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cff-version: 1.2.0
message: 'To cite package "Moonlight2R" in publications use:'
type: software
license: GPL-3.0-only
title: 'Moonlight2R: Identify oncogenes and tumor suppressor genes from omics data'
version: 1.3.0
abstract: 'The understanding of cancer mechanism requires the identification of genes
  playing a role in the development of the pathology and the characterization of their
  role (notably oncogenes and tumor suppressors). We present an updated version of
  the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns
  a list of candidate driver genes for specific cancer types on the basis of omics
  data integration. The Moonlight framework contains a primary layer where gene expression
  data and information about biological processes are integrated to predict genes
  called oncogenic mediators, divided into putative tumor suppressors and putative
  oncogenes. This is done through functional enrichment analyses, gene regulatory
  networks and upstream regulator analyses to score the importance of well-known biological
  processes with respect to the studied cancer type. By evaluating the effect of the
  oncogenic mediators on biological processes or through random forests, the primary
  layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor
  genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough
  to explain the deregulation of the genes, a second layer of evidence is needed.
  We have automated the integration of a secondary mutational layer through new functionalities
  in Moonlight2R. These functionalities analyze mutations in the cancer cohort and
  classifies these into driver and passenger mutations using the driver mutation prediction
  tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation
  are retained as the driver genes. As a consequence, this methodology does not only
  identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another)
  but also helps in elucidating the biological processes underlying their specific
  roles. In particular, Moonlight2R can be used to discover OCGs and TSGs in the same
  cancer type. This may for instance help in answering the question whether some genes
  change role between early stages (I, II) and late stages (III, IV). In the future,
  this analysis could be useful to determine the causes of different resistances to
  chemotherapeutic treatments.'
authors:
- family-names: Nourbakhsh
  given-names: Mona
- family-names: Saksager
  given-names: Astrid
- family-names: Tom
  given-names: Nikola
- family-names: Chen
  given-names: Xi Steven
- family-names: Colaprico
  given-names: Antonio
- family-names: Olsen
  given-names: Catharina
- family-names: Tiberti
  given-names: Matteo
  email: tiberti@cancer.dk
- family-names: Papaleo
  given-names: Elena
preferred-citation:
  type: article
  title: Interpreting pathways to discover cancer driver genes with Moonlight
  authors:
  - family-names: Colaprico
    given-names: Antonio
  - family-names: Olsen
    given-names: Catharina
  - family-names: Bailey
    given-names: Matthew H.
  - family-names: Odom
    given-names: Gabriel J.
  - family-names: Terkelsen
    given-names: Thilde
  - family-names: Silva
    given-names: Tiago C.
  - family-names: Olsen
    given-names: André V.
  - family-names: Cantini
    given-names: Laura
  - family-names: Zinovyev
    given-names: Andrei
  - family-names: Barillot
    given-names: Emmanuel
  - family-names: Noushmehr
    given-names: Houtan
  - family-names: Bertoli
    given-names: Gloria
  - family-names: Castiglioni
    given-names: Isabella
  - family-names: Cava
    given-names: Claudia
  - family-names: Bontempi
    given-names: Gianluca
  - family-names: Chen
    given-names: Xi Steven
  - family-names: Papaleo
    given-names: Elena
  journal: Nature Communications
  year: '2020'
  volume: 11(69)
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ELELAB/Moonlight2R
url: https://github.com/ELELAB/Moonlight2R
contact:
- family-names: Tiberti
  given-names: Matteo
  email: tiberti@cancer.dk
references:
- type: article
  title: A workflow to study mechanistic indicators for driver gene prediction with
    Moonlight
  authors:
  - family-names: Nourbakhsh
    given-names: Mona
  - family-names: Saksager
    given-names: Astrid
  - family-names: Tom
    given-names: Nikola
  - family-names: Chen
    given-names: Xi Steven
  - family-names: Colaprico
    given-names: Antonio
  - family-names: Olsen
    given-names: Catharina
  - family-names: Tiberti
    given-names: Matteo
  - family-names: Papaleo
    given-names: Elena
  journal: Briefings in Bioinformatics
  year: '2023'