Article ; Online: Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network.
PloS one
2019 Volume 14, Issue 5, Page(s) e0214868
Abstract: Lactic acid bacteria are Gram-positive bacteria used throughout the world in many industrial applications for their acidification, flavor and texture formation attributes. One of the species, Lactococcus lactis, is employed for the production of ... ...
| Abstract | Lactic acid bacteria are Gram-positive bacteria used throughout the world in many industrial applications for their acidification, flavor and texture formation attributes. One of the species, Lactococcus lactis, is employed for the production of fermented milk products like cheese, buttermilk and quark. It ferments lactose to lactic acid and, thus, helps improve the shelf life of the products. Many physiological and transcriptome studies have been performed in L. lactis in order to comprehend and improve its biotechnological assets. Using large amounts of transcriptome data to understand and predict the behavior of biological processes in bacterial or other cell types is a complex task. Gene networks enable predicting gene behavior and function in the context of transcriptionally linked processes. We reconstruct and present the gene co-expression network (GCN) for the most widely studied L. lactis strain, MG1363, using publicly available transcriptome data. Several methods exist to generate and judge the quality of GCNs. Different reconstruction methods lead to networks with varying structural properties, consequently altering gene clusters. We compared the structural properties of the MG1363 GCNs generated by five methods, namely Pearson correlation, Spearman correlation, GeneNet, Weighted Gene Co-expression Network Analysis (WGCNA), and Sparse PArtial Correlation Estimation (SPACE). Using SPACE, we generated an L. lactis MG1363 GCN and assessed its quality using modularity and structural and biological criteria. The L. lactis MG1363 GCN has structural properties similar to those of the gold-standard networks of Escherichia coli K-12 and Bacillus subtilis 168. We showcase that the network can be used to mine for genes with similar expression profiles that are also generally linked to the same biological process. |
|---|---|
| MeSH term(s) | Bacillus subtilis/genetics ; Escherichia coli K12/genetics ; Gene Regulatory Networks ; Lactococcus lactis/genetics ; Transcriptome |
| Language | English |
| Publishing date | 2019-05-22 |
| Publishing country | United States |
| Document type | Journal Article ; Research Support, Non-U.S. Gov't |
| ISSN | 1932-6203 |
| ISSN (online) | 1932-6203 |
| DOI | 10.1371/journal.pone.0214868 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
More links
Kategorien
Order via subito
This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.
Inter-library loan at ZB MED
Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.