ArrayExpress – functional genomics data
ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.
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!
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.
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.