Publications by authors named "Alexander M Simonov"
In gliomas, expression of certain marker genes is strongly associated with survival and tumor type and often exceeds histological assessments. Using a human interactome model, we algorithmically reconstructed 7494 new-type molecular pathways that are centered each on an individual protein. Each single-gene expression and gene-centric pathway activation was tested as a survival and tumor grade biomarker in gliomas and their diagnostic subgroups (IDH mutant or wild type, IDH mutant with 1p/19q co-deletion, MGMT promoter methylated or unmethylated), including the three major molecular subtypes of glioblastoma (proneural, mesenchymal, classical).
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- - OncoboxPD is an extensive database of human molecular pathways, featuring over 51,000 pathways that map out protein-protein interactions and metabolic reactions, totaling over 361,000 interactions among 64,000 molecules.
- - It categorizes pathways by biological processes and uses algorithms to annotate pathway nodes, allowing users to determine pathway activation levels based on specific RNA/protein expression profiles.
- - Users can visualize pathways as static or dynamic graphs, highlight differentially expressed nodes, and generate summary graphs that display the most significant upregulated and downregulated pathways for their comparisons.