Expression values of several known cancer genes in samples of the gliobastoma data set (log2 transformed absolute expression levels).

<p>This figure illustrates the Oncodrive-CIS analysis in different scenarios. MET and MDM4 are severely overexpressed when amplified, compared to both normal and tumor diploid samples, and they appear among the top-30 genes with larger expression change bias according to Oncodrive-CIS. However, the expression change due to CDK6 amplification was moderate and it was classified lower in the ranking list (position 138). PDGFRA was overexpressed when amplified, but the dispersion of the expression values lowered the expression impact scores calculated by Oncodrive-CIS (# 61 on the list). Thus, the two first genes should be considered as positives according to Oncodrive-CIS, whereas the remaining two genes should be considered as negatives according to our analysis criteria.</p

Same as in Figure 1 but for the assessment of homozygous deletions in the gliobastoma multiforme data set.

<p>All the <i>Z</i> scores obtained for the genes depicted in this figure are negative, i.e. they represent a bias towards underexpression.</p

Divergence of orthologs and homologs of representative functional categories

Molecular function and biological process. Colors towards red signify high relative conservation of the group of genes in a particular genome. Colors towards blue signify low relative conservation. Gray means no statistically significant difference in conservation level compared to the background of the rest of the genome. White cells denote that there is no gene with the GO term and with ortholog/homolog in the other organism. The colored lines on the left of the names of the functional classes correspond to the colors of the categories represented in Figure 5.<p><b>Copyright information:</b></p><p>Taken from "Functional protein divergence in the evolution of "</p><p>http://genomebiology.com/2008/9/2/R33</p><p>Genome Biology 2008;9(2):R33-R33.</p><p>Published online 15 Feb 2008</p><p>PMCID:PMC2374701.</p><p></p

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Spec commercial by Liz Kosowesky for FILM105 Intro to Filmmaking.https://digitalcommons.andrews.edu/auvad-film/1023/thumbnail.jp

Abstract overview of the chromosomal regions that were included and excluded from our analysis

<p><b>Copyright information:</b></p><p>Taken from "On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees"</p><p>http://genomebiology.com/2007/8/10/R230</p><p>Genome Biology 2007;8(10):R230-R230.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2246304.</p><p></p> A colinear and an inverted chromosome are presented. The inversion in the rearranged chromosome is highlighted in red. For every chromosome, regions considered in this paper are labeled in black. Regions excluded from the main analysis (telomeres, centromeres and breakpoints (BKP)) are within boxes and labeled in red

Additional file 2: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Supplementary methods, use cases description, Table S2. and Figures S1–S3. (PDF 6267 kb

Additional file 1: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Table S1. The features provided by different resources/methods and details about which of them are employed by the CGI. (XLS 21 kb