Assessement Of In Silico Methods For The Genomic Analysis Of Insulin Independent Glucose Uptake In Mucosal Epithelial Cells.

Transcription

1 Volume 119 No , ISSN: (on-line version) url: ijpam.eu Assessement Of In Silico Methods For The Genomic Analysis Of Insulin Independent Glucose Uptake In Mucosal Epithelial Cells. P.B.RameshBabu 1, Shankar Rao N 2 1 Professor and Head, 2 UG Student Dept. of Genetic Engineering BIHER, BIST, Bharath University Chennai rameshbabupb.gen@bharathuniv.ac.in ABSTRACT Recently a rapid development is observed in bioinformatics software tools in analysis of genomic analysis in diabetic mellitus. Recent large-scale common and rare variant genome-wide association studies (GWAS) suggest that substantially larger association studies are needed to identify most T2D loci in the population. The Cognitive gene diabetic database (CGDD) is going to enhance the way they work by simplifying the whole process of accessing several databases at several instances. As a boon to the researchers this database is going to be a free ware. As a fundamental requirement all the genes that are involved in causing this atopy is included in the database and can be retrieved at any moment if needed. And the corresponding conserved domain sequence, protein parameters as well as the protein motif, its positions and descriptions can be retrieved. The information that are found in future that contributes to this disorder will also be added to the database as and when they are discovered. Apart from this, some of the salient and significant information pertaining to diabetes can also be found. Keywords : Diabetes, CGDD, MySQL, Gene database, Snapshots INTRODUCTION Diabetes is a metabolic disorder where in human body does not produce or properly uses insulin, a hormone that is required to convert sugar, starches, and other food into energy. Diabetes mellitus is characterized by constant high levels of blood glucose (sugar). [1-5]Human body has to maintain the blood glucose level at a very narrow range, which is done with insulin and 2623

2 glucagon. The function of glucagon is causing the liver to release glucose from its cells into the blood, for the production of energy. Though, Diabetes mellitus is not completely curable but, it is controllable to a great extent. So, you need to have thorough diabetes information to manage this it successfully As for our database cognitive gene diabetic database (CGDD) is concerned, it is necessary to know about the genes, conserved domains,[6-11] motifs and protein parameters, which are discussed as follows. It is possible to obtain the information of all the genes responsible for diabetes disease in homo sapiens. Using this it is easy to retrieve the conserved domains, motifs and protein parameters. This database will enhance the way they work by simplifying the whole process of accessing several databases at several instances. As a boon to the researchers this database is going to be a free ware. These data are stored in MS SQL SERVER database. We have created a web interface to access these data easily.[12-14] For this purpose, PHP code is embedded into the HTML source document and interpreted by a web server with a PHP processor module, which generates the web page document. As a general-purpose programming language, PHP code is processed by an interpreter application in command-line mode performing desired operating system operations and producing program output on its standard output channel. It may also function as a graphical application. PHP is available as a processor for most modern web servers and as standalone interpreter on most operating systems and computing platforms. The control of diabetes mostly depends on the patient and it is his/her responsibility to take care of their diet, exercise and medication. Advances in diabetes research have led to better ways of controlling diabetes and treating its complications. Hence they include:- [15-19] New improved Insulin and its therapy, (external and implantable insulin pumps) have advanced well to manage elevated blood sugars without any allergic reactions. Oral hypoglycemic drug, controls diabetes type 2. New improved blood glucose monitor (new device for self blood glucose monitoring), and hemoglobin A1c laboratory test to measure blood glucose control during previous 3 months. Effective availability of the treatments for affected body organs due to diabetes. 2624

3 Diabetes Mellitus, commonly known as diabetes, comes in different forms and affects all age groups. In the United States, 18.2 million people, or 6.3% of the population, have been diagnosed with diabetes. Diabetes is the 7th leading cause of death in the United States and is the number one cause of blindness, chronic renal failure, and non-traumatic lower extremity amputations. In 2002, approximately $132 [20-28]billion was spent on direct and indirect costs of diabetes in the United States. These figures illustrate the need for better solutions in diabetes treatment and prevention. Currently, a large sector of the medical and research community is Development of cognitive gen diabetic database (CGDD) provides information about the genes responsible for diabetes, conserved domains, protein motifs and protein parameters. This database is going to enhance the way they work by simplifying the whole process of accessing several databases at several instances. As a boon to the researchers this database is going to be a free ware. Materials and Methods MySQL MySQL is a relational database management system (RDBMS) that runs as a server providing multi-user access to a number of databases. The MySQL development project has made its source code available under the terms of the GNU General Public License, as well as under a variety of proprietary agreements. MySQL is owned and sponsored by a single for-profit firm, the Swedish company MySQL AB, now owned by Sun Microsystems, a subsidiary of Oracle Corporation. Free-software projects that require a full-featured database management system often use MySQL. Such projects include (for example) WordPress,[29-32] phpbb, Drupal and other software built on the LAMP software stack. MySQL is also used in many high-profile, large-scale World Wide Web products including Wikipedia, Google and Facebook. MySQL code uses C and C++. The SQL parser uses yacc and a home-brewed lexer, sql_lex.cc. MySQL works on many different system platforms, including AIX, BSDi, FreeBSD, HP-UX, i5/os, Linux, Mac OS X, NetBSD, Novell NetWare, OpenBSD, OpenSolaris, ecomstation, OS/2 Warp, QNX, IRIX, Solaris, Symbian, SunOS, SCO OpenServer, SCO UnixWare, Sanos, Tru64 and Microsoft Windows. A port of MySQL to OpenVMS also exists. 2625

