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. 2015 Jul;12(7):615-621.
doi: 10.1038/nmeth.3440.

Pathway and network analysis of cancer genomes

Pau Creixell #  1 , Jüri Reimand #  2 , Syed Haider  3 , Guanming Wu  3   4 , Tatsuhiro Shibata  5 , Miguel Vazquez  6 , Ville Mustonen  7 , Abel Gonzalez-Perez  8 , John Pearson  9 , Chris Sander  10 , Benjamin J Raphael  11 , Debora S Marks  12 , B F Francis Ouellette  3   13 , Alfonso Valencia  6 , Gary D Bader  2 , Paul C Boutros  3   14   15 , Joshua M Stuart  16   17 , Rune Linding  1   18 , Nuria Lopez-Bigas  8   19 , Lincoln D Stein  3   20 ; Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium
Collaborators, Affiliations

Pathway and network analysis of cancer genomes

Pau Creixell et al. Nat Methods. 2015 Jul.

Abstract

Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.

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Figures

Figure 1
Figure 1. Major approaches to pathway and network analysis of cancer data
Figure 2
Figure 2. Pathway and network representation of EGF signaling
(A) In the simplified pathway representation, heterogeneous nodes and edges correspond to genes, proteins, small molecules, and their regulatory and catalytic relationships. Nodes do not interact directly but participate in reaction events designated by white squares. (B) In the network representation, all nodes correspond to the same type of biological entity (gene products). Edges derived from curated pathways are shown as bold arrows. Additional gene-gene interactions derived from gene co-expression and physical protein interactions are shown as light lines.
See this image and copyright information in PMC

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