Abstract
We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns. We provide evidence for SEAweb's fidelity by (i) generating a set of 591 tissue specific miRNAs across 29 tissues, (ii) finding known and novel bacterial and viral infections across diseases and (iii) determining a Parkinson's disease-specific blood biomarker signature using novel data. We believe that SEAweb's simple semantic search interface, the flexible interactive reports and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases and organisms.
Highlights
Small RNAs are a class of short, non-coding RNAs with important biological functions in most aspects of organismal development in health and disease
The introduction of sRNA deep sequencing allowed for the quantitative analysis of sRNAs of a specific organism, but its generic nature enables the simultaneous detection of microbial and viral reads. sRNA-seq data naturally lends itself for the analysis of host-pathogen interactions, which has been recently exemplified for RNA-seq
SEAweb provides users with an option to perform on the fly analysis such as overlapping differentially expressed (DE) sRNAs or pathogens across different studies or the most important features identified with classification
Summary
Small RNAs (sRNAs) are a class of short, non-coding RNAs with important biological functions in most aspects of organismal development in health and disease. The increasing number of deep sequencing sRNA studies (sRNA-seq) is reflecting the importance of sRNAs in biological processes as well as disease diagnosis and therapy. Recent evidence highlights the pivotal roles of viral and bacterial-derived sRNAs in the pathogenesis of infectious diseases, across the animal and plant kingdoms [2,3,4]. The introduction of sRNA deep sequencing (sRNA-seq) allowed for the quantitative analysis of sRNAs of a specific organism, but its generic nature enables the simultaneous detection of microbial and viral reads. SRNA-seq data naturally lends itself for the analysis of host-pathogen interactions, which has been recently exemplified for RNA-seq The introduction of sRNA deep sequencing (sRNA-seq) allowed for the quantitative analysis of sRNAs of a specific organism, but its generic nature enables the simultaneous detection of microbial and viral reads. sRNA-seq data naturally lends itself for the analysis of host-pathogen interactions, which has been recently exemplified for RNA-seq
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