Database Of The Interaction Between MicroRNA And Target Gene In Stem Cells

Research backgroundWith the rise of bioinformatics,literature mining slowly become auxiliary means of biomedical research, and also become one of the important means of a wide range of raw data acquisition; A key role for the propulsion of disease diagnosis, prevention and treatment research. literature mining has a key role for Many important biological information range(For example, the interaction between a source of protein, annotation of gene function and biological pathways).With the further development of human genome plan, the non coding sequence accounted for 99%ofthe human genome more and more aroused the concern of researchers, one of the most attracting somebody’s attention is microRNA (miRNA) discovery. MicroRNA (miRNA)is a class of small molecule RNA, which is non coding strand length in eukaryotes about 21-25nucleotide(NT), and combined with target mRNA’s 3’UTR region or coding region by base pairing to degrade or stop mRNA’s protein synthesis, thereby it can regulate gene expression after transcription.Stem cell research has been as the top of the world’s ten largest technology advances in twentieth century by Time. In the process of differentiation, cells because of highly differentiation lost the ability to split again completely, and finally die. In the process of adapting to the growth of the body in order to change the defect, they save a part of the original undifferentiated cells, which are called stem cells. Stem cells are the biological initiating cells, which have potency of proliferation, reproduction and differentiation. Stem cells from differentiation of fertilized zygote form the primitive embryonic stem cells,and then differentiate into blastocyst-likes structures. The inner cells of the embryonic stem cells is versatile in forming all sorts of human body tissue, they can slowly differentiate and develop into the tissue and organ of fetal each stage. Stem cells lost totipotency, and become the multipotential stem cells or tissue specialised cells having specific function.Bio informatics analysis showed that a third of all human genes are modulated by micro RNA, suggesting that the miRNA is the core component of gene regulatory network. MicroRNA plays a key role in a variety of biological to adjust early development, cell proliferation and stem cell differentiation and apoptosis, and mutations of microRNA are connected to various diseases and tumor. It has the function of approximate oncogene gene or tumor suppressor gene. In the organism, the specificity of the microRNA is not obvious, it is often that a miRNA adjusts and controls multiple target genes, or multiple microRNAs adjust and control a target gene. The regulating effect of microRNA may constitute a kind of complex network, and it has also been the readjustment of other conditions. All normal cell differentiation process can be changed with the change of the miRNA expression, the anomaly of change is characteristic of various kinds of cancer. So, microRNA may become the new marker about the classification and staging of cancer. Because of its many different and large number target genes, the miRNA intervenes many cellular signal transduction system, and forms huge regulatory networks with target genes, which display a variety of biological functions.materials and methodsA. Data screening With the rise of bio informatics, literature mining slowly become auxiliary means of biomedical research, and also become one of the important means of a wide range of raw data acquisition; A key role for the propulsion of disease diagnosis, prevention and treatment research. literature mining has a key role for Many important biological information range(For example, the interaction between a source of protein, annotation of gene function and biological pathways). GenCLiP2.0 combines the ability of literature mining and database mining, can provide one-stop service for biomedical researchers, at the same time be able to use their professional knowledge on the depth of information mining, from a single gene lookup to batch gene analysis; keywords from the gene functional annotation to literature comments; from automatic word document keywords annotation to manually add annotations; finding word related gene from according to the sentence according to the total; automatically from the batch of gene networks building into the human gene networks involved in constructing a specific word; from batch genetic fuzzy clustering to the average level of chain cluster.a) To find out about the vocabulary of Stem Cells on NCBI MeSH website:[Stem Cell], [Stem Cells], [Cell, Stem], [, Stem Cells], [Mother Cell], [Mother Cells]], [Cell, Mother], [Cells, Mother], [Progenitor Cell], [Progenitor Cells]], [Progenitor Cell,], [Cells, Progenitor], [Colony-Forming Unit], [Colony Forming Units], [Colony Forming Unit], [Colony Forming Units], [Unit, Colony Forming], [Units, Colony Forming].b) Get the gene containing keywords for stem cells on GenClip2.0 (http://cismu.edu.cn/GenCLip/analysis.php).c) copy the genes into Excel 2007 for filtrating, choose to the genes beginning with "MIR".d) The genes beginning with "MIR" input GenClip2.0, respectively select keywords, get relevant literatures.e) Read the related literature in this paper detailedly, collect title, PMED,stem cell types, species, type, target genes, the relationship between miRNA and target