Analysis Results
Date Name of Analysis Samples Processed View Results
2018/02/02 Identifying novel small RNA biomarkers for electrical and mechanical remodeling post-MI (myocardial infarction) 43 Click to View
2018/02/02 Identifying urinary RNA as non-invasive biomarkers for progression of chronic kidney disease 80 Click to View
2018/02/02 Identifying and analyzing circulating extracellular RNA found in human serum. 5 Click to View
2018/02/02 Identifying novel small RNA biomarkers unique to patients with placental dysfunction 48 Click to View
2018/02/02 Identifying novel small RNA biomarkers unique to patients with gastric cancer 198 Click to View
2018/02/02 Extracellular RNA levels for glioblastoma multiforme patients via extracellular exosomes in conditioned media 4 Click to View
2018/02/02 High-Density Lipoproteins - small RNA Signatures in Systemic Erythematosus Lupus. 6 Click to View
2018/02/02 Diverse human extracellular RNAs are widely detected in human plasma. 39 Click to View
2018/02/02 Plasma extracellular RNA profiles in healthy and cancer patients 192 Click to View
2018/02/02 The Complex Exogenous RNA Spectra in Human Plasma: An Interface with Human Gut Biota? 9 Click to View
2018/02/02 ULMC Plasma and serum exRNA from healthy donors at University of Michigan 197 Click to View
2018/02/02 small RNA Sequencing of CSF Samples from Patients with IVH 70 Click to View
2018/02/02 Profiles of Extracellular RNA in Cerebrospinal Fluid and Plasma from Subarachnoid Hemorrhage Patients 523 Click to View
2018/02/02 Identifying and analyzing extracellular RNA found in mouse samples 3 Click to View
2018/02/02 Small RNA-seq during acute maximal exercise reveal RNAs involved in vascular inflammation and cardiometabolic health 62 Click to View
2018/02/02 Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects. 428 Click to View
2018/02/02 RNAseq analysis of colorectal cancer cells: KRAS regulation of secreted RNAs. 18 Click to View
2018/06/08 Plasma small RNASeq comparison with Illumina TruSeq and Biooscientific NextFlex 12 Click to View
2018/02/02 Profiles of Extracellular miRNA in Cerebrospinal Fluid and Serum from Patients with Alzheimer's and Parkinson's Diseases Correlate with Disease Status and Features of Pathology 345 Click to View
2018/02/02 Large differences in small RNA composition between human biofluids - parotid and SMSL saliva 28 Click to View
2018/02/02 Large differences in small RNA composition between human biofluids - 10 biofluids 101 Click to View
2018/02/02 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - PD vs. CONTROLS - CSF Only 119 Click to View
2018/02/02 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - AD vs. PD - CSF Only 119 Click to View
2018/02/02 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - AD vs. PD - Serum Only 102 Click to View
2018/02/02 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - PD vs. CONTROLS - Serum Only 112 Click to View
2018/02/02 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - AD vs. CONTROLS - CSF Only 124 Click to View
2018/02/02 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - AD vs. CONTROLS - Serum Only 114 Click to View
2017/03/18 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - Serum Only 164 Click to View
2017/03/18 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) 345 Click to View
2017/03/18 Tushar Patel - Healthy vs. Cancer (EXR-TPATE1OqELFf-AN) 192 Click to View
2018/06/08 All Human RNA-seq Data (With EXR-TPATE1OqELFf-AN Removed as Outlier) 2528 Click to View
2018/05/23 All Human RNA-seq Data Processed by miRNeasy Kit (One Sample Excluded) 797 Click to View
2017/10/12 Saumya Das - Post-Myocardial Infarction Study (EXR-SADAS1UJ0CzW-AN) 43 Click to View
2018/06/08 All Human RNA-seq Data Processed by mirVana PARIS Kit 1440 Click to View
2017/03/18 David Wong - Gastric Cancer vs. Healthy (EXR-DWONG1qf3tcS-AN) 198 Click to View
2017/03/18 Kendall Jensen - aSAH Study (EXR-KJENS1WBaSro-AN) 523 Click to View
2018/05/23 Thomas Tuschl - Reference Profiling Study (EXR-TTUSC1gCrGDH-AN) 312 Click to View
