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REVIEW ARTICLE
Year : 2012  |  Volume : 1  |  Issue : 2  |  Page : 87-91

Database and tools for nutrigenomics: A brief summary


Wiwanitkit House, Bangkhae, Bangkok Thailand, Visiting University Professor, Hainan Medical University, China, Adjunct Professor, Joseph Ayobabalola University; Nigeria

Date of Web Publication22-Sep-2012

Correspondence Address:
Viroj Wiwanitkit
Wiwanitkit house, Bangkhae, Bangkok Thailand

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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/2278-019X.101293

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  Abstract 

The advance in bioinformatics brings several new "omics" sciences that can be applied in medicine. An important new "omics" science in present biomedicine is the nutrigenomics, which is the specific "omics" that deals with the nutrition and genomics issue. Similar to other "omics" sciences, the basic requirements for manipulation is the database and tool. Here, the author briefly reviews and discusses on some important computational online databases and tools in nutrigenomics.

Keywords: Nutrigenomics, database, tool


How to cite this article:
Wiwanitkit V. Database and tools for nutrigenomics: A brief summary. J Med Nutr Nutraceut 2012;1:87-91

How to cite this URL:
Wiwanitkit V. Database and tools for nutrigenomics: A brief summary. J Med Nutr Nutraceut [serial online] 2012 [cited 2019 Dec 7];1:87-91. Available from: http://www.jmnn.org/text.asp?2012/1/2/87/101293


  Introduction Top


Bioinformatics is the new science with combination between biology and informatics technology. [1] It is the use of advancement in computer science for explanation and study of the complex biology question. [1] The concept of bioinformatics is based on the classical theory of biological science. [1] Classically, the biology is the study of the biome via the standard scientific methods, in vitro and vivo study. In vitro study means the study in the experimental condition outside the living body while in vivo study means the study within the living body. These two approaches have been used for a very long times. Recently, due to the advancement of another science, computer science, the application of computer in other sciences is possible and this is a really helpful progression in scientific world. Computer can help shorten the study process in scientific assessment. Computer also helps predict and clarify the scientific phenomena that cannot be tested by simple classical approaches. The application of computer for helping biology work is the fundamental of bioinformatics.

About 1 decade, the modern era of science occurs when bioinformatics is launched. Due to the completeness of human genome project, [2-3] scientists realized for the need of an ultra-tool for analysis of the heap of data and the computational approach, bioinformatics, is the answer. [4],[5] At first, the "genomics" is the primitive "omics" science that existed in our world. [6],[7] After that, several new "omics" sciences have been continuously launched. The advance in bioinformatics brings several new "omics" sciences that can be applied in many fields including to medicine. An important new "omics" science in present biomedicine is the nutrigenomics, which is the specific "omics" that deals with the nutrition and genomics issue. [8],[9],[10],[11],[12] Similar to other "omics" sciences, the basic requirements for manipulation is the database and tool. [1] The database is the useful source of data using for primary searching on existed knowledge that can be further used for clarification and prediction of the problems. The tool is the computational analyzer for analysis of data. This is called in silico analysis. This can help shorten and replace the unnecessary in vivo and vitro studies. Here, the author briefly reviews and discusses on some important computational online databases and tools in nutrigenomics (more details can be seen in reference [12] ).

What is nutrigenomics?[12]

Before an in depth details will be presented, the basic concept of nutrigenomics should be mentioned. As already noted, nutrigenomics is a new "omics" science. By term, it can be a subset of genomics that directly deals with nutrition. Genomics is the study of gene and genetic phenomena via the computational approach. Nutrition is the study on nutrient, eating, physiology as well as disease. Hence, the nutrigenomics is an interesting computational study on nutrition and gene. Indeed, the interrelation between nutrition and gene is complex. [1] Basically, every living thing has gene and gene is the smallest unit that determine the appearance of every living thing. By term, the genotype is an old terminology for describing the genetic characteristic of a living thing. This cannot be seen by naked eye but can be revealed by the standard genetic technique. Before the completeness of human genome project, the old pattern of genetic study focuses on finding the gene. However, when the genome project is complete, the new paradigm to study on the effect of the gene on living thing is of concern. Indeed, the study of the expression of the gene has been mentioned for a long time. In classical genetic, it is called phenotype. Phenotype is the overt appearance that can be visualized and realized. However, it should be noted that genotype and phenotype has a complex relationship. There has to be a linkage process or pathway connecting between genotype and phenotype. It has also to be noted that a phenotype can be from several genotype and a genotype can also result into many phenotypes. The same phenotypes might be from different genotypes and the same genotype might have different final phenotypes.

