RESET is a computational methodology to identify aberrant DNA methylation and associated cis-transcriptional changes across tumors. All the material is available here.
If you use this tool or data, please cite:
Saghafinia S., Mina M., Riggi N., Hanahan D. and Ciriello G. (2018) Pan-cancer landscape of aberrant DNA methylation across human tumors. Cell Reports (In Press)
SELECT is a computational methodology to identify mutual exclusive and co-occurrent interactions between functional alterations in cancer. All the material is available here.
If you use this tool or data, please cite:
Mina M., Raynaud F., Tavernari D., Battistello E., Sungalee S., Saghafinia S., Laessle T., Sanchez-Vega F., Schultz N., Oricchio E., Ciriello G. (2017) Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies. Cancer Cell, 32(2), 155-168
MEMo (Mutual Exclusivity Modules) allows to search and test for mutual exclusive and functionally related genomic alterations in cancer.
A complete description on how to use MEMo can be found here.
If you use MEMo please cite:
Ciriello G., Cerami E.G., Sander C. & Schultz N. (2012), Mutual Exclusivity Analysis Identifies Oncogenic Network Modules.
Genome Res., 22, 398-406.
OncoSign (Oncogenic Signatures) is a network modularity based approach to hierarchically cluster sparse binary data.
OncoSign has been previously used to identify tissue-independent tumor classes characterized by specific combination, or signatures, of selected functional events.
If you use OncoSign please cite:
Ciriello G., Miller L.M., Aksoy B.A., Senbabaoglu Y., Schultz N. & Sander C. (2013) Emerging landscape of oncogenic signatures across human cancers.
Nat. Genetics, 45, 10, 1127-1133.
The Pan-cancer Genomics Archive PanGeA groups selected event calls associated to pan-cancer genomics studies from our group.
Here you will find all the data used in (Ciriello et al. Nat. Genetics 2013).
The TCGA breast cancer data snapshot summarizes all data and analyses results from the latest TCGA breast cancer data freeze.
Molecular and clinical data available at this page were used within in (Ciriello et al. Cell 2015).
If you use this data, please cite:
Ciriello G., Gatza M.L., Beck A.H., Wilkerson M.D., Rhie S.K., Pastore A., Zhang H., McLellan M., Yau C., Kandoth C., Bowlby R., Shen H., Hayat S., Fieldhouse R., Lester S.C., Tse G.M.K., Factor R.E., Collins L.C., Allison K.H., Chen Y.Y., Jensen K., Johnson N.B., Oesterreich S., Mills G.B., Cherniack A., Robertson G., Benz C., Sander, C., Laird P.W., Hoadley K.A., King T.A., TCGA Research Network, Perou C.M., (2015) Comprehensive molecular portraits of invasive lobular breast cancer. Cell, 163, 2 506-519