2017/05/11 Kendall Jensen - IVH Study (EXR-KJENS12WGutU-AN) 70 Click to View
2017/03/18 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - Healthy Controls Only 124 Click to View
2017/03/18 Jane Freedman - Framingham Heart Study (EXR-JFREE1eZDUKB-AN) 39 Click to View
2017/03/18 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - Alzheimer's Only 114 Click to View
2017/10/12 Muneesh Tewari - Plasma and Serum from Healthy Donors (EXR-MTEWA1cHYLo6-AN) 197 Click to View
2017/03/18 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - CSF Only 181 Click to View
2017/10/12 Markus Bitzer - Chronic Kidney Disease Study (EXR-MBITZ12SHVlr-AN) 80 Click to View
2018/05/23 David Erle - 10 Biofluid Study (EXR-DERLE1PHASE1OPEN-AN) 101 Click to View
2017/03/18 Kendall Jensen - Alzheimer's vs. Parkinson's (EXR-KJENS1sPlvS2-AN) - Parkinson's Only 107 Click to View
2017/03/18 Louise Laurent - Placental Dysfunction Study (EXR-LLAUR1s0A1mX-AN) 48 Click to View
2018/06/08 All Human RNA-seq Data 2720 Click to View
2017/05/11 Kendall Jensen - Biofluids from Healthy Controls (EXR-KJENS1RID1-AN) 428 Click to View
2017/10/12 Saumya Das - Exercise Study (EXR-SADAS1EXER1-AN) 62 Click to View
2018/05/23 David Erle - Parotid and SMSL Saliva Study (EXR-DERLE1PHASE1PROT-AN) 28 Click to View
2019/04/14 Tushar Patel - Plasma - Carcinoma (from Dataset EXR-TPATE1OqELFf-AN) 142 Click to View
2019/04/14 Saumya Das - Plasma - Post-Myocardial Infarction (from Dataset EXR-SADAS1UJ0CzW-AN) 43 Click to View
2019/04/14 Kendall Jensen - CSF - Alzheimer's Disease (from Dataset EXR-KJENS1sPlvS2-AN) 62 Click to View
2019/04/14 Thomas Tuschl - Serum and EDTA Plasma - Healthy Subjects (from Dataset EXR-TTUSC1gCrGDH-AN) 312 Click to View
2019/04/14 Markus Bitzer - Urine - Nephrotic Syndrome (from Dataset EXR-MBITZ12SHVIr-AN) 80 Click to View
2019/04/14 David Wong - Saliva - Healthy (from Dataset EXR-DWONG1qf3tcS-AN) 100 Click to View
2019/04/14 Tushar Patel - Plasma - Healthy (from Dataset EXR-TPATE1OqELFf-AN) 50 Click to View
2019/04/14 Muneesh Tewari - Plasma - Healthy (from Dataset EXR-MTEWA1cHYLo6-AN) 143 Click to View
2019/04/14 Kendall Jensen - CSF - Parkinson's Disease (from Dataset EXR-KJENS1sPlvS2-AN) 57 Click to View
2019/04/14 Saumya Das - Plasma - Healthy (from Dataset EXR-SADAS1EXER1-AN) 62 Click to View
2019/05/16 Kendall Jensen - Plasma - Stroke and Healthy Subjects (from Dataset EXR-KJENS10lPClY-AN) 203 Click to View
2019/04/14 Kendall Jensen - Plasma - Healthy (from Dataset EXR-KJENS1RID1-AN) 180 Click to View
2019/04/14 Kendall Jensen - Plasma - Subarachnoid Hemorrhage (from Dataset EXR-KJENS1WBaSro-AN) 266 Click to View
2019/04/14 Kendall Jensen - CSF - Subarachnoid Hemorrhage (from Dataset EXR-KJENS1WBaSro-AN) 257 Click to View
2019/04/14 Kendall Jensen - Serum - Parkinson's Disease (from Dataset EXR-KJENS1sPlvS2-AN) 50 Click to View
2019/04/14 David Wong - Saliva - Gastric Cancer (from Dataset EXR-DWONG1qf3tcS-AN) 98 Click to View
2019/04/14 Alessio Naccarati - Healthy Controls (from Dataset EXR-ANACC1S6lJ1C-AN) 209 Click to View
2019/04/14 Muneesh Tewari - Serum - Healthy (from Dataset EXR-MTEWA1cHYLo6-AN) 54 Click to View
2019/04/14 Kendall Jensen - Saliva - Healthy (from Dataset EXR-KJENS1RID1-AN) 45 Click to View
2019/04/14 Kendall Jensen - Urine - Healthy (from Dataset EXR-KJENS1RID1-AN) 203 Click to View
2019/04/14 Kendall Jensen - CSF - Intraventricular Brain Hemorrhage (from Dataset EXR-KJENS12WGutU-AN) 70 Click to View
2019/04/14 Kendall Jensen - Serum - Healthy (from Dataset EXR-KJENS1sPlvS2-AN) 62 Click to View
2019/04/14 Kendall Jensen - Serum - Alzheimer's Disease (from Dataset EXR-KJENS1sPlvS2-AN) 52 Click to View
2019/04/14 Kendall Jensen - CSF - Healthy (from Dataset EXR-KJENS1sPlvS2-AN) 62 Click to View
2019/04/14 Markus Bitzer - Prospective - Urine - Kidney Transplant (from Dataset EXR-MBITZ1KPWIgP-AN) 228 Click to View
2019/04/14 Markus Bitzer - Biopsy Associated - Urine - Kidney Transplant (from Dataset EXR-MBITZ1WCKgCw-AN) 207 Click to View

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.