In medicine, although gene is the primary determinant of the characteristic of living thing, the final expression can be modified by external insult or environment. Nutrition is considered as an important external insult. Indeed, nutrient is the necessary that for every living thing. Nutrient has to be used for construction and repair of cells. Without adequate and proper nutrient, the disorder can be expected. For sure, this means the aberration of the finalized phenotype. However, it should also be said that effect of nutrition on different individual can be different. The main determinant is the background genetic content. With some genetic underlying patterns, such as some polymorphisms, some individuals might be tolerable to nutritional impairment or fluctuation. On the other hand, the other individual might be highly prone to get the nutritional problem. Hence, it is no doubt that the study on the complex relationship between gene and nutrition can be useful in medicine and this is the basic concept of introduction of nutrigenomics. [13],[14],[15],[16],[17]

To help the reader more understand on the usefulness of nutrigenomics, here are some good examples of applied nutrigenomics concept in present medicine:

  • Assessment of genetic polymorphism, mutant and variant that affect the nutritional-related diseases (such as metabolic disorder, cardiovascular disorder and cancer)
  • Searching for new biomarker for early diagnosis of nutrition related disorder
  • Study on the effect of food and supplement on health status of healthy and sick persons
  • Selection of proper pharmacological and nutritional therapy for each individual, which is the present concept of individualized medicine
  • Study the relationship between host gastrointestinal tract and pathogen in the complexity of food and nutrition
  • Prediction of the risk of nutrition related disorder in screening of healthy individual.
Databases in nutrigenomics[12]

Database is the source of data. It is the classical practice to collect the data at one side for using as reference. Database is also developed based on this concept. In computer science, database is very important because the data is the core in any computational activities. Without database, any computer function cannot be successfully done (computer has to work based on the known information or "database" and further apply its activity based on formatted direction via mathematical modeling of the stored data). Hence, the database is very important for bioinformatics which is an actual applied computer science. As already noted, database is required as primary source for further manipulation in bioinformatics.

Focusing on database in bioinformatics, these activities have to be covered:

Data collection

This is the collecting of information. The information might be number, word, figure, signal or etc.

Data verification

This is the approval of correctness of the information. This is the validation step of quality control of the process.

Data registration

This is the preparation step for further storage of the data. The input of the data into the memory of the computer has to be done. Without registration, a good pattern of data storage cannot be expected.

Data storage

This is the actual step for storing all derived information within the central processing unit of the computer. The storage is the back-up of the data as library source for future usage.

Data maintenance

This is the step to maintaining the data. Searching for error within the system and prompt correcting is required.

Data extraction

This is the important step. Without this step, the stored data cannot be useful. This is getting out the stored data from the computer into the manipulation process for actual usage.

To develop a database for bioinformatics, these activities have to be fully developed. With advancement in computer technology, there are many databases in bioinformatics. All databases in bioinformatics will share the common characteristics as a) collection of bioinformatics data, b) usually computer-based storage, c) usually public access with or without user payment or registration, d) continuous updated and e) can be used as basic informatics for bioinformatics manipulation.

Some databases are specific for nutrigenomics. Indeed, database is the exact starting points for computational study in nutrigenomics. [4] Here, the authors will discuss on some important nutrigenomics database.

A-yo 5

This database was developed by Saito et al. [18] This database is an open-source database that can be freely accessible at http://a-yo5.ch.a.u-tokyo.ac.jP /index.phtml. [18] It displays several contents in basic nutrigenomics. This is an early prototype of database in nutrigenomics. [12]

SGMD

This is the specific database for soybean genomics. [19] Genomics and expression profile in soybean and interaction with soybean cyst nematode is available in this database. This database is also an open-source database that can be freely accessible at http://psi081.ba.ars.usda.gov/SGMD/default.htm. [19]

Nutritional Phenotype database (dbNP)

Nutritional Phenotype database is the newly developed database by Nutrigenomics Organisation (NuGO) aiming at storage of biologically relevant, pre-processed-omics data, as well as study descriptive and study participant phenotype data. [20] It is the results from previous collaboration in developing nutritional network by NuGO. [21] This is the first database describing the interrelationship between genomics and phenotypics in nutrition. It becomes the referencing database at present.

