ABSTRACT
Protein-protein interactions (PPIs) and microRNA (miRNA)-target interactions are important for deciphering the mechanisms of tumorigenesis. However, current PPI databases do not support cancer-specific analysis. Also, no available databases can be used to retrieve cancer-associated miRNA-target interactions. As the pathogenesis of human cancers is affected by several miRNAs rather than a single miRNA, it is needed to uncover miRNA synergism in a systems level. Here for each cancer type, we constructed a miRNA-miRNA functionally synergistic network based on the functions of miRNA targets and their topological features in that cancer PPI network. And for the first time, we report the cancer-specific database CancerNet (http://bis.zju.edu.cn/CancerNet), which contains information about PPIs, miRNA-target interactions and functionally synergistic miRNA-miRNA pairs across 33 human cancer types. In addition, PPI information across 33 main normal tissues and cell types are included. Flexible query methods are allowed to retrieve cancer molecular interactions. Network viewer can be used to visualize interactions that users are interested in. Enrichment analysis tool was designed to detect significantly overrepresented Gene Ontology categories of miRNA targets. Thus, CancerNet serves as a comprehensive platform for assessing the roles of proteins and miRNAs, as well as their interactions across human cancers.
ABSTRACT
The demand for evidence-based health informatics and benchmarking of 'good' information systems in health care gives an opportunity to continue reporting on recent papers in the German journal GMS Medical Informatics, Biometry and Epidemiology (MIBE) here. The publications in focus deal with a comparison of benchmarking initiatives in German-speaking countries, use of communication standards in telemonitoring scenarios, the estimation of national cancer incidence rates and modifications of parametric tests. Furthermore papers in this issue of MIM are introduced which originally have been presented at the Annual Conference of the German Society of Medical Informatics, Biometry and Epidemiology. They deal as well with evidence and evaluation of 'good' information systems but also with data harmonization, surveillance in obstetrics, adaptive designs and parametrical testing in statistical analysis, patient registries and signal processing.
Subject(s)
Delivery of Health Care/standards , Delivery of Health Care/trends , Health Information Systems/standards , Health Information Systems/trends , Quality Assurance, Health Care/standards , Quality Assurance, Health Care/trends , Epidemiologic Methods , GermanyABSTRACT
The publication of a memorandum on improving medication safety by information technology in both the German journal GMS Medical Informatics, Biometry and Epidemiology (MIBE) and the journal Methods of Information in Medicine (MIM) gives reason to strengthen cooperation of MIBE and MIM and to report on more publications of MIBE here. The publications in focus deal with simulation-based optimization of emergency processes, handling of research data in publications, open access to research metadata, reliability of digital patient records in medical research, assessment methods for physical activity, using of insurance databases for epidemiological studies, certificates for epidemiological professionals, regression models, computer based training, and performance management in Swiss hospitals. Finally determining factors for scientific careers are discussed.
Subject(s)
Medical Errors/prevention & control , Medical Informatics , Medication Therapy Management/standards , Patient Safety , Quality Improvement , HumansABSTRACT
The publication of German competency-based learning objectives "Medical Informatics" for undergraduate medical education gives reason to report on more publications of the German journal GMS Medical Informatics, Biometry and Epidemiology ( MIBE ) in Methods. The publications in focus deal with support of medical education by health and biomedical informatics, hospital information systems and their relation to medical devices, transinstitutional health information systems and the need of national eHealth strategies, epidemiological research on predicting high consumption of resources, and with the interaction of epidemiologists and medical statisticians in examining mortality risks in diabetes, in genome wide association studies and in dealing with limits and thresholds. This report is the beginning of an annual series intending to support better international cooperation to achieve good information as a basis for good medicine and good healthcare.
Subject(s)
Guidelines as Topic , Medical Informatics/education , Publications , Students, Medical , Education, Medical, Undergraduate , Germany , HumansABSTRACT
Today different database systems for molecular structures (genes and proteins) and metabolic pathways are available. All these systems are characterized by the static data representation. For progress in biotechnology, the dynamic representation of this data is important. The metabolism can be characterized as a complex biochemical network. Different models for the quantitative simulation of biochemical networks are discussed, but no useful formalization is available. This paper shows that the theory of Petrinets is useful for the quantitative modeling of biochemical networks.
Subject(s)
Metabolic Networks and Pathways , Models, Biological , Biotechnology , Computer Simulation , Databases, Factual , Systems BiologyABSTRACT
We developed an information system for inborn metabolic diseases. The system consists of three parts. The first part is the MD-Cave for information on laboratory findings, genes, enzymes and metabolic pathways. The second part (ASDB) concerns with active agents and their different mechanisms of action inside the metabolic pathway and possible therapeutic treatment of these illnesses. The third part deals with the integration of these and other data bases for easy access to different information. This information system can be helpful for scientists and physicians working in the field of inborn metabolic diseases.
