BioSysBio:abstracts/2007/Jamie Allen

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Abstract: Predicting gene co-expression from CIS-regulatory regions

Author(s): Jamie Allen,Ajay Kohli,Ehsan Mesbahi
Affiliations: University of Newcastle upon Tyne
Contact:email: jamie.allen@ncl.ac.uk
Keywords: 'add-keyword_1' 'add_keyword_2' 'add_keyword_3' 'add_keyword_4'

Background/Introduction

Single Nucleotide Polymorphisms (SNPs) affecting phenotype are frequently found in the CIS regulatory factors of a gene. However current prediction tools ignore positional data and thus over estimate the co-expression of genes. In order to reduce this error, this work intends to produce a method of correlating quantitative trait loci (QTLs) simultaneously to their CIS element and the expressed phenotype.

To decipher the cryptic code in this non-coding DNA autoassociative neural network tools and multidimensional self-organising maps (Kohenen maps) are being used.

Preliminary work produced a tool using a 2 dimensional Kohenen map has produced some promising results. This work aims to further improve the prediction rate by increasing the dimensions used in the self-organising map so more positional data is incorporated.

Once an effective prediction tool has been developed it will be trained using existing genomic data from Arabidopsis pollen and its effectiveness assessed.

Once trained the prediction tool can then be used on novel data and the predictions, if not available in published literature can be tested in vitro using Transcript and Locus profiling techniques within the university.

The ultimate aim being to use the prediction tool on regions of the rice genome mapped for high density heterosis QTLs to predicted co-regulated genes. Then using in-house genomics techniques meaningful biological information may be assigned to the co-expression.

Results

Results are currently being analysed.

Images/Tables

n/a at present.

Materials/Methods

All work computer based. Scripts have been written in Perl, Kohenon map has been written in LabView and will be translated to Java.

Conclusion

References

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