GxE

GxE is a database for gene-environment interaction. Specific interactions for interactions relevant to nutrition, blood lipids, cardiovascular disease and type 2 diabetes are covered by this database. [22] This is a good example of database with clear and simple application on nutrition related disorder in medicine.

vProtein

vProtein is the database for identifying optimal amino acid complements from plant-based foods. [23] It is made based on information of several foods listed in the United States Department of Agriculture standard release aiming at determining the required quantity of each food. [23]

BarleyBase

BarleyBase is a specific database for plant microarrays with integrated tools for data visualization and statistical analysis. [24] It also covers the microarrays data from study on food plants including wheat, maize, soybean and rice. [24] This database is important for not only nutrigenomics but also plant genomics.

Indeed, there are other minor databases that are not well-known. Those databases might be specific for some conditions with limited usefulness in general. As a practitioner in nutritional science, it is required to understand the important databases and further uses it as a reference source in knowledge improvement.

Tools in nutrigenomics[12]

In bioinformatics, the computational tool is the heart for manipulating of data. Step by step, after searching for desired data from existed database, the manipulation of derived data by online computational tool lead to final clarification and prediction purposes. [25] Briefly, the first step is performing the data extraction from the collect database. At this step, user have to give some information, by keying some searching tool to start and stimulate the data extraction. This step is important because if there is no good key words, no good results cannot be derived. After this step, it is the actual phase of derived data manipulation. In computational medicine, in silico approach, there are two main kinds of manipulation:

Clarification

This is the manipulation of the derived data to answer the question on the existed scenario. The question might be the biological process, function or structure. The good example is the use of the structural genomics tool to find the secondary, tertiary and quarternary structures of the hemoglobin in red blood cell in anemia.

Prediction

This is the manipulation of the manipulation of the derived data to answer the question on the imaginary phenomena, which has never been existed. The question might be the interaction or effect of new drug or food new supplementation. The good example is the use of expression analysis to identify the biology process after interaction of new food supplementation and cancerous cells or the use of docking system to predict the complex molecule between food supplementation and gut immunity.

As already noted, there are many tools for in silico study. Many tools such as basic comparative genomics tools (focusing or comparison or alignment among molecules), functional genomics tools (focusing on function of molecules), structural genomics tools (focusing on structure of molecules) can be used in any field of "omics" including nutrigenomics. [1] For nutrigenomics, some specific important tools will be hereby presented.

BioConductor

BioConductor is the specific tool used for relative power and sample size analysis on gene expression profiling data. [12] The primary focus is on PPARalpha. [12] It is available online at http://bioconductor.org/packages/release/bioc/html/SSPA.html. [12]

GRS

GRS is a new compression tool for storing and analyzing Genome ReSequencing data. [13] It can be used for analysis of rice genome in researching. [13]

SMM

SMM-system is the new tool for study on an important food borne pathogen,  Salmonella More Details enterica. [26] It is available for downloaded at http://foodsafety.sjtu.edu.cn/SMM-system.html. [26]

Booly

Booly is a new tool for data integration. [27] It can be used by Food and Drug Administration (FDA) in nutrition, food and drug aspect. [27] Booly is available at http://booly.ucsd.edu. [27]

These tools are the examples that can be useful in nutrigenomics study. To select a tool, practitioner has to study the details of each tool and apply it to the point.


  Conclusion Top


Nutrigenomics is one of the newest "omics" sciences. It plays important role in the present nutritional medicine. Nutrigenomics can be the useful concept in managing of the nutrition related medical problems. To use nutrigenomics, the basic requirements for computational application are database and tool. The database is the actual primary source of information that is the basic requirement for further manipulation on the data. Several databases in nutrigenomics are available at present. Selection of appropriate database for each scenario is required. The tool is the key point for manipulation of the data. With computation tool, extracted data from database can be further processed. The tool can be used for either clarification of the existed scenario or prediction of the new phenomena. With tool, a short and simple in silio study in nutrigenomics can be done and this is the actual advantage to reduce the required time by classical approach. Similar to database selection, practitioner has to select appropriate tool for appropriate nutrigenomics job. With the non-stop progress in nutrigenomics, new databases and tools will be introduced and the practitioner in nutritional medicine has to follow those new ones to update the knowledge and use it for managing of the patients.

 
  References Top

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[Pubmed] | [DOI]



 

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