Subject(s)
Databases as Topic , Metabolism, Inborn Errors , Biochemical Phenomena , Enzymes/metabolism , Humans , Metabolism, Inborn Errors/diagnosis , Metabolism, Inborn Errors/genetics , Metabolism, Inborn Errors/metabolism , Metabolism, Inborn Errors/therapy , Research/organization & administration , Systems IntegrationABSTRACT
The very complex and specific knowledge about inborn errors of metabolism increases rapidly and is spread worldwide. Therefore an Internet platform for the acquisition of statistical knowledge (PATDB) and for the collection of the experience of experts (Metabolic diseases database) has been established. The success of diagnostic support highly depends on the way of knowledge representation. An information retrieval system for physicians will offer first insights about useful user interfaces and handling properties. Furthermore information fusion of biomedical systems to a Biomedical Workbench for the simulation of biochemical reactions is described.
Subject(s)
Artificial Intelligence , Decision Support Systems, Clinical , Diagnosis, Computer-Assisted , Expert Systems , Metabolism, Inborn Errors/diagnosis , Humans , Internet , Software , User-Computer InterfaceABSTRACT
Computer supported drug design is based on the biochemical information for the prediction of alternative bio-chemical pathways. Molecular information on genes, proteins, biochemical reactions, mutations, inborn errors and metabolic diseases are available via internet. Based on this information we developed an information retrieval and processing concept combining knowledge about metabolic diseases and biochemical effects.
Subject(s)
Drug Design , Drug Information Services , Internet , Metabolic Diseases/drug therapy , Pharmacokinetics , Artificial Intelligence , Databases as Topic , Expert Systems , Humans , Metabolic Diseases/genetics , Metabolic Diseases/metabolismABSTRACT
Methods of biotechnology allow the analysis of molecular structures and molecular processes. Different molecular database systems are available which allow worldwide data access. Methods and concepts of bioinformatics are important for the analysis of these molecular data, which represent complex regulatory networks. The detection of metabolic diseases is one application of information systems, which represents molecular and medical data and allows the stimulation of metabolic processes. In this paper we present the architecture of our molecular information system.
Subject(s)
Metabolism, Inborn Errors/metabolism , Database Management Systems , Humans , Models, Molecular , User-Computer InterfaceABSTRACT
Methods of biotechnology allow the isolation, sequencing, and synthesis of molecular structures. Molecular database systems are available, which allow the worldwide data access. Methods and concepts of bioinformatics are important for the analysis of these molecular data, which represent complex regulatory networks. In this paper we present the architecture of our molecular information system.
Subject(s)
Biotechnology , Information Systems , Molecular Biology , Computational Biology , Models, Molecular , Systems IntegrationABSTRACT
Today different database systems for molecular structures (genes and proteins) and metabolic pathways are available. All these systems are characterized by the static data representation. For progress in biotechnology the dynamic representation of this data is important. The metabolism can be characterized as a complex biochemical network. Different models for the quantitative simulation of biochemical networks are discussed, but no useful formalization is available. This paper shows that the theory of Petrinets is useful for the quantitative modeling of biochemical networks.
Subject(s)
Biochemistry , Computer Simulation , Biochemical Phenomena , Biotechnology , Catalysis , Computational Biology , Databases, Factual , Glycolysis , Models, Biological , Protein EngineeringABSTRACT
The analysis of biochemical processes can be supported using methods of modelling and simulation. New methods of computer science are discussed in this field of research. This paper presents a new method which allows the modelling and analysis of complex metabolic networks. Moreover, our simulation shell is based on this formalization and represents the first tool for the interactive simulation of metabolic processes.
Subject(s)
Biochemistry , Metabolism , Models, Chemical , Models, Genetic , Software , Biochemical Phenomena , Cell Communication/physiology , Databases, Factual , Enzymes/physiology , Gene Expression/physiology , Genes, Regulator/physiology , Genetic Diseases, Inborn/enzymology , Genetic Diseases, Inborn/genetics , Genetic Diseases, Inborn/metabolism , ProbabilityABSTRACT
In this paper, we will present the first model which supports the automatic detection of metabolic defects. Our model is based on the theory of formal languages and on the knowledge of metabolic networks. The simulation program is the first interactive simulation shell which allows the analysis and synthesis of metabolic networks. Moreover, this formalization is a new concept in the research field of metabolic engineering [8] which allows us to produce a hypothesis for the metabolic therapy.
Subject(s)
Diagnosis, Computer-Assisted , Expert Systems , Metabolic Diseases/diagnosis , Models, Biological , Cell Communication/physiology , Computer Simulation , Gene Expression Regulation/physiology , Humans , Metabolic Diseases/physiopathology , Systems IntegrationABSTRACT
In the field of biotechnology and medicine it is of interest to model and simulate metabolic processes. The usual methods to model metabolic pathways are chemical descriptions and differential equations. Moreover, the graph theoretical aspect is discussed and the development of expert systems is in process. In this paper we present the formalization of metabolic processes. Our formalization is based on the theory of formal languages. This formalization is called genetic grammar and represents an expansion of the Semi-Thue-System.