LiverAtlas is a comprehensive resource of biomedical knowledge related to the liver and various hepatic diseases. It provides a wealth of manually curated records, relevant literature citations and cross-references to other databases. LiverAtlas covers detailed information of liver-related genome, transcriptome, proteome, metabolome, pathways and liver diseases. Importantly, the database contains proteins and genes that specificly expressed in the liver. Especially, an expert-confirmed Human Liver Disease Ontology, including relevant information for 227 types of hepatic disease, has been constructed and is used to annotate and arrange the data in LiverAtlas. We also assigned reliability scores to the entries of liver-expressed genes and proteins, PPIs, PTMs, and molecular/genetic events of hepatic diseases by a semi-quantitative assessment in order to facilitate users to select data of their interests.
For more introduction of LiverAtlas, please see FAQ.
Users can browse, search or download each kind of data in LiverAtlas freely.
For the complete user’s manual, please see Sitemap, which contains the detailed information of each kind of webpage of LiverAtlas and points out the links between them.
For the demonstration of data analysis methods and applications of LiverAtlas, please see Examples for Data Analysis, which illustrates how to utilize LiverAtlas to find candidate biomarkers for hepatocellular carcinoma by a systems-biology based classifier. This analysis method combines the differential gene expression with topological features of human protein interaction networks to enhance the ability of differential diagnosis.
As one of the data sources of LiverAtlas and another liver-related database provided by BPRC, the Liverbase integrates information on the human liver proteome, including the function, abundance, and subcellular localization of proteins as well as associated disease information. The overall objective of the Liverbase is to provide a unique public resource for the liver community by providing comprehensive functional annotation of proteins implicated in liver development and disease. The central database features are manually annotated proteins localized in or functionally associated with human liver. In the first version of Liverbase, the associated data includes the human liver proteome (6788 proteins) and transcriptome (11205 significantly expressed genes: 10224 from CHIP and 5422 from MPSS, respecively) from the Chinese human liver proteome project (CNHLPP). Liverbase enables (i) the establishment of liver GO slim with 51 nonredundant items; (ii) systematic searches for proteins within specific functional or metabolic pathways; (iii) systematic searches that aim to find the proteins that underlie common and rare liver diseases; and (iv) the integration of detailed protein annotations derived from the literature. Liverbase also contains an external links page with links to other biological databases, including GO, KEGG, pfam, SWISS-PROT, and GNF databases.
