viper

The VIPER software tool infers aberrant protein activity in biological samples, which is crucial for identifying dysregulated oncoproteins in tumorigenesis and developing personalized treatment plans. Accurate assessment of protein activity is challenging due to the partial predictiveness of genetic alterations and the impracticality of direct measurements. VIPER introduces a novel algorithm, Virtual Inference of Protein Activity by Enriched Regulon Analysis, experimentally validated to evaluate the functional relevance of genetic alterations in regulatory proteins across The Cancer Genome Atlas (TCGA) samples. It accurately identifies aberrant protein activity induced by mutations, revealing tumors with druggable oncoproteins despite lacking mutations, and vice versa.

Topic

Gene regulation;Transcription factors and regulatory sites;Protein sites, features and motifs;Data mining;Transcriptomics

Detail

  • Operation: Network simulation;Gene expression profiling;Protein quantification

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: File license

  • Cost: Free

  • Version name: 1.36.0

  • Credit: The NIH Roadmap National Centers for Biomedical Computing, the NIH Library of Integrated Network-based Cellular Signatures program, the NCI Cancer Target Discovery and Development program,a fellowship grant from the Lauri Strauss Leukemia Foundation.

  • Input: -

  • Output: -

  • Contact: Mariano J Alvarez reef103@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

  • Functional characterization of somatic mutations in cancer using network-based inference of protein activity.
  • Alvarez MJ, et al. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. 2016; 48:838-47. doi: 10.1038/ng.3593
  • https://doi.org/10.1038/ng.3593
  • PMID: 27322546
  • PMC: PMC5040167
  • VIPER: a web application for rapid expert review of variant calls.
  • Wöste M and Dugas M. VIPER: a web application for rapid expert review of variant calls. VIPER: a web application for rapid expert review of variant calls. 2018; 34:1928-1929. doi: 10.1093/bioinformatics/bty022
  • https://doi.org/10.1093/bioinformatics/bty022
  • PMID: 29346510
  • PMC: PMC5972565

Download and documentation

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