The Voronoi diagram for graphs and its application in the Sickle Cell Disease research

Minireview: Multiomic candidate biomarkers for clinical manifestations of sickle cell severity: Early steps to precision medicine

“…Triangle shaped nodes belong to more than one cluster. Modified from Zivanik et al 85 with permission of the copyright holder must understand the genetics and epigenetics of individuals and as much as possible about the environment in which they live. These factors will influence amounts and modifications of components of the genome, transcriptome, microRNAome, proteome, and metabolome.…”

“…84 They demonstrated that multiple SCA altered proteins in the ROD Box group (proteasomal subunits and chaperonins) fell within large clusters. 84 In an effort to continue RBC interactome analysis and enhance methods utilized by Kurdia et al 83 and Ammann and Goodman, 84 Daescu and colleagues 85 proposed the use of Voronoi diagram for graphs (VDG) as a tool for analyzing SCD dependent changes in the RBC protein interactomic map. VDG provided an efficient way to cluster nodes in the network based on their distance to the members of a predetermined subset of cluster centers called Voronoi sites.…”

“…The VDG approach proved to be better at interpreting the influence that SCA affected proteins have on the global networks since those proteins were used as the Voronoi sites. 85 Following the recent strides in the field of proteomics analyses of red blood cells, D'Alessandro et al 86 and, more recently, Daescu and colleagues 85 compiled a list of 1789 and 1834 proteins, respectively, by assembling data from Roux-Dalvai et al, 87 Pasini et al, 88 and Goodman et al 67 Despite technical differences in these analyses that may affect the clinical validity of these datasets for diagnostic purposes, 89 a few recurring patterns have been highlighted by all of the in silico elaborations of red blood cell proteomics data. Again the chaperonin, proteasomal, and anti-oxidant proteins altered in SCA were all part of major clusters.…”

“…The VDG approach proved to be better at interpreting the influence that SCA affected proteins have on the global networks since those proteins were used as the Voronoi sites. 85

Figure 2Voronoi regions induced by the nodes corresponding to the proteins altered by sickle cell disease. Sixteen proteins (Voronoi sites) altered by sickle cell disease 74 yielded 16 Voronoi clusters.

…”

Spectrin’s chimeric E2/E3 enzymatic activity

“…[106][107][108] (5) The RBC proteomic and interactomic analyses to date have indicated 2289 unique proteins, with SpI/bSpI having moderate connectivity. [109][110][111][112] The RBC has no internal organelles except 20 S proteasomes. 113 The proteome of nucleated nonerythroid cells, with a complete complement of organelles, will have at least 10 times the number of unique proteins, as compared with RBCs, with far greater connectivity of SpII/bSpII spectrin.…”