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Figure 2 | Genome Medicine

Figure 2

From: Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme

Figure 2

Example of Anduril-generated result website and links to external sources. Anduril generates a browsable website based on analysis results. (a) A screenshot of the gene level view of the data. The genes are sorted according to the survival P-value on the exon platform. The data are divided into 13 fields corresponding to analysis results and data sources. For example, the field 'GeneExpression' illustrates fold changes between GBM and control samples using data from gene expression microarrays. Exon array values are computed at the gene ('MedianExonExpression') and transcript levels ('TranscriptExpression'). For the transcript data the minimum and maximum transcript expression values show GBM-specific alternative splice variant candidates. The fields 'TranscriptExpression:Survival' and 'MedianExonExpression:Survival' show survival analysis P-values for the best transcript and gene in the exon arrays, whereas 'SNPSurvival' contains P-values for the survival associated SNPs. The green color for 'GeneExpression', 'FoldChange', 'Min', 'Max', 'Gain', 'Loss' and 'Methylation' denote downregulation and red denotes upregulation. The red color for P-values for the fields 'Survival', 'SNPSurvival' and 'ExonIntegration' denotes low P-values. (b) A web page that opens after clicking the gene MSN. This page contains detailed results and external links. (c, d) Clicking 'GeneName' opens a website in Genecards [28] (c), and 'GeneID' connects to Ensembl [29] (d). (e) Clicking 'Protein Interactions' opens a page listing known protein-protein interactions in PINA [27]. (f) Clicking an entry in 'KEGG pathway' allows accessing pathways at the KEGG [26] website. (g) Each splice variant is listed separately and if the survival P-value is < 0.01, the users can view the Kaplan-Meier curves. The groups '1', '-1' and '0' denote overexpression, underexpression (not shown for MSN) and stable expression, respectively ('-1' is not present in the figure). The dotted lines are 95% confidence intervals.

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