Recommended Conferences

Genetic Engineering and Gene Therapy

Paris, France

Human Genetics and Genetic Disorders

Miami, USA

Tissue Engineering and Regenerative Medicine

Chicago, USA
Related Subjects
 

Gene network interconnectedness and the generalized topological overlap measure

Author(s): Yip AM, Horvath S

Abstract

Background: Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency) between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz et al. 1 can be interpreted as a measure of agreement between the m = 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness.

Results: We generalize the topological overlap measure from m = 1 step neighborhoods to m > or = 2 step neighborhoods. This allows us to define the m-th order generalized topological overlap measure (GTOM) by (i) counting the number of m-step neighbors that a pair of nodes share and (ii) normalizing it to take a value between 0 and 1. Using theoretical arguments, a yeast co-expression network application, and a fly protein network application, we illustrate the usefulness of the proposed measure for module detection and gene neighborhood analysis.

Conclusion: Topological overlap can serve as an important filter to counter the effects of spurious or missing connections between network nodes. The m-th order topological overlap measure allows one to trade-off sensitivity versus specificity when it comes to defining pairwise interconnectedness and network modules.

Similar Articles

Bladder cancer biomarkers: review and update

Author(s): Ghafouri-Fard S,Nekoohesh L, Motevaseli E

Recent advances in the diagnosis and treatment of bladder cancer

Author(s): Cheung G,Sahai A, Billia M, Dasgupta P, Khan MS

Primary bladder preservation treatment for urothelial bladder cancer

Author(s): Biagioli MC, Fernandez DC, Spiess PE, Wilder RB

Prediction of muscle-invasive bladder cancer using urinary proteomics

Author(s): Schiffer E,Vlahou A, Petrolekas A, Stravodimos K, Tauber R, et al.

Making sense of cancer genomic data

Author(s): Chin L, Hahn WC, Getz G, Meyerson M

Principles and methods of integrative genomic analyses in cancer

Author(s): Kristensen VN,Lingjærde OC,Russnes HG,Vollan HK,Frigessi A, et al.

affy--analysis of Affymetrix GeneChip data at the probe level

Author(s): Gautier L, Cope L, Bolstad BM, Irizarry RA

Biomarkers for bladder cancer aggressiveness

Author(s): Frantzi M,Makridakis M, Vlahou A

Gene profiling, biomarkers and pathways characterizing HCV-related hepatocellular carcinoma

Author(s): De Giorgi V, Monaco A, Worchech A, Tornesello M, Izzo F, et al.

The double bromodomain protein Brd2 promotes B cell expansion and mitogenesis

Author(s): Belkina AC, Blanton WP, Nikolajczyk BS, Denis GV

Inhibition of BET bromodomain proteins as a therapeutic approach in prostate cancer

Author(s): Wyce A,Degenhardt Y, Bai Y, Le B, Korenchuk S, et al.

A UPF3-mediated regulatory switch that maintains RNA surveillance

Author(s): Chan WK,Bhalla AD, Le Hir H, Nguyen LS, Huang L, et al.

Targeted therapies in urothelial carcinoma

Author(s): Ghosh M,Brancato SJ, Agarwal PK, Apolo AB

Gene expression profiling and pathway analysis of superficial bladder cancer in rats

Author(s): Arum CJ,Anderssen E, Tømmerås K, Lundgren S, Chen D, et al.

Activation of RAS family genes in urothelial carcinoma

Author(s): Boulalas I,Zaravinos A, Karyotis I, Delakas D, Spandidos DA

Ras mutation cooperates with ß-catenin activation to drive bladder tumourigenesis

Author(s): Ahmad I, Patel R, Liu Y, Singh LB, Taketo MM, et al.

Ras in cancer and developmental diseases

Author(s): Fernández-Medarde A, Santos E