Dataset Information

Seeking gene relationships in gene expression data using support vector machine regression.

ABSTRACT: Several genetic determinants responsible for individual variation in gene expression have been located using linkage and association analyses. These analyses have revealed regulatory relationships between genes. The heritability of expression variation as a quantitative phenotype reflects its underlying genetic architecture. Using support vector machine regression (SVMR) and gene ontological information, we proposed an approach to identify gene relationships in expression data provided by Genetic Analysis Workshop 15 that would facilitate subsequent genetic analyses. A group of related genes were selected for a shared biological theme, and SVMR was trained to form a regression model using the training gene expressions. The model was subsequently used to search for and capture similarly related genes. SVMR shows promising capability in modeling and seeking gene relationships through expression data.

SUBMITTER: Yu R

PROVIDER: S-EPMC2367560 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

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Seeking gene relationships in gene expression data using support vector machine regression.

Yu Robert R Dehoff Kevin K Amos Christopher I CI Shete Sanjay S

BMC proceedings 20071218

Several genetic determinants responsible for individual variation in gene expression have been located using linkage and association analyses. These analyses have revealed regulatory relationships between genes. The heritability of expression variation as a quantitative phenotype reflects its underlying genetic architecture. Using support vector machine regression (SVMR) and gene ontological information, we proposed an approach to identify gene relationships in expression data provided by Geneti ...[more]

PMID: 18466551

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Project description:Biological data are accumulating at a faster rate, but interpreting them still remains a problem. Classifying biological data into distinct groups is the first step in understanding them. Data classification in response to a certain treatment is an extremely important aspect for differentially expressed genes in making present/absent calls. Many feature selection algorithms have been developed including the support vector machine recursive feature elimination procedure (SVM-RFE) and its variants. Support vector machine RFEs are greedy methods that attempt to find superlative possible combinations leading to binary classification, which may not be biologically significant. To overcome this limitation of SVM-RFE, we propose a novel feature selection algorithm, termed as "sigFeature" (https://bioconductor.org/packages/sigFeature/), based on SVM and t statistic to discover the differentially significant features along with good performance in classification. The "sigFeature" R package is centered around a function called "sigFeature," which provides automatic selection of features for the binary classification. Using six publicly available microarray data sets (downloaded from Gene Expression Omnibus) with different biological attributes, we further compared the performance of "sigFeature" to three other feature selection algorithms. A small number of selected features (by "sigFeature") also show higher classification accuracy. For further downstream evaluation of its biological signature, we conducted gene set enrichment analysis with the selected features (genes) from "sigFeature" and compared it with the outputs of other algorithms. We observed that "sigFeature" is able to predict the signature of four out of six microarray data sets accurately, whereas the other algorithms predict less data set signatures. Thus, "sigFeature" is considerably better than related algorithms in discovering differentially significant features from microarray data sets.

Dataset Information

Seeking gene relationships in gene expression data using support vector machine regression.

Publications

Seeking gene relationships in gene expression data using support vector machine regression.

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