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This article is about how to understand the ArrayExpress database, the editor thinks it is very practical, so I share it with you to learn. I hope you can get something after reading this article.

Like GEO databases, ArrayExpress is a public database owned by EBI that holds data related to chips and high-throughput sequencing.

The data comes from the two parts shown in the following figure.

The first part is the data submitted by the researchers, and the second part is the data imported automatically from the GEO database. In this database, the data is in units of experimental experiments, and each experiment corresponds to a unique number, as shown in the following figure.

The Accession in the first column represents the corresponding number of each experimental design, Assays represents the total number of samples corresponding to the experiment, and Raw represents the original data. The amount of data in the current version is as follows

Through this database, we can

Retrieve data, find data sets of interest according to keywords, numbers, etc.

Download data, analyze and mine based on public data

Submit data and upload your own data to the database

Click on each experiment number to display the details, as shown below

The red box marks are the three parts that you usually pay attention to. The first part shows the details of the samples contained in the experiment. After clicking, you can view the metadata related to the samples, as shown below.

The second part is used to download the data, and the third part is used to import the results into other software, such as GenomeSpace, for analysis and viewing.

In addition to downloading and analyzing public datasets, you can also upload your own data to the database. Except for the results of metagenome / macro transcriptome and transcriptome assembly, most of the other data can be uploaded to the database, such as SNP typing, gene expression profile, chip_seq, atac_seq, methylation sequencing and so on.

The database is also equipped with corresponding API and R packages, which can retrieve and download data in batches and processes. In the absence of data, it can also be used for in-depth mining based on ArrayExpress public data.

The above is how to understand the ArrayExpress database, the editor believes that there are some knowledge points that we may see or use in our daily work. I hope you can learn more from this article. For more details, please follow the industry information channel.

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