Similarity network fusion for aggregating data types on a genomic scale.
Recent technologies have made it cost-effective to collect diverse types of genome-wide data. Computational methods are needed to combine these data to create a comprehensive view of a given disease or a biological process. Similarity network fusion (SNF) solves this problem by constructing networks of samples (e.g., patients) for each available data type and then efficiently fusing these into one network that represents the full spectrum of underlying data. For example, to create a comprehensive view of a disease given a cohort of patients, SNF computes and fuses patient similarity networks obtained from each of their data types separately, taking advantage of the complementarity in the data. We used SNF to combine mRNA expression, DNA methylation and microRNA (miRNA) expression data for five cancer data sets. SNF substantially outperforms single data type analysis and established integrative approaches when identifying cancer subtypes and is effective for predicting survival.
1] Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada. [2].
Bo
B
Wang
1] Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
Aziz M
AM
Mezlini
1] Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
Feyyaz
F
Demir
Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
Marc
M
Fiume
Department of Cognitive Science, University of California San Diego, San Diego, California, USA.
Zhuowen
Z
Tu
1] Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
Michael
M
Brudno
1] Institut de Recherches Cliniques de Montréal, Université de Montréal, Montréal, Quebec, Canada. [2].
Benjamin
0000000276840079
B
Haibe-Kains
1] Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada. [2] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
Anna
A
Goldenberg
D001932:Brain Neoplasms / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004194:Disease / Q000235:genetics; D053263:Gene Regulatory Networks; D023281:Genomics; D005909:Glioblastoma / Q000235:genetics; D006801:Humans; D013223:Statistics as Topic / Q000379:methods*