XDec (Computational Deconvolution Tool)

Description of XDec

XDec deconvolutes small RNA-seq data from complex biofluids or fractions to estimate the exRNA expression profiles of constituent cargo profiles as well as the per-sample proportions of each constituent cargo profile.

Output from XDec includes:

  • Stage 1 Deconvolution
    • Heatmap representing the correlation between the deconvoluted cargo profiles modeled for the current dataset and the cargo types (CT) estimated from the deconvolution of individual Atlas datasets across informative ncRNAs.
    • Table of estimated constituent cargo profiles across 20,000+ ncRNA [miRNA, piRNA, tRNA, Y RNA, lincRNA, snoRNA, snRNA] transcripts (expression is normalized to [0:1] range).
    • Heatmap representing the proportions of each cargo profile for each sample in the current dataset.
    • Table of estimated proportions of each cargo profile for each sample in the current dataset.
    • Boxplots representing the proportions of each cargo profile for each sample in the current dataset separated based on provided metadata features.
  • Stage 2 Deconvolution
    • Tables of estimated average cargo profiles across 20,000+ ncRNA (miRNA, piRNA, tRNA, Y RNA, lincRNA, snoRNA, and snRNA) transcripts in reads per million (RPM) separated based on provided metadata features. Tables include mean expression, std. errors, degrees of freedom, and per sample residuals.

A full description of the deconvolution method used by XDec can be found in the Cell paper "ExRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present Across Human Biofluids" (Murillo et al., 2019).


Using XDec

There are three ways to use XDec:

  1. Submit your small RNA-seq biofluid data to the exRNA Atlas. We will deconvolute your data before releasing it to the public. By contributing your data to the exRNA Atlas, you will be providing new insights into exRNA biology for the wider scientific community and publicizing your own research in one of the largest web repositories for exRNA data. To learn more, read the guide on submitting data (and accompanying metadata) to the Atlas. You can also view existing deconvoluted Atlas datasets on the Public Analysis Results page.
  2. Use the Genboree Workbench, a web platform that hosts a variety of bioinformatics tools and stores related data for users, for your own private analyses. To learn more, read the guide.
  3. Install the exceRpt pipeline and XDec on your own private machine.