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, 29 (1), 24-6

Integrative Genomics Viewer

Integrative Genomics Viewer

James T Robinson et al. Nat Biotechnol.

Figures

Figure 1
Figure 1. Copy number, expression, and mutation data grouped by tumor subtype
This figure illustrates an integrated, multi-modal view of 202 glioblastoma multiforme TCGA samples. Copy number data is segmented values from Affymetrix SNP 6.0 arrays. Expression data is limited to genes represented on all TCGA employed platforms and displayed across the entire gene locus. Red shading indicates relative up-regulation of a gene and the degree of copy gain of a region; blue shading indicates relative down-regulation and copy loss. Small black squares indicate the position of point missense mutations. Samples are grouped by tumor subtype (2nd annotation column) and data type (1st sample annotation column), and sorted by copy number of the EGFR locus. Linking via sample attributes insures that the order of sample tracks is consistent across data types within their respective tumor subtypes.
Figure 2
Figure 2. View of aligned reads at 20kb resolution
Coverage plot and alignments from paired-end reads for a matched tumor/normal pair. Sequencing was performed on an Illumina GA2 platform and aligned with Maq. Alignments are represented as gray polygons with reads mismatching the reference indicated by color. Loci with a large percentage of mismatches relative to the reference are flagged in the coverage plot as color-coded bars. Alignments with unexpected inferred insert sizes are indicated by color. There is evidence for an approximately 10kb deletion (removing 2 exons of AIDA) in the tumor sample not present in the normal.

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References

    1. Cancer Genome Atlas Research Network. Nature. 2008;455:1061–1068. - PMC - PubMed
    1. The ENCODE Project Consortium. Science. 2004;306:636–640. - PubMed
    1. Verhaak RG, et al. Cancer Cell. 2010;17:98–110. - PMC - PubMed
    1. Guttman M, et al. Nature. 2009;458:223–227. - PMC - PubMed
    1. Berger MF, et al. Genome Res. 2010;20 Epub ahead of print.

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