LITERATURE REVIEW


 Network-based approaches
 network based approach -produced to identify molecular interaction
of gene expression.
 Network based approaches outperformed than gene-based approaches
in cancer metastasis prediction (Chuang, et al., 2007).
 networks models are simple and crucial for understanding of complex
networks and help maintain biological systems.
 three types of network model
i. random networks,
ii. scale-free networks and
iii. hierarchical networks
 nodes/vertices :-Biomolecules such as genes, proteins and
metabolites are represented as in molecular network.
 edges/links of nodes:- physical or fucntional interactions of protein,
genetics

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 Types of network


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 Network based algorithms available are
as follows in the table 1 below.
Algorithms
Single protein analysis of
Description
Single protein analysis of network (SPAN) methodology used to
Reference
Chen, et al. 2013
network (SPAN) identify cancer genes and additionally, they computationally identified
pathways among interactors across signatures and validated them
using a similarity metric and patient survival.
Markov Clustering (MCL) MCL isa semi-supervised algorithm used to cluster the weighted Wu & Stein2012
network into a series of gene interaction modules.
NetRank NetRank is a derivative of PageRank algorithm to predict gen Roy, et al. 2012
interaction networks.
NetWalker A NEM signature-based Survival Support Vector Machine (SSVM) Shi, et al. 2012
prognostic model was trained using a microarray gene expression
dataset and genes were integrated using NetWalker algorithm.
Network Guilt-by-association GBA is Google’s PageRank algorithm which is used to detect disease Lee, et al. 2011
(GBA) genes in a particular dataset.
Gene network Inference with GENIE3, a new algorithm for the prediction of GRNs where tree- Huynh-Thu, et al. 2010
Ensemble of Trees (GENIE3) based ensemble methods Random Forests or Extra-Trees used to
predict expression pattern of one of the genes (target gene).
Maximum-expectation Gene This approach is basically adopted by the greedy approximation Karni, et al. 2009
Cover (MGC) algorithm to Weighted Set Cover.
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