Mining osmotic stress response genes from Arabidopsis genome

The five-chromosome sequence files of Arabidopsis thaliana, which included huge amounts of genetic sequences and annotation information. How to get the tap osmotic stress response gene is already unable to meet the needs of these algorithms. Based on analysis of plant genes' interaction principle, a reasonable technological line has been presented in this paper. First, we establish a basic function base in order to offer kinds of convenient tool functions. Then we produce index files of mRNA and gene sequence to predigest GenBank flat files and improve efficiency. We can get the range of promoters combining with predicted TSS. Finally, we design a reasonable algorithm to calculate P value. Hereby researchers can conclude if the cis element correlates with osmotic stress when it appears in promoter region, which can provide infromation for reachers to carry on the biological information scientific and the molecular biology aspect reserch.

[1]  J. K. Kim,et al.  Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment. , 2007, Journal of experimental botany.

[2]  Robert Gentleman,et al.  Using GOstats to test gene lists for GO term association , 2007, Bioinform..

[3]  Jungwon Yoon,et al.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community , 2003, Nucleic Acids Res..

[4]  Wyeth W. Wasserman,et al.  A new generation of JASPAR, the open-access repository for transcription factor binding site profiles , 2005, Nucleic Acids Res..

[5]  P. Pavlidis.  Using ANOVA for gene selection from microarray studies of the nervous system. , 2003, Methods.

[6]  Sunduz Keles,et al.  Statistical Applications in Genetics and Molecular Biology Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo , 2011 .

[7]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[8]  E. Bornberg-Bauer,et al.  The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. , 2007, The Plant journal : for cell and molecular biology.

[9]  Mark J. van der Laan,et al.  A new algorithm for hybrid hierarchical clustering with visualization and the bootstrap , 2003 .

[10]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.