Interpreting pathways to discover cancer driver genes with Moonlight
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Interpreting pathways to discover cancer driver genes with Moonlight. / Colaprico, Antonio; Olsen, Catharina; Bailey, Matthew H.; Odom, Gabriel J.; Terkelsen, Thilde; Silva, Tiago C.; Olsen, André V.; Cantini, Laura; Zinovyev, Andrei; Barillot, Emmanuel; Noushmehr, Houtan; Bertoli, Gloria; Castiglioni, Isabella; Cava, Claudia; Bontempi, Gianluca; Chen, Xi Steven; Papaleo, Elena.
In: Nature Communications, Vol. 11, 69, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Interpreting pathways to discover cancer driver genes with Moonlight
AU - Colaprico, Antonio
AU - Olsen, Catharina
AU - Bailey, Matthew H.
AU - Odom, Gabriel J.
AU - Terkelsen, Thilde
AU - Silva, Tiago C.
AU - Olsen, André V.
AU - Cantini, Laura
AU - Zinovyev, Andrei
AU - Barillot, Emmanuel
AU - Noushmehr, Houtan
AU - Bertoli, Gloria
AU - Castiglioni, Isabella
AU - Cava, Claudia
AU - Bontempi, Gianluca
AU - Chen, Xi Steven
AU - Papaleo, Elena
PY - 2020
Y1 - 2020
N2 - Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering dual role cancer genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as genes controlling biological processes. With them, we classify cancer driver genes, unveiling their roles in cancer mechanisms. To this end, we present Moonlight, a tool that incorporates multiple -omics data to identify critical cancer driver genes. With Moonlight, we analyze 8000+ tumor samples from 18 cancer types, discovering 3310 oncogenic mediators, 151 having dual roles. By incorporating additional data (amplification, mutation, DNA methylation, chromatin accessibility), we reveal 1000+ cancer driver genes, corroborating known molecular mechanisms. Additionally, we confirm critical cancer driver genes by analysing cell-line datasets. We discover inactivation of tumor suppressors in intron regions and that tissue type and subtype indicate dual role status. These findings help explain tumor heterogeneity and could guide therapeutic decisions.
AB - Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering dual role cancer genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as genes controlling biological processes. With them, we classify cancer driver genes, unveiling their roles in cancer mechanisms. To this end, we present Moonlight, a tool that incorporates multiple -omics data to identify critical cancer driver genes. With Moonlight, we analyze 8000+ tumor samples from 18 cancer types, discovering 3310 oncogenic mediators, 151 having dual roles. By incorporating additional data (amplification, mutation, DNA methylation, chromatin accessibility), we reveal 1000+ cancer driver genes, corroborating known molecular mechanisms. Additionally, we confirm critical cancer driver genes by analysing cell-line datasets. We discover inactivation of tumor suppressors in intron regions and that tissue type and subtype indicate dual role status. These findings help explain tumor heterogeneity and could guide therapeutic decisions.
U2 - 10.1038/s41467-019-13803-0
DO - 10.1038/s41467-019-13803-0
M3 - Journal article
C2 - 31900418
AN - SCOPUS:85077479923
VL - 11
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
M1 - 69
ER -
ID: 235774080