Circulating miRNA Changes in Alzheimer's and Parkinson's Diseases Analysis Workshop

Workshop focused on analyzing circulating miRNA changes associated with Alzheimer's and Parkinson's diseases using the Genboree Workbench and exceRpt small RNA-seq analysis pipeline. The study aimed to identify extracellular miRNA biomarkers correlating with disease status and progression, replicating differential expression analysis from previous research. Dataset details, biological question of interest, and differential expression results are provided.

• miRNA analysis
• Alzheimers disease
• Parkinsons disease
• Genboree Workbench
• small RNA-seq

hirh Follow

Uploaded on Sep 17, 2024 | 0 Views

Download Presentation

Please find below an Image/Link to download the presentation.

The content on the website is provided AS IS for your information and personal use only. It may not be sold, licensed, or shared on other websites without obtaining consent from the author. Download presentation by click this link. If you encounter any issues during the download, it is possible that the publisher has removed the file from their server.

Presentation Transcript

1. ERCC Data Analysis Workshop Use Case 2: Circulating miRNA Changes Associated with Alzheimer s and Parkinson s Diseases Organized and Hosted by the Data Management and Resource Repository (DMRR) Thursday, 23 April, 2015 7:30 pm Data and disease background slides kindly provided by Kendall Jensen, Translational Genomics Research Institute Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 1

2. Use Case 2: miRNA Changes in Alzheimer s and Parkinson s Disease The goal of this use case is to show that the Genboree Workbench and the exceRpt small RNA-seq analysis pipeline can replicate the results of Burgos et al. We have developed these pipelines because as the Extracellular RNA Communication Consortium (ERCC) begins to generate more datasets, it is vital that they be analyzed in a reproducible and comparable way. Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 2

3. Use Case 2: miRNA Changes in Alzheimer s and Parkinson s Disease Biological Question of Interest Alzheimer s and Parkinson s are two neurodegenerative diseases that are difficult to assess by biopsy, since the affected tissue is inaccessible. In their study, Burgos et al. assessed the miRNA content in cerebrospinal fluid (CSF) and serum from postmortem subjects with full neuropathology evaluations. The goal of the study was to identify extracellular miRNA biomarkers that correlate with disease status and progression. In this use case, we focus on biomarkers that correlate with disease status by replicating the differential expression analysis in Burgos et al. Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 3

4. Use Case 2: miRNA Changes in Alzheimer s and Parkinson s Disease 345 Biological Samples to Be Analyzed Number of Samples 62 52 57 50 62 62 Disease Alzheimer s Biofluid CSF Serum CSF Serum CSF Serum Alzheimer s Parkinson s Parkinson s Control Control The dataset analyzed in this use case is available from dbGap, accession phs000727.v1.p1. 4

