ArrayExpress – functional genomics data

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.

Data Content

Updated today at 07:00
  • 56612 experiments
  • 1680905 assays
  • 27.55 TB of archived data

Latest News

17 February 2015 - RNA-seq expression data of many human cancer cell lines now available in ArrayExpress and Expression Atlas

Have you ever wondered if a commonly used cancer cell line (e.g. MCF-7) shows similar gene expression patterns when profiled in different labs? Or how about the gene expression patterns across a series of cell line models for the same cancer (e.g. B-cell lymphoma)? Two new RNA-seq data sets in ArrayExpress will shed some light on these questions: RNA-seq of 675 commonly used human cancer cell lines from Genentech, and RNA-seq of 39 human cancer cell lines that are in the NCI-60 set from the Cancer Cell Line Encyclopedia at the Broad Institute.

For those of you who are unsure about how to analyse this large amount of data, we've done the legwork for you: both data sets have been carefully curated, and then processed by our in-house statistical analysis pipeline at EMBL-EBI. The results are publicly available from the Expression Atlas (Genentech data, Broad data), where you will find FPKM values for genes and be able to browse/filter data by cell line, tissue origin of the cancer, or disease type on the interactive graphical user interface. Happy mining!

Links

Information about how to search ArrayExpress, understand search results, how to submit data and FAQ can be found in our Help section.

Find out more about the Functional Genomics group.

Tools and Access

ArrayExpress Bioconductor package: an R package to access ArrayExpress and build data structures.

Programmatic access: query and download data using web services or JSON.

FTP access: data can be downloaded directly from our FTP site.

Related Projects

Discover up and down regulated genes in numerous experimental conditions in the Expression Atlas.

Explore the Experimental Factor Ontology used to support queries and annotation of ArrayExpress data.