Liverbase: A Comprehensive View of Human Liver Biology

Sun, Aihua; Jiang, Ying; Wang, Xue; Liu, Qi‐Jun; Zhong, Fan; He, Quanyuan; Guan, Wei; Li, Hao; Sun, Yulin; Shi, Liang; Yu, Hong; Yang, Dong; Xu, Yang; Song, Yanping; Tong, Wei; Liu, Dong; Lin, Chengzhao; Hao, Yunwei; Geng, Chao; Dong, Yun; Zhang, Xuequn; Yuan, Xiaoyan; Chen, Ping; Zhu, Yunping; Li, Yixue; Liang, Songping; Zhao, Xiaohang; Liu, Siqi; He, Fuchu

doi:10.1021/pr900191p

Cited by 42 publications

(46 citation statements)

References 58 publications

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“…In 2002, the Human Liver Proteome Project (HLPP) was started as the first initiative for the understanding organ-or tissue-specific proteomes in humans (38). The recent completion of proteome, transcriptome, CHIP and massively parallel signature sequencing (MPSS) studies from the Chinese human liver proteome project (CNHLPP) revealed that tens of thousands of proteins/genes are regulated in the human liver (39,40). Determining how these proteins/genes are temporally and spatially modulated is still a great challenge, and the functional roles of PTMs in the liver remain to be elucidated.…”

Section: Systematic Analysis Of the Human Liver Phosphoproteome And Ppn-mentioning

confidence: 99%

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

Song

Liu

et al. 2012

Molecular & Cellular Proteomics

172

197

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In eukaryotes, hundreds of protein kinases (PKs) specifically and precisely modify thousands of substrates at specific amino acid residues to faithfully orchestrate numerous biological processes, and reversibly determine the cellular dynamics and plasticity. Although over 100,000 phosphorylation sites (p-sites) have been experimentally identified from phosphoproteomic studies, the regulatory PKs for most of these sites still remain to be characterized. Here, we present a novel software package of iGPS for the prediction of in vivo site-specific kinase-substrate relations mainly from the phosphoproteomic data. By critical evaluations and comparisons, the performance of iGPS is satisfying and better than other existed tools. Based on the prediction results, we modeled protein phosphorylation networks and observed that the eukaryotic phospho-regulation is poorly conserved at the site and substrate levels. With an integrative procedure, we conducted a large-scale phosphorylation analysis of human liver and experimentally identified 9719 psites in 2998 proteins. Using iGPS, we predicted a human liver protein phosphorylation networks containing 12,819 potential site-specific kinase-substrate relations among 350 PKs and 962 substrates for 2633 p-sites. Further statistical analysis and comparison revealed that 127 PKs significantly modify more or fewer p-sites in the liver protein phosphorylation networks against the whole human protein phosphorylation network. The largest data set of the human liver phosphoproteome together with computational analyses can be useful for further experimental consideration. This work contributes to the understanding of phosphorylation mechanisms at the systemic level, and provides a powerful methodology for the general analysis of in vivo post-translational modifications regulating sub-proteomes. Molecular & Cellular

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Section: Systematic Analysis Of the Human Liver Phosphoproteome And Ppn-mentioning

confidence: 99%

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

Song

Liu

et al. 2012

Molecular & Cellular Proteomics

172

197

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“…There is a huge amount of data on liver function and much has been assembled in in a comprehensive database called Liverbase. 14 Liver diseases can arise due to a wide range of causes including toxins such as alcohol or paracetamol, viral infection, and metabolic dysregulation. In particular, here we discuss the liver damage resulting from the build-up of fats in the liver (steatosis) known as non-alcoholic fatty liver disease (NAFLD), which can result in inflammation (hepatitis), scar tissue formation (fibrosis), and irreversible cell death (cirrhosis).…”

Section: Diseases Of the Liver Systemmentioning

confidence: 99%

Liver function as an engineering system

et al. 2016

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Process Systems Engineering has tackled a wide range of problems including manufacturing, the environment, and advanced materials design. Here we discuss how tools can be deployed to tackle medical problems which involve complex chemical transformations and spatial phenomena looking in particular at the liver system, the body's chemical factory. We show how an existing model has been developed to model distributed behavior necessary to predict the behavior of drugs for treating liver disease. The model has been used to predict the effects of suppression of de novo lipogenesis, stimulation of b-oxidation and a combination of the two. A reduced model has also been used to explore the prediction of behavior of hormones in the blood stream controlling glucose levels to ensure that levels are kept within safe bounds using interval methods. The predictions are made resulting from uncertainty in two key parameters with oscillating input resulting from regular feeding. V C 2016 The Authors AIChE Journal published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers AIChE J, 62: 3285-3297, 2016 Keywords: mathematical modeling, biomedical engineering, systems biology, medical, controlThe liver, its regulation, and its diseases Why systems engineering of the liver?Systems Engineering is the discipline of the management of complex engineering systems over their whole life cycle. Process Systems Engineering is the study of complex process engineering systems involving chemical and physical change. Prof Roger Sargent was a pioneer from the 1950s in seeing the potential that computers could have to revolutionize the way that we tackled these problems.1 He also saw the way Chemical Engineering was broadening its base into molecular and biological systems to improve manufacturing. 1,2The liver is one part of a very complex processing system which ensures that all parts of the body receive the energy and nutrients that they need, that waste products are removed efficiently from the various streams, and that short and long term well being are maintained. It is the body's central chemical processing organ. Considering the liver system as one which controls chemical and physical change within the body, particularly of nutrition, makes it a legitimate area of study for Process Systems Engineers. A number of Chemical Engineers have also contributed to the use for Process Systems Engineering to a range of medical applications. Bogle 3 reviews recent

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“…After evaluation of individual variation in protein expression levels in normal liver, standard operating procedures (SOPs) for HLPP sample preparation were generated [6]. By collaborative and systematic analysis, a total of high confident 6788 proteins with at least two peptides matches were identified [7,8]. Of these, 3721 proteins were identified for the first time in the liver.…”

Section: Liver Proteome Expression Profilementioning

confidence: 99%

“…These results validated the great effort the Chinese proteomists had put forth and the sensitivity of the platform they used for this project, especially considering that mass spectrometry (MS) was not so powerful several years ago. The Journal of Proteome Research published one special issue for the outcome of the HLPP and greatly acknowledged the contribution of this international project [7,8].…”

Section: Liver Proteome Expression Profilementioning

confidence: 99%

Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development

Zhai

et al. 2014

Sci. China Life Sci.

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Proteomics focuses on the systematic identification and quantification of entire proteomes and interpretation of proteins' biological functions. During the last decade, proteomics in China has grown much faster than other research fields in life sciences. At the beginning of the second decade of the 21st century, the rapid development of high-resolution and high-speed mass spectrometry makes proteomics a powerful tool to study the mechanisms underlying physiological/pathological processes in organisms. This article provides a brief overview of proteomics technology development and representative scientific progress of the Human Liver Proteome Project in China over the past three years. proteomics, LC-MS/MS, HLPP, protein-protein interaction, protein posttranslational modification, bioinformaticsCitation:

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Liverbase: A Comprehensive View of Human Liver Biology

Cited by 42 publications

References 58 publications

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

Liver function as an engineering system

Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development

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