Recent News and Updates
- June 2016
We've updated MAGI to include 8,607 tumor samples from 31 cancer types downloaded from Firebrowse.
- March 2016
We've improved our mutation annotation framework with a new MAGI annotations website. Check it out from the link in the navbar at the top of every page!
MAGI is a tool for annotating, exploring, and analyzing gene sets that may be
associated with cancer.
The tool was authored by the Raphael Lab at Brown University.
Aberrations view of multiple cancer types. Aberrations view of a single cancer type.
The aberrations view shows the pattern of mutations in a set of genes (rows) in a cohort of tumor samples (columns) as a matrix.
Each cell in the mutation matrix contains shape, which represents whether or not a gene is mutated in the given sample.
Matrices are colored in different ways, depending on if the tumor cohort includes multiple cancers or not.
For a cohort with multiple cancer types each cell is colored by the cancer type of the sample,
while for a cohort with one cancer type each cell is colored by whether or not the gene is the only
gene to harbor a mutation in that sample.
Mutation datasets are provided, or you can upload your own
Subnetwork of five genes with edges from three interaction networks.
The subnetwork visualization shows the interactions among a set of nodes (proteins)
in one or multiple protein interaction networks. Edges that appear in multiple subnetworks
will appear together in the visualization. Nodes are colored by the number of samples in which
they are mutated.
We provide the HINT
, and iRefIndex
protein-protein interaction (PPI) networks.
To request additional PPI networks, please contact us
Heatmap of gene expression data for genes in the cohesin complex.
MAGI generates heatmaps for continuous valued data (e.g. gene expression, DNA methylation).
Single Nucleotide Variants (SNVs)
Transcript view for the SMAD4 transcript ENST00000342988 in multiple cancer types.
The transcript view shows locations at which mutations occur in a gene's transcript.
Mutations are color-coded by cancer type, and different mutation types (e.g. missense, nonsense)
are represented by different symbols. In addition, protein domains from different databases
are shown along the length of the transcript.
The mutation data for the transcript view is the same as for the aberrations view
. Protein domains are provided for the Conserved Domain
, and SMART
Screenshot of the MAGI annotations interface.
MAGI includes an interface for users to add annotations to aberrations or interactions
in the browser while they are exploring their data. Here we show an example of how
users can click on mutations in the transcript view to prepopulate the annotation form
with information about the mutation. Users can click on any of the data points in the
MAGI visualizations to prepopulate the form. Note that users must be logged in to
add new annotations or vote on existing annotations.
Copy number aberrations (CNAs)
CNA view for amplifications in the CDKN2A gene in glioblastoma.
The copy number aberration browser shows the amplified/deleted segments
that have been mapped to a particular gene. Since many segments span more than
the length of the gene, the segments are shown in the context of a
chromosome arm. Segments are colored by cancer type.
The mutation data for the CNA browser is the same as for the aberrations view