Author(s): Yip AM, Horvath S
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.
Referred From: https://pubmed.ncbi.nlm.nih.gov/17250769/
Author(s): Ghafouri-Fard S,Nekoohesh L, Motevaseli E
Author(s): Ploeg M,Aben KK, Kiemeney LA
Author(s): Cheung G,Sahai A, Billia M, Dasgupta P, Khan MS
Author(s): Biagioli MC, Fernandez DC, Spiess PE, Wilder RB
Author(s): Zhu XL, Ai ZH, Wang J, Xu YL, Teng YC
Author(s): Wang HF, Wang JS
Author(s): Schiffer E,Vlahou A, Petrolekas A, Stravodimos K, Tauber R, et al.
Author(s): Chin L, Hahn WC, Getz G, Meyerson M
Author(s): Horvath S, Dong J
Author(s): Langfelder P, Horvath S
Author(s): Kristensen VN,Lingjærde OC,Russnes HG,Vollan HK,Frigessi A, et al.
Author(s): Stranger BE, Stahl EA, Raj T
Author(s): Gautier L, Cope L, Bolstad BM, Irizarry RA
Author(s): Smyth, GK
Author(s): Song L, Langfelder P, Horvath S
Author(s): Zhang W, Zang Z, Song Y, Yang H, Yin Q
Author(s): Mason MJ, Fan G, Plath K, Zhou Q, Horvath S
Author(s): Zhang B, Horvath S
Author(s): Li L, Shiga M, Ching WK, Mamitsuka H
Author(s): Xiao X, Moreno-Moral A, Rotival M, Bottolo L, Petretto E
Author(s): Puniya BL, Kulshreshtha D, Verma SP, Kumar S, Ramachandran S
Author(s): Frantzi M,Makridakis M, Vlahou A
Author(s): Zeng T, Sun SY, Wang Y, Zhu H, Chen L
Author(s): Liu R, Wang X, Aihara K, Chen L
Author(s): He D, Liu ZP, Honda M, Kaneko S, Chen L
Author(s): Lezon-Geyda K,Najfeld V, Johnson EM
Author(s): De Giorgi V, Monaco A, Worchech A, Tornesello M, Izzo F, et al.
Author(s): Gout S,Brambilla E, Boudria A, Drissi R, Lantuejoul S, et al.
Author(s): An Y, Zhou Y, Ren G, Tian Q, Lu Y, et al.
Author(s): Belkina AC, Blanton WP, Nikolajczyk BS, Denis GV
Author(s): Wyce A,Degenhardt Y, Bai Y, Le B, Korenchuk S, et al.
Author(s): Chan WK,Bhalla AD, Le Hir H, Nguyen LS, Huang L, et al.
Author(s): Karam R,Carvalho J, Bruno I, Graziadio C, Senz J, et al.
Author(s): Wang J,Peng X, Peng W, Wu FX
Author(s): Ghosh M,Brancato SJ, Agarwal PK, Apolo AB
Author(s): Arum CJ,Anderssen E, Tømmerås K, Lundgren S, Chen D, et al.
Author(s): Oppezzo P,Dighiero G
Author(s): Boulalas I,Zaravinos A, Karyotis I, Delakas D, Spandidos DA
Author(s): Ahmad I, Patel R, Liu Y, Singh LB, Taketo MM, et al.
Author(s): Fernández-Medarde A, Santos E