Abstract
BackgroundA current challenge in gene annotation is to define the gene function in the context of the network of relationships instead of using single genes. The inference of gene networks (GNs) has emerged as an approach to better understand the biology of the system and to study how several components of this network interact with each other and keep their functions stable. However, in general there is no sufficient data to accurately recover the GNs from their expression levels leading to the curse of dimensionality, in which the number of variables is higher than samples. One way to mitigate this problem is to integrate biological data instead of using only the expression profiles in the inference process. Nowadays, the use of several biological information in inference methods had a significant increase in order to better recover the connections between genes and reduce the false positives. What makes this strategy so interesting is the possibility of confirming the known connections through the included biological data, and the possibility of discovering new relationships between genes when observed the expression data. Although several works in data integration have increased the performance of the network inference methods, the real contribution of adding each type of biological information in the obtained improvement is not clear.MethodsWe propose a methodology to include biological information into an inference algorithm in order to assess its prediction gain by using biological information and expression profile together. We also evaluated and compared the gain of adding four types of biological information: (a) protein-protein interaction, (b) Rosetta stone fusion proteins, (c) KEGG and (d) KEGG+GO.Results and conclusionsThis work presents a first comparison of the gain in the use of prior biological information in the inference of GNs by considering the eukaryote (P. falciparum) organism. Our results indicates that information based on direct interaction can produce a higher improvement in the gain than data about a less specific relationship as GO or KEGG. Also, as expected, the results show that the use of biological information is a very important approach for the improvement of the inference. We also compared the gain in the inference of the global network and only the hubs. The results indicates that the use of biological information can improve the identification of the most connected proteins.
Highlights
A current challenge in gene annotation is to define the gene function in the context of the network of relationships instead of using single genes
In this work we developed an algorithm to integrate biological information data for the inference of gene networks (GNs), evaluated and compared the relative gain of four biological information dataset for the P. falciparum organism: (a) Protein-protein interaction, (b) Rosetta Stone fusion proteins, (c) Kyoto Encyclopedia of Genes and Genomes (KEGG), (d) Combined KEGG and Gene Ontology (GO) dataset
Validation of the information gain In order to quantify the similarity between the goldstandard and inferred networks, it was adopted the positive predictive value (PPV) (Positive Predictive Value, known as accuracy or precision) and Sensitivity measurements presented by [21], which are based on a confusion matrix [36] and widely used to compare the results of the gene inference methods
Summary
We propose a methodology to include biological information into an inference algorithm in order to assess its prediction gain by using biological information and expression profile together. We evaluated and compared the gain of adding four types of biological information: (a) protein-protein interaction, (b) Rosetta stone fusion proteins, (c) KEGG and (d) KEGG+GO
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