Learn to use ArrayExpress, a resource for storage and sharing of gene expression and other microarray data. ArrayExpress provides interfaces that allow users to search for complete datasets, for gene expression profiles, and for differentially expressed genes. Data content can be downloaded in multiple ways. ArrayExpress is one of the core databases of EBI, the European Bioinformatics Institute, and it is a public archive for functional genomics data.

You will learn:

  • to query the archive of ArrayExpress for records of experiments, arrays, and protocols, and to export data
  • to query for expression profiles of genes, and identify groups of genes with similar expression profiles
  • to find conditions under which a gene is differentially expressed, and to find genes differentially expressed under certain conditions
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group Expression resources. You might find the other tutorials in the group interesting:

Functional Glycomics Gateway: The home for Functional Glycomics research

CleanEx: A Database of Heterogeneous Gene Expression Data Based on A Consistent Gene Nomenclature

Allen Mouse Brain Atlas: Mapped gene expression data in mouse brain

miRBase: microRNA sequences, targets and gene nomenclature

DBTSS: Database of Transcriptional Start Sites

Alternative Splicing and Transcript Diversity (ASTD) database: A bioinformatics resource for alternative splice events and transcripts for human, mouse, and rat

GENSAT: Provides an extensive amount of high quality images of gene expression in the central nervous system of the mouse.

Gene Expression Omnibus (GEO): A gene expression/molecular abundance repository and a curated, online resource for gene expression data

CATEGORIES

EBI : This category includes all resources maintained at the European Bioinformatics Institute (EBI)

Expression : This category may contain various expression data collections, annotation tools, or repositories of expression data.

BLOG POSTS

Tip of the Week: BioGPS for expression data and more: This week's tip introduces BioGPS, or Gene Portal System. We get a lot of questions about two things that BioGPS can help you to tackle: what do I do with a list of genes to find out what they are? An...

Tip of the Week: Genomic Data Resources: Today's tip isn't on just one resource or a part of one, it's a whirlwind tour of many! In fact, in less than 5 minutes I'll put you through ALL of the resources online on genomics. Ok, well, not all. ...

Tip of the Week: cast a SPELL and find your genes!: Today's tip is on a resource named SPELL, which stands for 'Serial Pattern of Expression Levels Locator'. You enter a small set of gene names. The SPELL search engine will analyze expression datasets c...

Tip of the Week: Gene Expression Data by Condition at ArrayExpress: In today's tip, I want to show you how to use a great looking beta tool that I just found at EBI's ArrayExpress Gene Expression repository (AE). The tool's name is the ArrayExpress Atlas. You may have ...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Zamani-Ahmadmahmudi Mohamad et al., Prognostic efficacy of the human B-cell lymphoma prognostic genes in predicting disease-free survival (DFS) in the canine counterpart Oncology. BMC Veterinary Research (2017) doi:10.1186/s12917-016-0919-x

Koper Andre et al., Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples. Respiratory Research (2017) doi:10.1186/s12931-016-0496-3

Wu Jian et al., Nomogram integrating gene expression signatures with clinicopathological features to predict survival in operable NSCLC: a pooled analysis of 2164 patients. Journal of Experimental Clinical Cancer Research (2017) doi:10.1186/s13046-016-0477-x

Du Wei et al., A feature selection method based on multiple kernel learning with expression profiles of different types. BioData Mining (2017) doi:10.1186/s13040-017-0124-x

Uboldi S. et al., Mechanism of action of trabectedin in desmoplastic small round cell tumor cells Cell and molecular biology. BMC Cancer (2017) doi:10.1186/s12885-017-3091-1