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. 2019 Jul 10;9:9968. doi: 10.1038/s41598-019-46355-w

Figure 4.

Figure 4

Definition of SALS subtype-specific genomic signature using pathway and network analyses. (a) A representative illustration showing the functional correlation between SALS associated CNV-driven genes and their biological processes. Interaction map represents the most promising candidate genes showing a positive correlation between gene expression and underlying genomic changes, grouped on the basis of the main biological processes associated with them. The map was created using the MetaCore Pathway Map Creator tool (GeneGo). Gene expression and CNV values are presented on the map as ‘thermometer-like’ figures with SALS1 patients data represented as thermometer #1 and SALS2 patients as #2. Genes associated with overexpression and CNV gain regions are labeled with red dots while genes associated with downregulated expression and homozygous or heterozygous deleted CNVs are labeled with blue dots. A detailed legend for the network objects is shown in the Supplementary Fig. 1. (b) Functional network of known and predicted interactions of the most promising candidate CNV-driven genes. The network was produced by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) v10 (http://string-db.org/) using default settings. Proteins are represented by spheres. Lines linking proteins indicate evidence for interactions: a red line indicates the presence of gene fusion (genes that are sometimes fused into single open reading frames); a green line – gene neighborhood (genes that reside within 300 bp on the same strand in the genome); a blue line – co-occurrence (gene families whose occurrence patterns across genomes show similarities); a purple line - experimental evidence (interaction extracted from protein-protein interaction databases); a yellow line – text mining (interaction extracted from scientific literature); a light blue line - database (interaction extracted from curated databases); a black line – co-expression (proteins whose genes are co-expressed in the same or in other species).