNA-Seq gene expression profiles and query tools.
The website offers free and easy access to RNA-Seq gene expression profiles and tools to both compare tissues and find genes with specific expression patterns. To enlarge the socpe of the RNA-Seq Atlas, the data were linked to common functional and genetic databases. Additionally, data were linked to multiple microarray gene profiles representing normal as well as pathological tissue states and our data search interface allows an integrative detailed comparison between our RNA-Seq data and the microarray information.
Cite RNA-Seq Atlas
RNA-Seq Atlas - A reference database for gene expression profiling in normal tissue by next generation sequencing. Bioinformatics (Oxford, England), 10.1093/bioinformatics/bts084 (Krupp et al.).
Data access and query tools
Table view of all entries within the database.
- Fullt text search.
- Comparison of specific tissues profiles; also allowing for comparative analysis not only between normal tissue information but also to NCI60 data and thus between normal and tumor tissues.
- Explore common (and diverse) gene expression profiles between tissues.
- Explore pathway profile; e.g. selecting one or multiple KEGG pathway resulting in a list of involved genes.
Download RNA-Seq Atlas in tab separated text file format.
- RNA-Seq: The provided genome-wide expression compendium originates from eleven, healthy, human tissues samples pooled from multiple donors spanning 32384 specific transcripts corresponding to 21399 unique genes. The tissues include adipose, colon, heart, hypothalamus, kidney, liver, lung, ovary, skeletal muscle, spleen and testes (for more information see: Castle et al. 2010).
- Normal tissues: Multiple microarrays were adopted from BioGPS (Wu et al. 2009) and the Normal Tissue Gene Expression Study (Ge et al. 2005) representing more than 39000 transcripts in the normal, human tissues: colon, heart, hypothalamus, kidney, liver, lung, ovary, skeletal muscle, spleen and testes.
- Cancer celllines:
A panel of 60 human cancer cell line microarrays, representing 9703 unique spots corresponding to 6649 unique genes, from the NCI were adopted and transormed into log2 fold change ratios (for more information see: Ross et al. 2000).