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. 2015 Nov 15;31(22):3679-81.
doi: 10.1093/bioinformatics/btv431. Epub 2015 Jul 25.

The MI bundle: enabling network and structural biology in genome visualization tools

Arnaud Céol  1 , Heiko Müller  1
Affiliations

The MI bundle: enabling network and structural biology in genome visualization tools

Arnaud Céol et al. Bioinformatics. .

Abstract

Prioritization of candidate genes emanating from large-scale screens requires integrated analyses at the genomics, molecular, network and structural biology levels. We have extended the Integrated Genome Browser (IGB) to facilitate these tasks. The graphical user interface greatly simplifies building disease networks and zooming in at atomic resolution to identify variations in molecular complexes that may affect molecular interactions in the context of genomic data. All results are summarized in genome tracks and can be visualized and analyzed at the transcript level.

Availability and implementation: The MI Bundle is a plugin for the IGB. The plugin, help, video and tutorial are available at http://cru.genomics.iit.it/igbmibundle/ and https://github.com/CRUiit/igb-mi-bundle/wiki. The source code is released under the Apache License, Version 2.

Contact: arnaud.ceol@iit.it

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Mapping RUNX1 variations to molecular interactions. (a) Genomic variations for RUNX1 are loaded from ClinVar and cBioPortal (purple tracks). (b) Some variations are identified at the interface with CBFB (yellow tracks), DNA (orange track) and RUNX1 (homodimer, blue track). (c) Network representation: the black circles on the edges indicate a variation on the interaction interface. (d) Structure visualization: affected residues in contact with DNA are displayed in red (PDB:1HD9)
See this image and copyright information in PMC

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