The ENCODE project is an enormous international collaboration (>400 researchers), the goal of which is:
to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active
On the 5th September 2012, the ENCODE project simultaneously published 30 papers in 3 journals, describing five years of progress towards this goal. The sheer amount of information available in, and associated with, these publications is overwhelming, and clearly very important in the process of understanding what so much of the human genome does. In addition to the papers, Nature has published an ENCODE mini-site, which has links to all of the papers, as well as a publishing innovation called “Threads“. The threads are 13 sub-categories of information, that pull together relevant sections from all of the ENCODE papers to provide an overview of a particular topic (for instance, transcription factor motifs – which incorporates information from 13 of the publications into a single, coherent piece). These threads are an extremely useful way of summarising information from across disparate publications, and saves someone interested only in a portion of the data ENCODE provides from having to trawl through all 30 publications in order to find the nuggets of information he/she is interested in.
There are many other resources available too, including an iPad App, and a Virtual Machine that efficiently packages the code and data required to reproduce much of the analysis (see the last BIOINF-SIG talk for why this is such a good development ).
I’m going to list all the papers in the bibliography here, as a hopefully convenient resource (http://dx.doi.org/10.1038/nature11247), (http://dx.doi.org/10.1038/nature11233), (http://dx.doi.org/10.1038/nature11232), (http://dx.doi.org/10.1038/nature11212), (http://dx.doi.org/10.1038/nature11245), (http://dx.doi.org/10.1038/nature11279), (http://dx.doi.org/10.1101/gr.137323.112), (http://dx.doi.org/10.1101/gr.136184.111), (http://dx.doi.org/10.1101/gr.134478.111), (http://dx.doi.org/10.1101/gr.134445.111), (http://dx.doi.org/10.1101/gr.133553.111), (http://dx.doi.org/10.1101/gr.135350.111), (http://dx.doi.org/10.1101/gr.136127.111), (http://dx.doi.org/10.1101/gr.134767.111), (http://dx.doi.org/10.1101/gr.134890.111), (http://dx.doi.org/10.1101/gr.135129.111), (http://dx.doi.org/10.1101/gr.134957.111), (http://dx.doi.org/10.1101/gr.127712.111), (http://dx.doi.org/10.1101/gr.139105.112), (http://dx.doi.org/10.1101/gr.132159.111), (http://dx.doi.org/10.1101/gr.136366.111), (http://dx.doi.org/10.1101/gr.136838.111), (http://dx.doi.org/10.1101/gr.136101.111), (http://dx.doi.org/10.1101/gr.127761.111), (http://dx.doi.org/10.1186/gb-2012-13-9-r49), (http://dx.doi.org/10.1186/gb-2012-13-9-r52), (http://dx.doi.org/10.1186/gb-2012-13-9-r53), (http://dx.doi.org/10.1186/gb-2012-13-9-r51), (http://dx.doi.org/10.1186/gb-2012-13-9-r50), (http://dx.doi.org/10.1186/gb-2012-13-9-r48).
There’s also many summaries and opinion pieces available that are worth perusing if you have the time, links below.
Ewan Birney’s blog post about the project – Ewan is a co-director of the EBI, and the lead analysis coordinator for ENCODE.
I’ll add more as I find them.
CitationPlease cite this article as: Simon Cockell (2012) ENCODE. Bioinformatics Special Interest Group. http://bsu.ncl.ac.uk/fms-bioinformatics/2012/09/encode/
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- ENCODE | Bioinformatics Special Interest Group on Reproducibility in Bioinformatics – Simon Cockell
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