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modENCODE

The National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements

The modENCODE Project will try to identify all of the sequence-based functional elements in the Caenorhabditis elegans and Drosophila melanogaster genomes.

The goal of the modENCODE project is to provide the biological research community with a comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster.

modENCODE is run as a Research Network and the consortium is formed by 11 primary projects , divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation.

The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness.

All the data is publicly available and can be accessed on this site, using modMine or the Dataset Search Tool, on the Amazon Cloud and on the Open Science Data Cloud (OSDC). There are some restrictions on its use for 9 months following publication (see our Publication Policy ).

All the software of the project is publicly available on the on-line public repository GitHub. In particular, please check the code for the integration of modENCODE data in Galaxi on the Amazon Cloud.

The modENCODE project's aims are described in Nature 2009 Jun 18;459(7249):927-30. Unlocking the Secrets of the Genome. Please use this reference to cite the project.



Integrative papers companion pages

In December 2010, the modENCODE consortium published integrative analysis papers on its data, and summary pages of the data presented in those papers are available for both fly and worm.

In modMine we reproduced the networks identified by the 2 integrative papers.

    
Fly
    
Worm



Fly Chromatin States

Kharchenko at al., Nature 471, pp. 480-485 produced a genome-wide map of 9 chromatin states for D. melanogaster in the S2 embryonic cell line the BG3 neuronal cell line. You can explore the map using 2 different tools:

    
GBrowse
    
Park Lab Viewer