miREV - Online Tool and Database
Description
miREV was developed as an easy to use online tool with a graphical user interface. Main goal is to uncover potential reference RNAs from EV studies in relation to different experimental conditions. Because suitable reference RNAs, for instance to validate findings from NGS experiments or to perform meaningful expression analyses by RT-qPCR, can vary from study to study because the RNA fingerprint strongly depends on the kind of experimental methods used. miREV also serves as a database. Interested parties can download the raw read counts and the associated metadata for further analyzes.
miREV contains data from publicly accessible sources as well as own data. The whole data set focuses on blood derived EVs and represents 9 different pathologies and 3 different isolation methods from both serum and plasma. The database only contains data sets with validated EV or exosome isolates. Data was processed to exclude poor quality data and reads mapping to other RNA species (e.g. rRNA, tRNA). In total 654 samples from 13 studies with 15 different physiological and pathophysological conditions were incorporated. 428 samples remained after the strict filtering procedure. To account for variable analysis setups, count lists were normalized by 6 commonly used normalization methods for abundance analyses and potential, stably expressed reference transcripts were evaluated by 3 different established algorithms. Raw count tables as well as the associated metadata for the selected sample set can be downloaded directly in the app. The code with which the results of the database were calculated is available on GitHub.