| Chronic hepatitis B is a worldwide disease caused by hepatitis B virus (HBV),it was originally called serum hepatitis.lt owns a high incidence in Asia and Africa and other developing countries, it is endemic in China. About one-third of people around the world once was infected with chronic hepatitis b in his life.Among them,the number of asymptomatic carriers of hepatitis b virus (HBsAg carriers) is more than350million, about130million are in our country. Most people who were infected were asymptomatic,only about a third of them manifest the clinical liver damage.At present,our country has30million patients with chronic hepatitis b. With a character of slower onset, the hepatitis b is relatively common with subclinical type and chronic type. The disease is mainly spread through blood, mother-baby and sexual contact."Chronic hepatitis to liver fibrosis, liver cirrhosis and liver cancer" is a evolution way of liver disease, forming a considerable threat to the patients’ survival. Chronic hepatitis caused by hepatitis b account for about80%～90%in chronic hepatitis caused by various causes. Chronic hepatitis duration can take several years, even decades. The disease are usually lighter, does not producing any symptoms or significant liver damage, but in some cases, persistent inflammation can slowly damage liver, eventually lead to cirrhosis and liver cancer, and then seduce poor prognosis of patients with the liver cancer.There is nearly none effective treatments for them. Nowadays, the application of the hepatitis b vaccine is the main measures to prevent and control the hepatitis b. However, due to a variety of reasons, such as the large number of hepatitis b infection in China,quite a lot of new hepatitis b infection appears. And in those countries whose economic and social development are slower than us,the second liver has continued to spread. For patients who had already infected with hepatitis b, vaccine can’t cure them. There are some widely knew treatments,however,their effects limited.The gene chip (DNA microarray) is a major technique in bioscience field in the21st century, which has the outstanding of high-throughput and rapid detection.Gene expression profiling chip has the superiority on the study of gene expression profiling mode of cells, which can be used to study the change of gene expression profiling in every stage of tumor cell development, understand the gene expression mode during the occurrence and development of tumors. Thus, gene expression profiling chip has widespread application in tumorigenesis, early diagnosis, tumor genotyping, directing therapy and prognosis evaluation, etc. With the rapid development and widespread application of gene expression profiling chip, redundant and complicate biological data was arised. How to analyze tens of thousands gene hybridization information on the gene-chip to reveal the life characteristics and regular pattern, which has become the major "bottleneck" restricting the further development of gene expression profiling chip. The analysis of tumor expression profiling chip is useful to clarify the mechanism of tumorigenesis, the diagnosis and therapy of tumor. Bioinformatics is a crossing science that conjunct computing-technology, statistics, mathematics, genetics, molecular biology, medical science, informatics, bio-physics and chemistry, which can be applied for the data-mining and explore the disease from the molecular level based on the bio-chips, sequences aligning, statistics methods, visualization, biological clustering, pathways analysis and promoter prediction. It is an important approach for functional genomics to obtain tumor-related genes and regulatory mechanism using gene-chip technologies and bioinformatics, which can integrate the gene expression network of tumors from the genome level, provide new insights and open up a new way to explore the pathogenesis of tumors.Because the expression profile chip has the advantage in research on gene expression patterns, use it for periods of tumor cell growth and tumor occurrence and development of related gene expression patterns in the process of change, therefore, gene expression profile chip has been widely used in mechanism of tumorigenesis, early diagnosis, tumor genotyping, guiding therapy and evaluating prognosis of research. As the expression profile chip technology extensively developed, and the produced abundant, vast and complex biological information data. How to interpret the tens of thousands of genes point on the chip hybridization, reveal the implied characteristics and law of life has become restricted gene chip technology application and development of the main "bottleneck". Bioinformatics is the comprehensive utilization of biology, computer science and information technology to reveal numerous and complicated biological data holds the biological mysteries of a cross subject, which based on the biological chip, with sequence alignment, statistical analysis method, clustering, path analysis and visualization mapping, biological promoter prediction method as the means, data mining, to the disease in molecular level, to broaden the study of tumor molecular pathogenesis is a new research idea, thus more comprehensive study of disease as a whole.Bioinformatics is a new frontier discipline formed on the base of the mutual infiltration and highly crosss of the modern biology and medical science, such as biochemistry, cell biology, developmental biology, genetics, genomics, physiology) and information science, computer