NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger
2015 Database: The Journal of Biological Databases and Curation  
These authors contributed equally to this work. Citation details: Bagewadi,S., Adhikari,S., Dhrangadhariya,A. et al. NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. Abstract Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the
more » ... fymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary V C The Author(s)
doi:10.1093/database/bav099 pmid:26475471 pmcid:PMC4608514 fatcat:r5sachf3wjhqzcgb6lycqo6gre