5. Differential Expression of miRNAs in Cerebrospinal Fluid (CSF) Control vs. AD Burgos? et? al exceRpt? +? DESeq2 Burgos? et? al exceRpt? +? DESeq2 miR? Name miR-124-3p miR-138-5p miR-127-3p miR-132-3p miR-127-5p miR-136-3p miR-381(-3p)* miR-101-5p miR-199b-5p miR-136-5p miR-184 miR-181a-5p miR-598(-3p)* miR-218-5p miR-9-3p miR-769-5p miR-95(-3p)* miR-760 miR-181a-3p log2(FC) -1.56 -1.46 -1.17 -0.89 -1.15 -1.02 -1.14 -0.92 -1.22 -0.91 -0.97 -0.71 -0.96 -0.79 -0.84 -0.84 -0.95 -0.88 -0.74 P-value 1.00E-06 1.00E-06 1.90E-05 1.90E-05 3.10E-05 4.00E-05 4.90E-05 6.70E-05 6.70E-05 1.91E-04 2.69E-04 3.57E-04 4.15E-04 4.93E-04 4.95E-04 6.20E-04 6.20E-04 8.46E-04 1.01E-03 log2(FC) -1.68 -1.48 -1.11 -0.86 -1.09 -0.88 -1.05 -0.85 -1.36 -0.91 -0.92 -0.62 -1.01 -0.76 -0.96 -0.80 -1.00 -0.87 -0.67 P-value 2.00E-06 7.00E-06 2.55E-04 1.29E-04 3.07E-04 1.16E-03 9.86E-04 9.86E-04 1.29E-04 7.73E-04 1.73E-03 3.49E-03 4.24E-04 2.56E-03 3.07E-04 3.49E-03 9.86E-04 1.94E-03 7.55E-03 miR? Name miR-124-3p miR-138-5p miR-127-3p miR-132-3p miR-127-5p miR-136-3p miR-381(-3p)* miR-101-5p miR-199b-5p miR-136-5p miR-184 miR-181a-5p miR-598(-3p)* miR-218-5p miR-9-3p miR-769-5p miR-95(-3p)* miR-760 miR-181a-3p log2(FC) -1.56 -1.46 -1.17 -0.89 -1.15 -1.02 -1.14 -0.92 -1.22 -0.91 -0.97 -0.71 -0.96 -0.79 -0.84 -0.84 -0.95 -0.88 -0.74 P-value 1.00E-06 1.00E-06 1.90E-05 1.90E-05 3.10E-05 4.00E-05 4.90E-05 6.70E-05 6.70E-05 1.91E-04 2.69E-04 3.57E-04 4.15E-04 4.93E-04 4.95E-04 6.20E-04 6.20E-04 8.46E-04 1.01E-03 log2(FC) -1.68 -1.48 -1.11 -0.86 -1.09 -0.88 -1.05 -0.85 -1.36 -0.91 -0.92 -0.62 -1.01 -0.76 -0.96 -0.80 -1.00 -0.87 -0.67 P-value 2.00E-06 7.00E-06 2.55E-04 1.29E-04 3.07E-04 1.16E-03 9.86E-04 9.86E-04 1.29E-04 7.73E-04 1.73E-03 3.49E-03 4.24E-04 2.56E-03 3.07E-04 3.49E-03 9.86E-04 1.94E-03 7.55E-03 miR-181b-5p miR-488-3p miR-495(-3p)* miR-708-3p miR-874(-3p)* miR-873-5p miR-129-5p miR-181d(-5p)* miR-139-5p miR-3200-3p miR-431-3p miR-9-5p miR-326 miR-377-5p miR-433(-3p)* miR-323a-3p miR-134(-5p)* miR-329(-3p)* miR-10a-5p miR-33b-5p miR-410(-3p)* miR-708-5p -0.75 -0.88 -1.07 -0.84 -0.75 -0.81 -0.84 -0.72 -0.84 -0.75 -0.91 -0.75 -0.76 -0.81 -0.85 -0.73 -0.7 -0.83 -0.84 -0.74 -0.71 -0.78 1.01E-03 1.01E-03 1.01E-03 1.01E-03 1.01E-03 1.48E-03 1.65E-03 1.89E-03 1.96E-03 2.77E-03 3.72E-03 4.97E-03 5.18E-03 6.87E-03 7.77E-03 8.53E-03 8.98E-03 8.98E-03 1.16E-02 1.24E-02 1.47E-02 1.51E-02 -0.63 -0.79 -1.13 -0.74 -0.79 -0.74 -0.87 -0.41 -0.86 -0.73 -1.06 -0.60 -0.71 -0.87 -0.78 -0.75 -0.69 -0.92 -0.29 -0.73 -0.54 -0.89 1.42E-02 1.08E-02 2.28E-03 1.31E-02 1.39E-03 9.08E-03 4.32E-03 6.86E-02 4.55E-03 9.09E-03 1.71E-03 3.32E-02 1.68E-02 9.09E-03 2.96E-02 1.54E-02 1.90E-02 1.09E-02 4.35E-01 2.66E-02 8.82E-02 1.27E-02 Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 5

