The small RNA Expression Atlas

SEA 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...

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Examples
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. We examined the expression of these miRNAs using SEA. Click on the links for searching these examples and see 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.
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Samples in GSE33584 and GSE59944 are known to be infected by Human herpesvirus 5 and Human immunodeficiency virus 1 viruses, respectively.
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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, which is a 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.
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For results in detail, please see the SEA manuscript.