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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.

A quick start guide to navigating modMine

Welcome to modMine! The purpose of modMine is to provide an interface for accessing modENCODE project data, as well as hosting a range of analysis tools to be used with it.

Here is a quick guide to getting started. For a more detailed overview of modMine features, please check our publication modMine: flexible access to modENCODE data.

What data exists?

At present, modMine contains submissions, organised in experiments. There are fly submissions and worm ones.

Each submission corresponds to one experiment done under a particular set of conditions. To get an idea of the scope of the modENCODE project, you can browse data by category. From there, you can find links to specific projects such as nucleosome mapping in C. elegans or gene model prediction in Drosophila.

How do I find a specific dataset?

If you're interested in a specific protein, modification or category of molecules, you can use the Search box in the top right corner to retrieve a range of information about it including any submissions found. modMine home page also has a search box that allows you to search through datasets based on the associated metadata, so for example, you can search for all 'ChIP-chip' experiments, or for data produced by a particular lab.

Further to that, the main section of the modENCODE project website allows browsing by category, experiment and organism. The same page links also to the Dataset search tool, where you can specify a range of filters (such as technique or developmental stage), as well as view and download data.

How do I download modENCODE data?

To download an individual dataset: each submission has a report page. In the top right corner, under 'Data Files Download', there are links to all the data files associated with that submission, which you can download by clicking on them. There are usually both raw data files from the experiments and a file of processed results.

To bulk download data: The easiest tool to use is the FTP interface on the modENCODE website. Alternatively, the Dataset search tool allows a user to select and download multiple datasets.

Can I upload my own data?

You can upload gene lists which can then be used for further queries. Your gene lists will be automatically saved if you're logged in. You can also upload a set of genome regions (e.g. as a .bed or .gff file) and investigate particular sets of features in those regions.

How do I analyse data with modMine?

The powerful thing about modMine is that it integrates a huge range of different datasets, which can then be compared and analysed together to draw biological conclusions. As well as offering access to the data, modMine also provides tools for analysing it. Template forms for answering the more common questions (e.g. which transcription factor binding sites are associated with a particular gene or list of genes) can be found in the Templates section of the website. If you have a question that's not covered in this section, you can also construct custom queries.

If you've uploaded a gene list, there is a page with a range of analysis results, e.g. an overview of chromosomal locations and GO enrichment. In the case of Drosophila, this page also includes a heatmap of gene expression throughout development for the genes in question [example]. Further questions can then be answered using templates or custom queries.

Further available analysis tools include uploading a set of genome regions of interest and comparing them to modENCODE data, browsing through a visualization of Drosophila chromatin states, and exploring a hierarchical view of physical regulatory networks for worm and fly.

Further questions?

Please check our Frequently Asked Questions, or contact us.