6. Differential Expression of miRNAs in Cerebrospinal Fluid (CSF) Control vs. AD Comparison of Differential Expression Results 0.4 The plot to the left compares the differential expression results from Burgos et al. (x-axis) and the exceRpt pipeline (y- axis). miRNAs with absolute log2 fold changes < 0.7 were not reported in the article. exceRpt log2(FC) 0.8 1.2 1.6 1.4 1.2 1.0 0.8 Burgos et al (1) log2(FC) Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 6

7. Differential Expression of miRNAs in Cerebrospinal Fluid (CSF) Control vs PD Burgos? et? al exceRpt? +? DESeq2 miR? Name miR-132-5p miR-19a-3p miR-19b-3p miR-485-5p miR-127-3p miR-128(-3p)* miR-409-3p miR-433(-3p)* let-7g-3p miR-370(-3p)* miR-431-3p miR-873-3p miR-136-3p miR-212-3p miR-10a-5p miR-1224-5p log2(FC) -1.02 0.98 0.92 -1.08 -0.98 -0.85 -0.77 -0.86 0.82 -0.83 -0.81 -0.83 -0.72 -0.73 -0.76 -0.76 P-value 3.93E-04 3.93E-04 3.93E-04 3.93E-04 4.48E-04 3.45E-03 3.45E-03 6.29E-03 8.41E-03 8.41E-03 8.41E-03 8.68E-03 1.20E-02 2.29E-02 2.37E-02 3.29E-02 log2(FC) -1.11 0.97 1.05 -1.24 -1.06 -0.92 -0.80 -0.90 0.93 -0.88 -0.74 -0.89 -0.68 -0.78 -0.27 -0.73 P-value 3.31E-04 3.77E-03 3.31E-04 3.31E-04 5.28E-04 3.70E-03 4.20E-03 1.05E-02 9.40E-03 1.05E-02 2.99E-02 1.38E-02 3.03E-02 3.03E-02 4.76E-01 9.88E-02 *In some cases, Burgos et al reports results for the parent form of a miRNA. The sRNAbench tool used by exceRpt always estimates which mature product of the miRNA is most likely expressed based on the position of reads in the miRNA sequence. Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 7

8. Differential Expression of miRNAs in Cerebrospinal Fluid (CSF) Control vs PD Comparison of Differential Expression Results 1.0 The plot at left compares the differential expression results from Burgos et al (x axis) and the exceRpt pipeline (y axis). miRNAs with absolute log2 fold changes < 0.7 were not reported in the article. exceRpt log2(FC) 0.5 0.0 miR-10a-5p 1.0 0.0 0.5 1.0 1.0 0.5 Burgos et al (1) log2(FC) Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 8

9. Differential Expression of miRNAs in Cerebrospinal Fluid (CSF) AD vs PD Burgos? et? al exceRpt? +? DESeq2 miR? Name miR-19b-3p miR-19a-3p miR-127-5p miR-873-5p miR-32-5p log2(FC) 0.98 0.94 0.83 0.82 0.71 P-value 2.34E-04 6.84E-04 1.57E-02 1.57E-02 3.06E-02 log2(FC) 1.03 1.07 0.89 0.80 0.80 P-value 7.39E-04 1.93E-03 1.95E-02 3.39E-02 2.02E-02 1.2 exceRpt log2(FC) miR 19a 3p 1.0 miR 19b 3p miR 127 5p 0.8 miR 32 5p miR 873 5p 0.6 0.6 0.7 0.8 0.9 1.0 Burgos et al (1) log2(FC) Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 9

