Presentation is loading. Please wait.

Presentation is loading. Please wait.

Use Case 5: Biomarker Potential and Limitations of Circulating miRNA Performed by the Data Management and Resource Repository (DMRR) ERCC Data Analysis.

Published byRalph Townsend Modified over 8 years ago

Similar presentations

Presentation on theme: "Use Case 5: Biomarker Potential and Limitations of Circulating miRNA Performed by the Data Management and Resource Repository (DMRR) ERCC Data Analysis."— Presentation transcript:

1 Use Case 5: Biomarker Potential and Limitations of Circulating miRNA Performed by the Data Management and Resource Repository (DMRR) ERCC Data Analysis 1 Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260.

2 Use Case 5: Biomarker Potential and Limitations of Circulating miRNA Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260. 2 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 Williams 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. The dataset from Williams et al is freely available in the Short Read Archive (SRA), so it makes a good practice dataset for becoming familiar with the Workbench and exceRpt.

3 Biological Question of Interest 3 This work from the Tuschl lab at Rockefeller University is mainly a technical study. They examined extracellular RNA from the bloodstream of mothers and fathers, their newborn babies, and the placenta. They were interested in quantitating how much exRNA could be found, and whether it would be possible to detect biomarker RNAs at that level. The placenta acted as a model of a tumor; their thinking was that if detecting exRNAs from placenta is feasible, the same should be true of tumors. Use Case 5: Biomarker Potential and Limitations of Circulating miRNA Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260.

4 Biological Samples to Be Analyzed Use Case 5: Biomarker Potential and Limitations of Circulating miRNA 4 The dataset analyzed in this use case is available from the Short Read Archive (SRA) under Bioproject PRJNA187509. http://www.ncbi.nlm.nih.gov/bioproject/PRJNA187509

5 To match the sample names from the article with SRA accessions from the exceRpt output, we visit the Bioproject page at the SRA: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA187509 Use Case 5: Data Scrubbing Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260. 5

6 To match the sample names from the article with SRA accessions from the exceRpt output, we visit the Bioproject page at the SRA: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA187509 Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260. 6 Use Case 5: Data Scrubbing

7 Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260. 7 Use Case 5: Data Scrubbing

8 After matching sample IDs between the two pipelines, we can import both tables into Excel and start generating comparison plots. Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260. 8 Use Case 5: Data Comparison

9 Results from the Article’s analysis pipeline Use Case 5: Biomarker Potential and Limitations of Circulating miRNA Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260. 9

10 We can compare the number of reads mapped to various categories of RNA in Table S1 from the article with the same data from the exceRpt read mapping summary. Categories in common are total input reads, microRNA, ribosomal RNA, and transfer RNA. Use Case 5: Biomarker Potential and Limitations of Circulating miRNA Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260. 10

11 11 Use Case 5: exceRpt Pipeline Results - Number of Input Reads

12 12 Use Case 5: exceRpt Pipeline Results – MicroRNA

13 13 Use Case 5: exceRpt Pipeline Results - Ribosomal RNA

14 14 Use Case 5: exceRpt Pipeline Results - Transfer RNA

15 The exceRpt analysis pipeline recapitulates the analysis from Williams et al. except for significant differences in the number of reads mapped to transfer RNA. Use Case 5: Summary 15 http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Version_Updates

16 We used exceRpt version 2.8.8; the latest version is 3.1.9. At the Genboree Workbench there is a version history. Use Case 5: Summary 16 http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Version_Updates v2.2.8 We moved the alignment against endogenous repetitive elements (RE) to occur after the main smallRNA alignments performed by sRNABench. This is because we noticed that the RE library was able to ‘compete’ for reads that would be better annotated/interpreted as coming from tRNAs, piRNAs, or other transcripts. This competitive alignment did not ever affect miRNAs as these are always aligned to before other annotated RNAs, but we expect that this update will faithfully capture reads aligning to repetitive small-RNAs, especially tRNAs, piRNAs, and snoRNAs. exceRpt still aligns to REs as a final step before aligning to exogenous sequences as this is critical to remove highly repetitive endogenous sequences that might otherwise be confused as exogenous sequences.

17 Acknowledgements 17 Baylor College of Medicine, Houston, TX Aleksandar Milosavljevic Matthew Roth Genboree Team at Baylor Andrew Jackson Sai Lakshmi Subramanian William Thistlethwaite Sameer Paithankar Neethu Shah Aaron Baker Yale University, New Haven, CT Mark Gerstein Joel Rozowsky Rob Kitchen Fabio Navarro Gladstone Institute Alexander Pico Anders Riutta Pacific Northwest Diabetes Research Institute, Seattle, WA David Galas Roger Alexander Rockefeller University, New York, NY Tom Tuschl NIH John Satterlee Lillian Kuo Dena Procaccini

18 Use Case 5: References 18 1.Williams Z., et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. PNAS 110: 4255–4260. 2.Farazi T.A., et al. (2012) Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing. Methods 58: 171-187. 3.ExRNA Portal Software Resources (http://exrna.org/resources/software)http://exrna.org/resources/software

19 19 Useful Links exRNA Portal Software Resources – http://exrna.org/resources/software exRNA Atlas – http://genboree.org/exRNA-atlas/ 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/

Download ppt "Use Case 5: Biomarker Potential and Limitations of Circulating miRNA Performed by the Data Management and Resource Repository (DMRR) ERCC Data Analysis."

