(Candidate Gene Selection Protocol for Pig cdna Chip Manufacture Using TIGR Gene Indices)

Transcription

1 (Candidate Gene Selection Protocol for Pig Chip Manufacture Using TIGR Gene Indices) Chip Chip Chip Red Hat Linux 80 MySQL Perl Script TIGR(The Institute for Genome Research SsGI (Sus Scrofa Gene Index) DB 1 DB TIGR SsGI DB (ftp://ftptigrorg/pub/data/tgi/sus_scrofa/) 2 5 ( ) DB ( 5765 ) 3 Perl script Excel Chip 500~1000bp 3436 : DNA TIGR Abstract DNA microarray or c experiment is now considered to be one of the best gene expression profiling method because it takes advantage of handling large number of genes with one time experiment We present here an efficient way that is able to pick the candidate genes for pig c manufacture We expect that this method will be very useful to design a chip because this method utilizes the gene itself rather than the shorter s It was achieved by using SSGI (Sus Scrofa Gene Index) DB of TIGR (The Institute for Genome Research and Perl script we developed on the Linux PC cluster The more detailed procedure steps are as follows: 1 The SsGI DB file was downloaded from TIGR (ftp://ftptigrorg/pub/data/tgi/sus_scrofa/) 2 Libraries file list was also downloaded from TIGR Porcine Gene Index website and compared to the SsSI DB fro the five different tissues (fat muscle ovary uterus adipocyte) The 5765 sequences were obtained from the five tissues in the condition that the overlaps between tissues were allowed 3 Using the homemade Perl scripts the overlap was removed and the result data files were converted and saved to 'Excel' file format Finally for c manufacture only the sequences of which the sequence length is between 500 and 1000bp were obtained The number of final DNA sequence was 3436 Keywords: DNA Chip Pig Bioinformatics TIGR Swine Gene 174

2 (Bashiardes 2001) c (Leung (Jet 2002; Carroll 2003) (functional genomics) (structural genomics) nomics) (functional ge- NCBI TIGR(The Institute for Genome Research http: //wwwtigrorg) (Gene Index) (Quackenbush 2000) UniGene (Hemberger 2001) (Expressed Sequence Tag (Mount 2001) 2003) ) 2000) (Gill post genome TIGR 31 DNA (Southern 2001) Southern DNA sequencing 2002) ; Franca c Northern blot (Southern 500bp bp c Southern Northern blot nitrocellulose (Huttenhofer 2006) 1 mrna c (Gyeongsang National Univerisity) mrna DNA DNA mrna : / NCRC)" DNA TIGR SsGI (Sus scrofa Gene Index) DB Perl script(tisdall 2001) Red Hat Linux 80 TIGR ( jglee@gnuackr) 21 (#: R ) SsGI DB MySQL Perl 3 TIGR (EB- ftptigrorg/pub/data/tgi/sus_scrofa/ 175 DB FTP ftp:// SsGI DB

3 TIGR Porcine Gene Index libraries DB (refinement) 5765 Perl script Perl script Excel Chip 500bp 1000bp 3436 TIGR DB SsGI DB (ftp://ftptigrorg/pub/data/tgi/sus _scrofa/) 5 ( ) DB ( 5765 ) Perl script Excel Chip 500~1000bp 3436 : 1 176

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7 1 TIGR SsGI DB [1] Bashiardes S and Lovett M (2001) detection and analysis Curr Opin Chem Biol 5(1):15-20 [2] Carroll SB (2003) Genetics and the making of Homo sapiens Nature 422: [3] Franca LT et al (2002) A review of DNA sequencing techniques Q Rev Biophys 35(2): [4] Gill RW and Sanseau P (2000) Rapid in silico cloning of genes using expressed sequence tags (s) Biotechnol Annu Rev 5:25-44 [5] Hemberger M et al (2001) UniGene array-based monitoring of transcriptome changes during mouse placental development Proc Natl Acad Sci U S A 98(23): [6] Huttenhofer A and Vogel J (2006) Experimental approaches to identify non-coding RNAs Nucleic Acids Res 34(2): [7] Kim TH et al (2006) Generation and analysis of large-scale expressed sequence tags (s) from a full-length enriched library of porcine backfat tissue BMC Genomics 7(1):36 [8] Leung YF and Cavalieri D (2003) Fundamentals of microarray data analysis Trends Genet 19(11): [9] Mount DW (2001) Bioinformatics: Sequence and Genome Analysis Cold Spring Harbor Laboratory Press [10] Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis J Mol Biol 98(3): [11] Southern EM (1979) Analysis of restriction-fragment patterns from complex deoxyribonucleic acid species Biochem Soc Symp 44:37-41 [12] Southern EM (2001) DNA microarrays History and overview Methods Mol Biol 170:1-15 [13] Tisdall JD (2001) Beginning Perl for Bioinformatics O'Reilly [14] Quackenbush J et al (2000) The TIGR Gene Indices: reconstruction and representation of expressed gene sequences Nucleic Acids Res 28:141-5 [15] Vet JA et al (2002) Molecular beacons: colorful analysis of nucleic acids Expert Rev Mol Diagn 2(1):