10. Differential Expression of miRNAs in serum Control vs Alzheimer s Burgos? et? al exceRpt? +? DESeq2 miR? Name miR-34b-3p miR-219-2-3p miR-22-5p miR-125b-1-3p miR-1307-5p miR-34c-5p miR-34b-5p miR-887(-3p)* miR-182-5p miR-135a-5p miR-184 miR-30c-2-3p miR-873-3p miR-125a-3p miR-671-3p miR-21-5p miR-1285-3p miR-375 miR-3176 miR-127-3p log2(FC) 2.36 1.93 1.38 1.32 1.39 1.57 1.71 1.34 -1.01 1.66 1.43 1.22 1.30 1.27 1.21 -0.82 1.03 -0.94 1.06 0.92 P-value 1.90E-05 5.37E-04 5.37E-04 8.03E-04 1.28E-03 1.96E-03 2.57E-03 3.31E-03 3.82E-03 4.84E-03 4.84E-03 4.84E-03 4.84E-03 9.65E-03 9.65E-03 2.35E-02 2.45E-02 3.26E-02 3.35E-02 3.74E-02 log2(FC) 1.95 2.62 1.11 1.29 0.81 2.04 2.33 1.58 -1.14 2.73 2.50 1.31 1.43 1.74 0.75 -0.88 1.60 -1.00 1.01 0.94 P-value 4.77E-03 9.20E-05 4.77E-03 1.10E-03 7.82E-02 2.52E-04 8.70E-04 1.06E-03 9.36E-04 3.22E-04 5.00E-06 6.41E-03 4.77E-03 8.70E-04 1.53E-01 1.58E-02 2.52E-04 2.89E-02 6.07E-02 3.49E-02 Burgos K., et al. (2014) 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. 10 PLoS ONE 9: e94839.

11. Differential Expression of miRNAs in serum Control vs Alzheimer s Comparison of Differential Expression Results 3 The plot at left compares the differential expression results from Burgos et al (x axis) and the exceRpt pipeline (y axis). miRNAs with absolute log2 fold changes < 0.7 were not reported in the article. exceRpt log2(FC) 2 1 0 1 0.0 0.5 1.0 1.5 2.0 1.0 0.5 Burgos et al (1) log2(FC) Burgos K., et al. (2014) 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. 11 PLoS ONE 9: e94839.

12. Differential Expression of miRNAs in serum Control vs Parkinson s Burgos? et? al exceRpt? +? DESeq2 miR? Name miR-338-3p miR-16-2-3p miR-1294 miR-30e-3p miR-30a-3p log2(FC) 1.35 -1.09 -1.04 0.97 0.95 P-value 1.06E-03 3.96E-03 1.17E-02 1.33E-02 1.54E-02 log2(FC) 0.37 -1.12 -1.10 0.40 0.74 P-value 5.64E-01 2.10E-02 2.10E-02 4.70E-01 1.63E-01 1.0 0.5 exceRpt log2(FC) 0.0 1.0 0.0 0.5 1.0 1.5 1.0 0.5 Burgos et al (1) log2(FC) Burgos K., et al. (2014) 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. 12 PLoS ONE 9: e94839.

13. Differential Expression of miRNAs in serum Alzheimer s vs Parkinson s Comparison of Burgos? et? al exceRpt? +? DESeq2 miR? Name miR-320a miR-320b miR-378d miR-378f miR-378a(-3p)* miR-378b miR-378c miR-193a-5p miR-320c miR-1285-3p miR-550a-3-5p miR-874(-3p)* miR-125a-5p miR-21-5p miR-671-3p let-7i-3p log2(FC) -1.81 -1.84 -1.69 -1.70 -1.54 -1.62 -1.47 -1.32 -1.45 -1.25 -1.09 -1.06 -1.01 0.98 -1.19 -0.86 P-value 4.60E-05 4.60E-05 4.60E-05 4.60E-05 7.70E-05 1.32E-04 4.53E-04 2.22E-03 3.48E-03 6.90E-03 1.36E-02 1.39E-02 1.69E-02 1.69E-02 1.69E-02 2.77E-02 log2(FC) -2.04 -1.66 -1.83 -1.89 -1.56 -1.76 -1.72 -1.35 -1.12 -1.58 -0.54 -0.65 -1.04 1.12 -0.58 -0.88 P-value 3.10E-05 1.92E-03 5.80E-05 4.10E-05 2.07E-04 1.17E-03 1.42E-04 3.25E-03 5.60E-02 1.03E-03 2.25E-01 1.65E-01 1.54E-02 6.74E-03 3.08E-01 2.80E-02 Differential Expression Results 1.0 exceRpt log2(FC) 0.0 1.0 2.0 0.0 0.5 1.0 1.5 1.0 0.5 Burgos et al (1) log2(FC) Burgos K., et al. (2014) 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. 13 PLoS ONE 9: e94839.

