DPPN-SVM: Computational Identification of Mis-Localized Proteins in Cancers by Integrating Differential Gene Expressions With Dynamic Protein-Protein Interaction Networks

Frontiers in Genetics
Guang-Ping LiTao Luo

Abstract

Eukaryotic cells contain numerous components, which are known as subcellular compartments or subcellular organelles. Proteins must be sorted to proper subcellular compartments to carry out their molecular functions. Mis-localized proteins are related to various cancers. Identifying mis-localized proteins is important in understanding the pathology of cancers and in developing therapies. However, experimental methods, which are used to determine protein subcellular locations, are always costly and time-consuming. We tried to identify cancer-related mis-localized proteins in three different cancers using computational approaches. By integrating gene expression profiles and dynamic protein-protein interaction networks, we established DPPN-SVM (Dynamic Protein-Protein Network with Support Vector Machine), a predictive model using the SVM classifier with diffusion kernels. With this predictive model, we identified a number of mis-localized proteins. Since we introduced the dynamic protein-protein network, which has never been considered in existing works, our model is capable of identifying more mis-localized proteins than existing studies. As far as we know, this is the first study to incorporate dynamic protein-protein interaction...Continue Reading

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Citations

Dec 18, 2020·Life·Ravindra Kumar, Sandeep Kumar Dhanda

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Datasets Mentioned

BETA
GSE9476
GSE27567
GSE121248

Methods Mentioned

BETA
environmental stress
Assay

Software Mentioned

PL
libSVM
Bioconductor
Hum
DPPN
mPLoc
affymetrix
PROLocalizer
SVM

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