Explanation of Public Analysis Results

• This page contains all public analysis results submitted through the exRNA Atlas analysis tools.
• These results are available to everyone and cover much of the Atlas data.
• They should be useful for an initial examination of what the Atlas has to offer.
• Note that public analyses were last run on 2018/06/08, so certain results may be slightly outdated and/or missing newer samples. We will update these jobs in the near future.
• Use each Click to View link to view the results associated with a given analysis.

---

List of Tools

Below, you can read more about the different analysis tools offered by the exRNA Atlas.
Currently, all analysis tools work solely with RNA-seq profiles.

Deconvolution (Currently Only Available for Public Analyses)

• Download an archive containing the results of the deconvolution analysis.
• Result files include:
• Stage 1 Deconvolution Results
• Stage1_Results_Boxplots.pdf - Boxplots of the per-sample proportions for each estimated constituent cargo profile (rows) numbered 1 through k. Boxplots are separated based on metadata columns (e.g., disease, biofluid, etc.).
• Stage1_Results_Expression.txt - exRNA expression in transformed transcript abundance values (rows) for each estimated constituent cargo profile (columns) numbered 1 through k (profiles modeled for the input dataset).
• Stage1_Results_Heatmap_Correlations.pdf - Estimated constituent cargo profiles (rows) are correlated using the exRNA expression in transformed transcript abundance values across the informative RNAs (see Murillo et al., 2019) against the 6 CTs (columns) previously identified through the deconvolution of the exRNA Atlas (see Murillo et al., 2019).
• Stage1_Results_Heatmap_Proportions.pdf - Heatmap of the per-sample proportions (columns) for each estimated constituent cargo profile (rows) numbered 1 through k. Dendrogram is included to cluster similar composed samples.
• Stage1_Results_Proportions.txt - Per-sample proportions (columns) for each estimated constituent cargo profile (rows) numbered 1 through k (profiles modeled for the input dataset).
• Stage 2 Deconvolution Results
• NOTE: Stage 2 deconvolution is performed for each metadata value that is associated with at least 20 samples.
• Stage2_[METADATA COLUMN]_[METADATA VALUE]_miRNA_RPM.txt - Tables of estimated average cargo profiles across miRNA transcripts in reads per million (rows) separated based on provided metadata values. Columns include mean expression and std. errors for each estimated constituent cargo profile (numbered 1 through k) as well as degrees of freedom, explained variances, and per sample residuals.
• A full description of the deconvolution method 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).
• Tool designed and implemented by Oscar D. Murillo at the Bioinformatics Research Lab, Baylor College of Medicine, Houston, TX.
• Integrated into the exRNA Atlas by William Thistlethwaite at the Bioinformatics Research Lab, Baylor College of Medicine, Houston, TX.

DESeq2

• View a table containing differentially expressed miRNAs for selected Atlas data.
• Sort data by a variety of different metrics (adjusted p-value by default).
• Select some subset of miRNAs and use the Pathway Finder tool to find pathways containing miRNAs of interest (or protein targets of those miRNAs).
• Currently, our integration of the tool allows for pairwise comparisons of sample profiles (two conditions, two RNA isolation kits, etc.).
• Tool designed and implemented by Michael Love, Simon Anders, and Wolfgang Huber (PubMed).
• Integrated into the exRNA Atlas by William Thistlethwaite and Neethu Shah at the Bioinformatics Research Lab, Baylor College of Medicine, Houston, TX.

Dimensionality Reduction Plotting Tool (Currently Only Available for Public Analyses)

• Visualize selected Atlas data via PCA and tSNE embedding.
• Choose between three different plotting styles (ggplot2, plotly 2D, and plotly 3D).
• Pick between four different RNA categories (miRNA, piRNA, tRNA, snRNA) for your visualization.
• Color your plots by various metadata categories like dataset, anatomical location, condition, and biofluid name.
• Use filters to add or remove different datasets and biofluids from a given plot (with dynamically adjusted counts for each option).
• Note that these filters are purely visual and do not recompute the PCA or tSNE values.
• Tool designed and implemented by James A. Diao and Joel Rozowsky at the Gerstein Lab, Yale University, New Haven, CT.
• Integrated into the exRNA Atlas by William Thistlethwaite and Andrew R. Jackson at the Bioinformatics Research Lab, Baylor College of Medicine, Houston, TX.

Generate Summary Report

• Download an archive containing a collection of summary files describing the output from exceRpt for selected samples.
• Summary files include:
  • Plots including read count distributions, biotype distributions, miRNA abundance distributions, etc.
  • Read count tables for each library (miRNA / tRNA / piRNA / etc.) that span all selected samples. Both raw counts and normalized counts (reads per million mapped reads) are available.
  • Visualized taxonomy trees for exogenous rRNA and exogenous genomic reads.
• A full list of summary files can be found on the exceRpt Tutorial Page.
• Tool designed and implemented by Robert R. Kitchen and Joel Rozowsky at the Gerstein Lab, Yale University, New Haven, CT.
• Integrated into the exRNA Atlas by William Thistlethwaite and Neethu Shah at the Bioinformatics Research Lab, Baylor College of Medicine, Houston, TX.