14. Digging Deeper: Parkinson s vs. Parkinson s with Dementia Burgos? et? al exceRpt? +? DESeq2 Burgos? et? al exceRpt? +? DESeq2 miR? Name miR-30b-5p miR-30c-5p miR-30a-3p miR-664-3p miR-26a-5p miR-34c-5p miR-582-3p miR-26b-5p miR-1298(-3p)* let-7f-1-3p miR-375 miR-1247-5p miR-1911-5p miR-374a-5p miR-34b-5p miR-152(-3p)* miR-7-1-3p miR-135a-5p miR-18b-5p miR-23c miR-135b-5p miR-374a-3p miR-148b-3p miR-18a-5p miR-204-5p miR-374b-5p miR-3960 miR-3605-5p miR-101-3p miR-34b-3p miR-503(-5p)* miR-132-3p miR-142-5p miR-582-5p miR-1246 miR-1260a miR-208b(-3p)* log2(FC) 1.939733 1.791096 1.886821 2.350324 1.698547 2.123616 1.861379 1.763952 2.05341 1.89744 -1.610137 -1.819452 1.980395 1.896724 2.007146 1.357329 1.675576 1.862747 1.783578 1.367051 1.824455 1.627059 1.27146 1.704245 1.71578 1.46507 1.436168 -1.437123 1.285599 1.707851 1.666408 1.046738 1.065144 1.460105 -1.433216 1.20334 1.424901 P-value 0.000367 0.000367 0.000479 0.000685 0.001409 0.002262 0.002897 0.003231 0.005541 0.006943 0.00807 0.009217 0.009217 0.009217 0.009562 0.010709 0.012898 0.016956 0.016956 0.016956 0.017638 0.021943 0.022047 0.022047 0.022047 0.031505 0.033061 0.033136 0.03471 0.034753 0.034753 0.051849 0.052703 0.062794 0.065986 0.067076 0.067076 log2(FC) 2.101559 1.861623 2.000182 -0.21 0.71 0.43 0.21 1.05 1.21 0.42 -0.34 0.76 -0.79 --- --- --- -0.14 0.03 1.17 1.36 0.53 -1.11 1.67 2.03 1.05 1.26 P-value 0.000371 0.000492 0.003382 8.58E-01 4.91E-01 8.29E-01 9.31E-01 9.72E-02 5.61E-02 8.26E-01 8.29E-01 4.96E-01 5.26E-01 --- --- --- 9.64E-01 9.84E-01 1.92E-01 1.71E-01 8.23E-01 1.80E-01 6.64E-02 4.85E-02 1.80E-01 1.71E-01 miR? Name miR-30b-5p miR-30c-5p miR-30a-3p miR-664-3p miR-26a-5p miR-34c-5p miR-582-3p miR-26b-5p miR-1298(-3p)* let-7f-1-3p miR-375 miR-1247-5p miR-1911-5p miR-374a-5p miR-34b-5p miR-152(-3p)* miR-7-1-3p miR-135a-5p miR-18b-5p miR-23c miR-135b-5p miR-374a-3p miR-148b-3p miR-18a-5p miR-204-5p log2(FC) 1.94 1.79 1.89 2.35 1.70 2.12 1.86 1.76 2.05 1.90 -1.61 -1.82 1.98 1.90 2.01 1.36 1.68 1.86 1.78 1.37 1.82 1.63 1.27 1.70 1.72 P-value 3.67E-04 3.67E-04 4.79E-04 6.85E-04 1.41E-03 2.26E-03 2.90E-03 3.23E-03 5.54E-03 6.94E-03 8.07E-03 9.22E-03 9.22E-03 9.22E-03 9.56E-03 1.07E-02 1.29E-02 1.70E-02 1.70E-02 1.70E-02 1.76E-02 2.19E-02 2.20E-02 2.20E-02 2.20E-02 log2(FC) 2.10 1.86 2.00 --- 1.84 1.53 0.49 1.04 1.01 2.18 -1.10 -2.20 1.00 2.29 1.26 1.61 1.94 -0.12 0.62 --- --- 1.87 1.32 0.46 1.55 P-value 3.71E-04 4.92E-04 3.38E-03 --- 1.66E-03 6.55E-02 7.36E-01 2.53E-01 5.43E-01 1.62E-02 1.71E-01 1.62E-02 4.86E-01 1.62E-02 4.28E-01 9.79E-03 1.94E-02 9.71E-01 8.17E-01 --- --- 4.07E-02 3.88E-02 8.24E-01 7.65E-02 miR-374b-5p miR-3960 miR-3605-5p miR-101-3p miR-34b-3p miR-503(-5p)* miR-132-3p miR-142-5p miR-582-5p miR-1246 miR-1260a miR-208b(-3p)* miR-196a-5p miR-548d-5p miR-548am-5p miR-1264 miR-424-5p miR-98(-5p)* miR-214-3p miR-34c-3p miR-486-3p let-7f-2-3p miR-124-3p miR-199a-3p miR-340-5p 1.47 1.44 -1.44 1.29 1.71 1.67 1.05 1.07 1.46 -1.43 1.20 1.42 -1.50 1.04 1.15 1.46 1.29 1.13 1.22 1.47 -1.05 1.18 1.44 0.99 1.11 3.15E-02 3.31E-02 3.31E-02 3.47E-02 3.48E-02 3.48E-02 5.18E-02 5.27E-02 6.28E-02 6.60E-02 6.71E-02 6.71E-02 7.35E-02 7.48E-02 7.48E-02 7.69E-02 7.69E-02 7.69E-02 8.20E-02 8.33E-02 8.33E-02 9.16E-02 9.21E-02 9.79E-02 9.79E-02 1.64 --- 5.61E-02 --- 0 0 1.836147 1.532867 0.487248 1.036815 1.010962 2.182452 -1.098313 -2.197584 0.997008 2.293509 1.260189 1.608754 1.940839 -0.124056 0.618491 0.001659 0.06545 0.735536 0.253081 0.543247 0.016231 0.171406 0.016231 0.485975 0.016231 0.428362 0.009791 0.019443 0.970966 0.816702 0 0 0 0 1.874623 1.317292 0.462525 1.547009 1.636204 0.040713 0.038828 0.824074 0.076549 0.056118 0 0 Burgos K., et al. (2014) 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. -0.209193 0.713873 0.426134 0.205409 1.046828 1.212802 0.419758 -0.341807 0.760768 -0.789706 0.857932 0.491222 0.828741 0.930952 0.097198 0.056118 0.825734 0.828741 0.495857 0.526064 14 PLoS ONE 9: e94839.

