The small RNA Expression Atlas

SEA (also SEAweb) is a searchable database for the expression of small RNA (miRNA, piRNA, snoRNA, snRNA, siRNA) and pathogens. Publically available sRNA sequencing datasets were analysed with Oasis 2 pipelines and the results are stored here for easy and comparable search. Our curated, ontology connected metadata enables powerful searches within this database. Learn more in the documentation and publication.

miRNAs enriched in tissues

Several studies have shown tissue-specificity for miRNAs. Recently, Ludwig et al. analyzed 61 human tissue biopsies of different organs to define the distribution of miRNAs using tissue specificity index (TSI) and found several groups of miRNAs with tissue-specific expression. In particular, high expression of hsa-miR-124-3p and hsa-miR-9-5p was detected in brain and hsa-miR-133a-3p and hsa-miR-1-3p were detected in muscle. Click on the links for examining these examples with SEA and confirm that expression is highest in brain tissue samples or in heart and skeletal muscle tissue samples, respectively.

Bacterial and viral infections

We validated our approach of pathogen detection using seven datasets with known infection status. Samples in GSE72769 and GSE69837 are known to be infected by Mycobacterium abscessus and Chlamydia trachomatis bacteria, respectively.
Search Example

Analyzing in-house data and comparing with SEA data

In-house sRNA-seq data from well-characterised 47 Parkinson disease (PD) and 53 frequency-matched healthy controls is presented as User Demo Data. It is baseline data from the longitudinal de novo Parkinson disease (DeNoPa) cohort. SEA gives us a unique opportunity to identify PD-specific biomarkers associated with early-stage PD that can eventually help us in early diagnosis, therefore, better treatment of the disease. For detailed results, please see the SEA manuscript.
Search Example

snoRNA and piRNA in cancer datasets

Krishnan et al. explored piRNA as biomarkers for breast cancer. We can confirm this kind of study with SEA. In this example, we search their top differentially expressed piRNA hsa_piR_008114 in our cancer datasets and indeed find it differentially expressed in various different conditions in various cancer datasets.
Similarly, Baral et al. examined the role of snoRNA in hepatocellular carcinoma. SNORD126 is on top of their list of the upregulated ones and again, we can confirm this in several cancer datasets.

This section gives an overview of the number of datasets and samples with specific annotations. Click on the buttons or parts of the graph for requesting the dataset information.

Number of samples by:

browse searchable terms  
SEA can be browsed for small RNAs such as miRNA, piRNA, snoRNA, snRNA and rRNA (first table), tissues, cell lines, cell types, diseases and organisms (second table) and pathogens (e.g. bacteria or viruses, third table). This browsing index contains around 200,000 terms (most of them for different small RNA classes), therefore we only show a subset of terms (max 250 per type) request-able through the filter bars below. The initial terms displayed, are filtered for "a" or "hsa-". With these table all possible terms can be browsed that exists in SEA, for example, we can filter for “p-hsa” to see the predicted human miRNA, or "cancer" to obtain cancer related dataset stored in SEA. A click on any term adds it to the SEA search bar and will be used in the next request. These three table do not influence eachother. Not every combination of search terms will lead to results since it may be that certain sRNA or pathogens are not expressed in the datasets annotated with another requested term.
Explore sRNA, experiment's annotation or pathogens below or browse for   all datasets.