science, biology, statistics, mathematics and other disciplines, and is often referred to as the genome informatics.It is based on the biochip research and is usually used to acquire, process, store, retrieve, manage, distribute, analyze, and interpret the biological information, to understand the biological meaning of contained in the data. Because currently the object of the study is mainly focused on nucleotide and amino acid, so narrowly said, bioinformatics is applying computer science and mathematics to the biological macromolecular information acquisition, processing, storage, classification, retrieval and analysis, to understand the biological significance of the information biological macromolecules of interdisciplinary.Main research contents of bioinformatics include biomolecular data collection and management, database search and sequence comparison, genome sequence information analysis, gene expression data analysis and processing, protein structure prediction, the system analysis, comparative genomics, etc. In particular, bioinformatics research includes the following aspects:(1) genome information acquisition, storage, management, processing, distribution and interpretation.(2) the discovery of a new gene and positioning, function annotations, regulation mechanism and network research.(3) non-coding region information structure analysis.(4) research of biological evolution.(5) Complete genome comparative studies.(6) Genome information analysis method research.7) functional genomics information analysis, including associated with large-scale gene expression profile analysis algorithms, software research, studies of gene expression regulation network, etc.As today’s life science and one of the important frontier fields of natural science, bioinformatics is also one of the core areas of natural science in the21st century, its research focus mainly on Genomics and Proteomics. Nowadays,is research center shift now:one is to associate the known gene sequences and function with functional genomics research.One is from the drawing on the basis of separation separation to based on the sequence of genes. The third is from the cause of the disease research to explore the pathogenesis. The fourth is from diagnosis to disease susceptibility research. Among them, the functional genomics has become a new research hotspot after the mapping and sequencing of human genome project was completed.My research has three main parts.The first part:chronic hepatitis b expression profile chip research. Collecting blood specimens of patients with chronic hepatitis b and unaffected volunteer each for three cases, using the Human Genome U133Array Plus2.0gene expression profile chip produced by Affymetrix companies in the United States to test the expression of genes.First,extract the total RNA of chronic hepatitis b patients and volunteers blood WBC by one-step extraction method,and then purify, synthesizing cDNA synthesis probes by reverse transcription, and chip hybridization and then washing, using fluorescence scanning to analyze the differentially expressed genes of chronic hepatitis b patients and normals. After careful analysis,37542genes were checked out. Upon examination, the result is accurate, effective and can be used for further analysis.The second part:screening of differentially expressed genes related to chronic hepatitis B.Using gene chip data analysis software BRB-ArrayTools4.2.1,to analyze the chip data acquired in the first part.Data were imported to BRB-Array Tools4.2.1,and then were filtered and clustered.Then we can identify the differentially expressed genes, which were annotated by GO and KEGG pathway later.Totally51genes were found,among them,31were up-regulated and the other20were down-regulated.The third part:the analysis of the protein-protein interaction network related to the differentially expressed genes.For microarray data, obtaining differentially expressed genes is only the first step, but these differentially expressed gene transcription regulation relationship and the expression of protein interactions is not acquired from gene expression profile analysis. How to carry on the fitting comments for these differentially expressed genes is more important to reveal the genetic relationship under certain conditions.In this chapter,we construct the PPI network with the software STRING and Cytoscape.With STRING,we found11differentially genes are more important in the network.Then,with Cytoscape,we found6proteins were interacted with most proteins among the up-regulated genes,and some of them are same with those in the11proteins,confirming their importance in the the development of chronic hepatitis b,they are:FLNC,MDK,TK1,THBS1,MAPK12and CD93.To sum up, our study successful screened some genes associated with CHB metastasis using gene expression data mining and bioinformatics tools which may play important roles in the process. In terms of biological pathways,we also found a few pathways throughout the CHB, each signal path may cross each other mutual connection, mutual influence, between formed the complex organic signaling network, common work on the occurrence of CHB; Finally, respectively, to build the occurrence and metastasis related gene transcription regulation network diagram, we can clearly identify in the core position of genes and transcription factors. These findings may provide a meaningful exploration and basis for further understanding of the molecular pathogenesis, drugs and treatment of CHB. |
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