15. Digging Deeper: Parkinson s vs. Parkinson s with Dementia Comparison of Differential Expression Results 3 2 exceRpt log2(FC) 1 0 Significant in 1 Both Burgos exceRpt Neither 2 3 0 1 2 3 2 1 Burgos et al (1) log2(FC) Burgos K., et al. (2014) 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. 15 PLoS ONE 9: e94839.

16. Use Case 2: Summary Differential expression analysis of all pairwise comparisons shows that the exceRpt pipeline does a good job of reproducing the results from Burgos et al. AD vs control in CSF rPearson = 0.89 PD vs control in CSF rPearson = 0.98 AD vs PD in CSF rPearson = 0.90 1.2 1.0 0.4 exceRpt log2(FC) exceRpt log2(FC) 0.5 exceRpt log2(FC) miR 19a 3p 0.8 1.0 miR 19b 3p 0.0 miR 127 5p 1.2 0.8 miR 32 5p miR 873 5p 1.0 1.6 0.6 0.0 0.5 1.0 1.4 1.2 1.0 0.8 1.0 0.5 0.6 0.7 0.8 0.9 1.0 Burgos et al (1) log2(FC) Burgos et al (1) log2(FC) Burgos et al (1) log2(FC) AD vs PD in Serum rPearson = 0.93 AD vs control in Serum rPearson = 0.93 PD vs control in Serum rPearson = 0.97 1.0 3 1.0 exceRpt log2(FC) 0.5 exceRpt log2(FC) 2 exceRpt log2(FC) 0.0 0.0 1 1.0 0 1.0 1 2.0 0.0 0.5 1.0 1.5 1.0 0.5 0.0 0.5 1.0 1.5 2.0 1.0 0.5 0.0 0.5 16 1.0 1.5 1.0 0.5 Burgos et al (1) log2(FC) Burgos et al (1) log2(FC) Burgos et al (1) log2(FC)

17. Use Case 2: Summary Alzheimer s CSF vs control: all 41 of the miRNAs identified in Burgos et al as significantly differentially expressed were also so identified by exceRpt. Pearson correlation of log2(fold change) for those top 41 miRNAs between exceRpt and Burgos et al is 0.89. 30 / 41 (~75%) of the miRNAs have been identified in the literature as deregulated in Alzheimer s. Thus, this set of miRNAs represent useful candidates for further study and development into clinical biomarkers of AD disease status. See Burgos et al. for discussion of the other comparisons: AD vs PD and PD vs Control in CSF, and all serum cases. Burgos K., et al. (2014) 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. PLoS ONE 9: e94839. 17

18. Acknowledgements Baylor College of Medicine, Houston, TX Aleksandar Milosavljevic Matthew Roth Pacific Northwest Diabetes Research Institute, Seattle, WA David Galas Roger Alexander Genboree Team at Baylor Andrew Jackson Sai Lakshmi Subramanian William Thistlethwaite Sameer Paithankar Neethu Shah Aaron Baker TGen, Phoenix, AZ Kendall Van Keuren-Jensen Sean Allen Ashish Yeri NIH John Satterlee Lillian Kuo Dena Procaccini Yale University, New Haven, CT Mark Gerstein Joel Rozowsky Rob Kitchen Fabio Navarro Gladstone Institute Alexander Pico Anders Riutta 18

19. Use Case 2: References 1. Burgos K., Malenica I., Metpally R., Courtright A., et al. (2014)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. PLoS ONE 9:e94839. Barturen et al. (2014)sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments. Methods in Next Generation Sequencing. Volume 1, Issue 1 Ben Langmead, Cole Trapnell, Mihai Pop and Steven L Salzberg (2009)Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3):R25. Kozomara A, Griffiths-Jones S. (2011)miRBase: integrating microRNA annotation and deep-sequencing data. NAR 39 (Database Issue) Langmead B, Salzberg SL. (2012)Fast gapped-read alignment with Bowtie 2. Nature Methods. 9 : 357-359. Love M.I., Huber W., and Anders S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15: 550. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003)Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13(11):2498-504 ExRNA Portal Software Resources (http://exrna.org/resources/software) 2. 3. 4. 5. 6. 7. 8. 19

20. Useful Links exRNA Portal Software Resources http://exrna.org/resources/software exRNA Atlas http://genboree.org/java-bin/exRNAAtlas.jsp Genboree Workbench - http://genboree.org/java-bin/workbench.jsp Data Coordination Center Wiki - http://genboree.org/theCommons/projects/exrna-mads/wiki exRNA Data Analysis Tools Wiki - http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki Use Case Tutorials exRNA Portal Data Resource http://exrna.org/resources/data/ 20