The ENCODE project has produced a massive amount of transcriptome data, made possible by the collaboration of a world wide consortium of laboratories. During the project it was critical to immediately know what data was being produced by which lab. The ENCODE RNA dashboard kept the researchers informed about new results, even before they were officially registered with the ENCODE Data Coordination Center (DCC). It was instrumental for management to have direct insight into the current state of the project at any given point in time. Collaborators could quickly proceed with their own analysis steps once the raw data and processed results were published on the dashboard by other groups. The dashboard was also enriched with direct links to additional summary statistics that had been published using the Grape RNA-Seq pipeline. Now that the project has yielded its results, the ENCODE dashboard still remains the only central place collecting all the RNA data produced by the ENCODE project. The international research community can explore the wide range of experiments, and quickly find and download the exact data sets they need for their own data analysis. The dashboard is not only useful for web access, but command line users will enjoy the friendly batch processing capabilities. There is a huge demand to provide the same kind of dashboard for additional ENCODE projects, and with the new version of our dashboard software package, the system can even be extrapolated to any other bioinformatics project having to deal with a lot of data. For example, the ENCODE Mouse (Mus musculus) dashboard is one of the upcoming dashboards, replicating the success of the ENCODE hg19 (Homo sapiens) dashboard.

1. ENCODE RNA Dashboard
HUB5 - Heidelberg
21. March 2013
Maik Röder
Python Consultant
roeder@berg.net
http://genome.crg.es/
encode_RNA_dashboard
Thursday, March 21, 13

2. ENCODE RNA Dashboard
• The ENCODE project has produced
massive amount of transcriptome data
• How to keep up to date during
production, even before submission to the
ENCODE Data Coordination Center
(DCC)?
• Direct links to additional summary statistics
produced by the Grape RNA-Seq pipeline
Thursday, March 21, 13

3. USCS Genome
Browser - ENCODE
• First, a look at the current
UCSC genome browser
Experiment Matrix for
ENCODE
• http://genome.ucsc.edu/
ENCODE/
Thursday, March 21, 13

4. ENCODE Experiment
Matrix (UCSC)
Files
RNA-Seq
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5. Search + List (UCSC)
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6. Mouse Experiment
Matrix (UCSC)
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7. Search + List (UCSC)
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8. ENCODE
RNA dashboard
• http://genome.crg.es/encode_RNA_dashboard/hg19/
• Summary of transcriptome data production
• Overview
• Exploration
• Batch Download
Thursday, March 21, 13

9. ENCODE RNA Dashboard
Human (hg19)
Exploration
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10. Exploration
Click to make file
details appear in
place
Click again to make list disappear and continue exploring
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11. ENCODE RNA Dashboard
Mouse (mm9)
Thursday, March 21, 13

12. Exploration
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13. Batch Download
• http://genome.crg.es/
encode_RNA_dashboard/HOWTO_batch-
download.html
Thursday, March 21, 13

14. Today
• ENCODE dashboard still remains the only
central place collecting all the RNA data
produced by the ENCODE project
• The international research community can
explore the wide range of experiments
• Quickly find and download the exact data
sets they need for their own data analysis.
• command line users will enjoy the friendly
batch processing capabilities
Thursday, March 21, 13

15. Upcoming
• Dashboard generation tool
• Reimplementation in Python using Pandas
• Methods Paper to be published soon
Thursday, March 21, 13

16. Thanks
• This work has been supported by the Centre for
Genomic Regulation (CRG) in Barcelona
• Roderic Guigó
• Julien Lagarde
• Learn about Pandas at the Python Meetup:
• Monday, April 15th
• http://www.meetup.com/HeidelbergPython
Thursday, March 21, 13