modMine: flexible access to modENCODE data

Abstract

In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.

Figure 1.

Experiment search: entering ‘chip–chip AND ctcf AND 0–12’ into the experiment search box on the front page returns the two CTCF ChIP-chip experiments using material from 0 to12 h embryos. The check boxes have been ticked in preparation for making them into a list of submissions.

Figure 2.

A Template Search which, given a gene (or a list of genes) and a ChIP experiment submission (or a list of submissions), returns ChIP positive annotation in the upstream intergenic region. Options have been selected so that the template search is accepting a list of genes as input, and also a list of submissions. Thus, a single template search can retrieve data corresponding to the product of a gene list and a submission list. The example used finds 1666 regions identified in 12 ChIP experiments as being upstream of the 540 C. elegans transcription factor genes. Links to additional features: link (A) ‘< embed results/>’, generates text that can be pasted into a web page so that the results appear there; (B) ‘web service URL’, provides a URL to fetch results for the template from the command line or a script; (C) ‘perl | python | java’ generates code in the selected language that will run the template query; (D) ‘export XML’ exports an XML version of the template search (Import is available via the QueryBuilder, or in the ‘Query History’ section of MyMine).

Figure 3.

Gene expression heatmap tool. Viewing a list of Drosophila genes results in a number of interactive analysis tools being run with default settings including the heatmap tool shown here displaying gene expression across different cell lines and across different developmental stages. This tool is implemented with canvasXpress (http://www.canvasxpress.org).