genesf) take out datas without the target gene and stem cell types.B. Database buildingThe MySQLdatabase is according to the structured query language to realize the communication between database. SQL main function is to build a variety of database system operating instructions, used to insert, query, modify, or delete all kinds of database objects. The most convenient and rapid method is to communicate directly with the database through the command line. On the premise of the SQL, the user can operate by programming interface for large amount of data. The user of unfamiliar with SQL or wanting to convenient for daily management can use the client, for visualization of the operation.a) Download WampServer and install and debug.b) Build a new database, named for "anaysis_of_microRNA".c) Build a new table in the database, named for "microrna_stemcell_targetgene".d) Load the datas into the database.e) data processing Browse the datas loaded into the database, the datas which don’t display properly corrected.C. The website constructionIn high performance computing cluster server, LANGCHAO uses a combination of LAMP (Linux+Apache+MySQL+PHP/Perl), namely the whole system work on the Linux platform, Web server is the Apache, MySQL is the database system, at the same time PHP/Perl develop system with HTML and JavaScript. The users design a stable and easy the network system in the biggest limitation.a) Layout. Web page is divided into five parts altogether, respectively:header1, header2, header3, menu, cytoscapeweb.b) Connect to the database. The the success or failure of subject is whether the web can smoothly connecte to the corresponding database.c) Set the combination between miRNA, stem cells and target genes, a total of eight kinds of combination relations.d) The image shows about miRNAs and target genes matching. Put corresponding miRNAs and target genes in the same array, where miRNAs are named to $geneNode [$id1], target genes are named to $geneNode [$id2].Resultsa) Get genes for containing keywords for stem cell, the number is 498.b) copy the genes into Excel2007 for filtrating, choose to the genes beginning with "MIR", the number is 63.c) The genes beginning with "MIR" input GenClip2.0, respectively select keywords, get relevant literatures,the number is 286d) Read the related literature in this paper detailedly, collect title, PMID,stem cell types, species, type, target genes, the relationship between miRNA and target genese) take out datas without the target gene and stem cell types, the number is 356. From the above data can be:a) Involving 118 articles;b) Involve four kinds of animal models, respectively, for the human, mice, rats, trans genic mice;c) Collect 58 kinds of miRNAs, the top three are MR145 (a total of 55 record), MIR2131 (records), MIR34A(a total of 16 records);d) Collect 153 kinds of target genes, the top three are Oct4 (a total of 19 records), Nanog (a total of 19 records), Sox2 (a totalof 17 records);e) Collect 53 kinds of stem cell types, the top three, the top three are mesenchymal stem cells (a total of 66 records), embryonic stem cells (a total of 38 records), breast cancer stem cells (a total of 27 records).f) Database of the interaction between microRNA and target gene in stem cells provides three word choice searching, stem cells, miRNA, target genes, etc., can be formed eight different combinations.g) The result shows that the number of conditions of the retrieval word collocation are retrieved, a table display that the serial number of the results and the experimental animal, the types of stem cells, microRNA, target genes, as well as the source document, which miRNA and target genes can be linked to the corresponding web in GENE, source documents can be linked to the corresponding page in PubMed, which can allow users to know the related information retrieval information quickly and effectively. At the same time, it forms a diagram at the bottom of the page, which can show the retrieval of the relationship between miRNAs and target genes, the diagram can be zoom in normal operation, etc.Conclusion The result shows that the number of conditions of the retrieval word collocation are retrieved, a table display that the serial number of the results and the experimental animal, the types of stem cells, microRNA, target genes, as well as the source document, which microRNA and target genes can be linked to the corresponding web in GENE, source documents can be linked to the corresponding page in PubMed, which can allow users to know the related information retrieval information quickly and effectively. At the same time, it forms a diagram at the bottom of the page, which can show the retrieval of the relationship between microRNAs and target genes, the diagram can be zoom in normal operation, etc. It can Solve the problem about many littery experimental data, unable to quickly get the required type of stem cell on the mutual relationship between microRNAs and target genes, to provide the reference to the user’s subsequent experiment, reduce the experiment cost. However, the database also exists some shortage, collecting a total of 118 references, not well in terms of the highlight the advantages of the experiment. Not involved in the collection literature materials and methods of experiment, experiment for the experimenter future guidance weakened obviously, cannot effectively update, not according to the materials and methods of web page are beautiful enough.