determination of biomarkers for neonatal sepsis based on differential modules

conclusions in the present study, we identified a key gene rps16 and a significant module involved in ribosome biogenesis in eukaryotes that were related to neonatal sepsis, which might be potential biomarkers for early detection and therapy for neonatal sepsis. background the exact interacting factor that response to the infection for neonatal sepsis is still needed to urgently to be disclosed. objectives this research was aimed to explore the potential biomarkers and illuminate the underlying molecular mechanisms associated with neonatal sepsis via identifying differential modules (dms). methods this is a case-control bioinformatics analysis using already published microarray data of neonatal sepsis. this study was conducted in qingdao, china from september 2015 to may 2016. we recruited the gene expression profile of neonatal sepsis from the array express database (http://www.ebi.ac.uk/arrayexpress) under the accessing number of e-geod-25504, which included 27 neonatal samples with a confirmed blood culture-positive test for sepsis (bacterial infected cases) as well as 35 matched controls. meanwhile, the human protein-protein interaction (ppi) data was collected from the database of search tool for the retrieval of interacting genes/proteins (string, http://string-db.org). all of the data was preprocessed. then, the differential co-expression network (dcn) was constructed by integrating co-expression analysis and differential expression analysis. next, a systemic module searching strategy, which contained seed genes selection, module searching and refinement of modules, was performed by select dms. results starting from the gene expression data and ppi data, the dcn that included 430 edges (covering 324 nodes) was constructed, in which each edge was assigned a weight value. from the dcn, we selected a total of 16 seed genes. starting from these seed genes, a total of 3 modules were identified from the dcn based on the systemic module algorithm. of them, only one module (module 3) was considered as dm under p < 0.05. this dm was involved in the progress of ribosome biogenesis in eukaryotes.