Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion

• Published in: BMC Bioinformatics Vol. 20; no. Suppl 2; pp. 104 - 43
• Main Authors: Roy, Sujoy, Zaman, Kazi I., Williams, Robert W., Homayouni, Ramin
• Format: Journal Article
• Language: English
• Published: London Springer Science and Business Media LLC 14.03.2019; BioMed Central; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Aging; Algorithms; Bioinformatics; Biology (General); Biomedical and Life Sciences; Brain; BXD mice; Cohesion; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Computer applications to medicine. Medical informatics; Correlation analysis; Data Mining; Data processing; Datasets; DNA microarrays; DNA probes; Gene expression; Gene Expression Profiling; GeneNetwork.org; Genes; Genetic aspects; Genomics; Ground truth; Humans; Inbreeding; Indexing (Content analysis); Latent Semantic Indexing; Life Sciences; Liver; Metabolic pathways; Metabolism; Methods; Mice; Microarray; Microarrays; Mitochondria; Ontology; Physiological aspects; Probes; Protein research; Proteomics; QH301-705.5; Quality; R858-859.7; Researchers; Semantics; Signaling peptides and proteins; Sirt3; Sirtuin 3; Text mining; Transcription; Transcription factors; Uniqueness; United States; Text mining; Sirt3; BXD mice; Latent Semantic Indexing; Microarray; GeneNetwork.org
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2621-z

Background Gene co-expression studies can provide important insights into molecular and cellular signaling pathways. The GeneNetwork database is a unique resource for co-expression analysis using data from a variety of tissues across genetically distinct inbred mice. However, extraction of biologically meaningful co-expressed gene sets is challenging due to variability in microarray platforms, probe quality, normalization methods, and confounding biological factors. In this study, we tested whether literature derived functional cohesion could be used as an objective metric in lieu of ‘ground truth’ to evaluate the quality of probes and microarray datasets. Results We examined Sirtuin-3 (Sirt3) co-expressed gene sets extracted from either liver or brain tissues of BXD recombinant inbred mice in the GeneNetwork database. Depending on the microarray platform, there were as many as 26 probes that targeted different regions of Sirt3 primary transcript. Co-expressed gene sets (ranging from 100–1000 genes) associated with each Sirt3 probe were evaluated using the previously developed literature-derived cohesion p -value (LPv) and benchmarked against ‘gold standards’ derived from proteomic studies or Gene Ontology classifications. We found that the maximal F-measure was obtained at an average window size of 535 genes. Using set size of 500 genes, the Pearson correlations between LPv and F-measure as well as between LPv and mitochondrial gene enrichment p -values were 0.90 and 0.93, respectively. Importantly, we found that the LPv approach can distinguish high quality Sirt3 probes. Analysis of the most functionally cohesive Sirt3 co-expressed gene set revealed core metabolic pathways that were shared between hippocampus and liver as well as distinct pathways which were unique to each tissue. These results are consistent with other studies that suggest Sirt3 is a key metabolic regulator and has distinct functions in energy-producing vs. energy-demanding tissues. Conclusions Our results provide proof-of-concept that literature cohesion analysis is useful for evaluating the quality of probes and microarray datasets, particularly when experimentally derived gold standards are unavailable. Our approach would enable researchers to rapidly identify biologically meaningful co-expressed gene sets and facilitate discovery from high throughput genomic data.