4 PHP: Hypertext Preprocessor is a widely used, general-purpose scripting language that was originally designed for web development to produce dynamic web pages. For this purpose, PHP code is embedded into the HTML source document and interpreted by a web server with a PHP processor module, which generates the web page document. [33-36]As a general-purpose programming language, PHP code is processed by an interpreter application in command-line mode performing desired operating system operations and producing program output on its standard output channel. It may also function as a graphical application. PHP is available as a processor for most modern web servers and as standalone interpreter on most operating systems and computing platforms. WAMPs are packages of independently-created programs installed on computers that use a Microsoft Windows operating system. WAMP is an acronym formed from the initials of the operating system Microsoft Windows and the principal components of the package: Apache, MySQL and PHP (or Perl or Python). Apache is a web server. MySQL is a database management software. PHP is a scripting language that can manipulate information held in a database and generate web pages dynamically each time content is requested by a browser. Other programs may also be included in a package, such as phpmyadmin which provides a graphical user interface for the MySQL database manager, or the alternative scripting languages Python or Perl. Front end coding: html I. collection of information: The following gene information from NCBI is obtained as show above. >ref NC_ : Homo sapiens chromosome 8, GRCh37 primary referenceassemblyagcagtttttgtaggtgaaaacaatgaagccaggtaatattgcaa GGAGGCTGTAATTTTAGCAGACCTACCAACAACACTGATGTAGGAAGCTCATTATTT TAATTTCTGGAGCCTTTTAATTTTTTCTTTAGAAAGTGTATAAATAATTGCAGTGCTG CTTTGCTTCCAAAACTGGGCAGTGAGTTCAACAACAACGACAACAACAGCCGCAGC TCATCCTGGCCGTCATGGAGTTTCTTGAAAGAACGTATCTTGTGAATGATAAAGCTG CCAAGAT 2626

5 We have obtained the conserved domain sequences from uniprot using the id from NCBI and motifs from Motif search as shown below. 2627

6 II. The above information is stored in the database using MYSQL as shown below. CREATE TABLE `diabetes_table` ( `SLNO` int(5) NOT NULL auto_increment, `GeneID` int(10) NOT NULL, `GeneName` varchar(600) NOT NULL, `GeneSeq` longblob NOT NULL, `Domain` longblob NOT NULL, `MotifLocDesc` longblob NOT NULL, `Proteinparam` longblob NOT NULL,PRIMARY KEY (`SLNO`)) INSERT INTO `diabetes_table` VALUES (1, , 'solute carrier family 30 (zinc transporter), member 8 [Homo sapiens]', [37-39]gene sequence, domain sequence, motif locations and descriptions, protein parameters ); 3. Designing web interface is shown below along with the snapshots. Snap shots: index.html (main page): 2628

7 disease.html Cognitive gen diabetic database: CGDD is a free database devoted to genes, conserved domains and protein motifs responsible for diabetes in human beings. Goal: to allow automatic identification and recognition of domains,[22-26] motifs and protein parameters in user-supplied protein way. Protein motifs and domains are important as they provide clues as to possible functions of the protein, and possible interactions of the protein. If the protein for example has a domain for DNA binding, you would predict that that protein may act by binding to DNA sequences. </h3> Results & Discussion 1. CGDD is a free database availed for the user requirement. 2. Open the database through the browser. 3. Choose the required gene id or gene name and click enter. 4. We will get all the information like gene sequence, conserved domain sequence, protein parameters, motifs its locations and descriptions for a particular gene, which will be shown below. 2629

8 This page contains the following results: GeneID: Gene Name: solute carrier family 30 (zinc transporter), member 8 [Homo sapiens] ConservedDomain: MEFLERTYLVNDKAAKMYAFTLESVELQQKPVNKDQCPRERPEELESGGMYHCHSGSK PTEKGANEYAYAKWKLCSASAICFIFMIAEVVGGHIAGSLAVVTDAAHLLIDLTSFLLSL FSLWLSSKPPSKRLTFGWHRAEILGALLSILCIWVVTGVLVYLACERLLYPDYQIQATVM IIVSSCAVAANIVLTVVLHQRCLGHNHKEVQANASVRAAFVHALGDLFQSISVLISALIIY FKPEYKIADPICTFIFSILVLASTITILKDFSILLMEGVPKSLNYSGVKELILAVDGVLSVHS LHIWSLTMNQVILSAHVATAASRDSQVVRREIAKALSKSFTMHSLTIQMESPVDQDPDC LFCEDPCD[40-45] References 1. Nimal, R.J.G.R., Hussain, J.H., Effect of deep cryogenic treatment on EN24 steel,, V-116, I-17, PP , Parameswari, D., Khanaa, V., Deploying lamport clocks and linked lists, International Journal of Pharmacy and Technology, V-8, I-3, PP , Parameswari, D., Khanaa, V., Case for massive multiplayer online role-playing games, International Journal of Pharmacy and Technology, V-8, I-3, PP , Parameswari, D., Khanaa, V., Deconstructing model checking with hueddot, International Journal of Pharmacy and Technology, V-8, I-3, PP , Parameswari, D., Khanaa, V., The effect of self-learning epistemologies on theory, International Journal of Pharmacy and Technology, V-8, I-3, PP , Pavithra, J., Peter, M., GowthamAashirwad, K., A study on business process in IT and systems through extranet,, V-116, I-19, PP , Pavithra, J., Ramamoorthy, R., Satyapira Das, S., A report on evaluating the effectiveness of working capital management in googolsoft technologies, Chennai, International Journal of Pure and Applied Mathematics, V-116, I-14, PP , Pavithra, J., Thooyamani, K.P., A cram on consumer behaviour on Mahindra two wheelers in Chennai,, V-116, I-18, PP-55-57,

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