Bioinformatics and database resources in hepatology

Abstract

Lately, advances in high-throughput technologies in biomedical research have led to a dramatic increase in the accessibility of molecular insights at multiple biological levels in hepatology. Much of this information is available in publications, but an increasing number of large-scale analyses are currently being stored in databases. Scopes of these databases are very divergent and may range from large, general databases collecting information on almost every known disease, to very specialized databases covering only a specific liver disease or aspect of hepatology. Over recent years, these bioinformatics data repositories have rapidly evolved into an essential aid for molecular hepatology. However, although publicly available through the internet, many of these databases are only known to a few experts. To facilitate access to these resources, the publicly available databases supporting research on liver diseases are summarized in this review.

Proteomic profiling of liver tissue from the mdx-4cv mouse model of Duchenne muscular dystrophy

“…As the largest multi-functional internal organ in the body, the liver has a very broad variety of biochemical functions, including digestion, nutrient storage, the integration of key metabolic pathways, the essential detoxification of xenobiotic substances, protein synthesis and immunity [ 46 ]. The transcriptome and proteome of human liver tissue has been extensively categorised by large-scale profiling studies [ 47 – 50 ] and detailed bioinformatics databases have been established that specifically focus on molecular hepatology in health and disease [ 51 , 52 ]. Building on these data banks of liver protein expression, including findings from detailed cataloguing studies of the mouse liver proteome [ 53 – 55 ], we have used here a comparative proteomic approach to study potential changes in liver proteins due to X-linked muscular dystrophy.…”

CCNB2, TOP2A, and ASPM Reflect the Prognosis of Hepatocellular Carcinoma, as Determined by Weighted Gene Coexpression Network Analysis

“…To date, thousands of HCC genomes have been sequenced globally, and most driver gene mutations, structural variants, fusion genes, copy number alterations, and viral integration events have been established [4]. This vast amount of new data provides an opportunity to understand the molecular basis of HCC better [5]. However, to utilize this scientific information, knowledge of the available database resources and bioinformatics tools are indispensable.…”

Upregulation of BUB1B, CCNB1, CDC7, CDC20, and MCM3 in Tumor Tissues Predicted Worse Overall Survival and Disease-Free Survival in Hepatocellular Carcinoma Patients

“…This tremendous amount of molecular data provides a rich source to better understand the molecular basis of HCC and to identify novel genomic targets for therapeutic intervention. Over the past two decades, advances in high-throughput technologies in biomedical research have led to a dramatic increase in the accessibility of molecular insights at multiple biological levels in HCC [ 9 ].…”