Similar presentations

Modules 6 and 7: Genboree and Epigenome Comparison Aleksandar Milosavljevic Epigenomics Data Analysis and Coordination Center (EDACC) Presented at the.

Modules 6 and 7: Genboree and Epigenome Comparison Aleksandar Milosavljevic Epigenomics Data Analysis and Coordination Center (EDACC) Presented at the.
Exploring the Human Transcriptome

Exploring the Human Transcriptome
Creating NCBI The late Senator Claude Pepper recognized the importance of computerized information processing methods for the conduct of biomedical research.

Creating NCBI The late Senator Claude Pepper recognized the importance of computerized information processing methods for the conduct of biomedical research.
Genome databases and webtools for genome analysis Become familiar with microbial genome databases Use some of the tools useful for analyzing genome Visit.

Genome databases and webtools for genome analysis Become familiar with microbial genome databases Use some of the tools useful for analyzing genome Visit.
01 The sRNA Workbench project date 20/07/2012 Matthew. B. Stocks.

01 The sRNA Workbench project date 20/07/2012 Matthew. B. Stocks.
Transcriptomics Breakout. Topics Discussed Transcriptomics Applications and Challenges For Each Systems Biology Project –Host and Pathogen Bacteria Viruses.

Transcriptomics Breakout. Topics Discussed Transcriptomics Applications and Challenges For Each Systems Biology Project –Host and Pathogen Bacteria Viruses.
Peter Tsai Bioinformatics Institute, University of Auckland

Peter Tsai Bioinformatics Institute, University of Auckland
Bi-correlation clustering algorithm for determining a set of co- regulated genes BIOINFORMATICS vol. 25 no.21 2009 Anindya Bhattacharya and Rajat K. De.

Bi-correlation clustering algorithm for determining a set of co- regulated genes BIOINFORMATICS vol. 25 no Anindya Bhattacharya and Rajat K. De.
Use Case 3: Circulating miRNA Changes Associated with Alzheimer’s and Parkinson’s Diseases Thursday, 23 April, 2015 7:30 pm Organized and Hosted by the.

Use Case 3: Circulating miRNA Changes Associated with Alzheimer’s and Parkinson’s Diseases Thursday, 23 April, :30 pm Organized and Hosted by the.
Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520

Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520
Small RNA-Seq Data Analysis Tools in the Genboree Workbench Sai Lakshmi Subramanian Lab of Prof. Aleksandar Milosavljevic Bioinformatics Research Laboratory.

Small RNA-Seq Data Analysis Tools in the Genboree Workbench Sai Lakshmi Subramanian Lab of Prof. Aleksandar Milosavljevic Bioinformatics Research Laboratory.
Use Case 1: Exogenous exRNA in plasma of patients with Colorectal Cancer and Ulcerative Colitis Wednesday, Nov 5 th, 2014 6:00 – 8:30 pm Organized and.

Use Case 1: Exogenous exRNA in plasma of patients with Colorectal Cancer and Ulcerative Colitis Wednesday, Nov 5 th, :00 – 8:30 pm Organized and.
Use Case 2: HDL-bound small RNA in Lupus 1 Data and background slides kindly provided by Kasey Vickers, Vanderbilt University. Use Case 2: High-Density.

Use Case 2: HDL-bound small RNA in Lupus 1 Data and background slides kindly provided by Kasey Vickers, Vanderbilt University. Use Case 2: High-Density.
Next generation sequencing Why? What? How? Marcel Dinger Developmental Biology Divisional Seminar 7 October 2010.

Next generation sequencing Why? What? How? Marcel Dinger Developmental Biology Divisional Seminar 7 October 2010.
mRNA-Seq: methods and applications

mRNA-Seq: methods and applications
Supplementary Material Supplementary Tables Supplementary Table 1. Sequencing statistics for ChIP-seq samples. Supplementary Table 2. Pearson correlation.

Supplementary Material Supplementary Tables Supplementary Table 1. Sequencing statistics for ChIP-seq samples. Supplementary Table 2. Pearson correlation.
Diabetes and Endocrinology Research Center The BCM Microarray Core Facility: Closing the Next Generation Gap Alina Raza 1, Mylinh Hoang 1, Gayan De Silva.

Diabetes and Endocrinology Research Center The BCM Microarray Core Facility: Closing the Next Generation Gap Alina Raza 1, Mylinh Hoang 1, Gayan De Silva.
Before we start: Align sequence reads to the reference genome

Before we start: Align sequence reads to the reference genome
NGS Analysis Using Galaxy

NGS Analysis Using Galaxy
BACKGROUND Have a gene involved in neurological disease, its function unclear Knockout is lethal, so… Designed a conditional knockout (cKO) mouse where.

BACKGROUND Have a gene involved in neurological disease, its function unclear Knockout is lethal, so… Designed a conditional knockout (cKO) mouse where.

Similar presentations

Ads by Google