ENCODEdb
Data generated by members of the ENCODE Consortium is housed in a number of public databases, such as the UCSC Genome Browser and NCBI's Gene Expression Omnibus (GEO). Since issuing queries to these databases is often not intuitive, the ENCODEdb portal was developed to allow biologists to more easily query and retrieve data generated by the Consortium. This portal provides users a single, unified point-of-access to data generated by the ENCODE Consortium, regardless of which public database the primary data is housed in.
ENCODEdb users can both browse data in genomic regions of interest, as well as easily assemble custom data sets that can be used for downstream analysis with tools such as the Galaxy platform for interactive, large-scale genome analysis.
Two types of searches can be performed:
| Genomic Context | The Genomic Context search allows for the retrieval of information on functional elements that have been annotated within ENCODE regions of the human genome. These elements include NCBI mRNA Reference Sequences (RefSeqs), mRNA, EST, and STS sequences, single nucleotide polymorphisms (SNPs), and UniGene clusters, as well as links to gene expression databases, Online Mendelian Inheritance in Man (OMIM), and genome sequence browsers. |
| Consortium Data | The Consortium Data search allows users to perform queries on data generated by the ENCODE Consortium. Query results include array-based data stored in NCBI's Gene Expression Omnibus, as well as data available through the UCSC Genome Browser. |
An ideogram showing the position of each of the ENCODE regions is also available.
All ENCODE data submitted to NCBI's Gene Expression Omnibus (GEO) is listed here.
More information on how to use ENCODEdb can be found in the answers to Frequently Asked Questions.
Additional information on the ENCODE Project and consortium members can be found on the ENCODE Project Home Page.
Comments, suggestions and problems to bioinformatics@nhgri.nih.gov
