Gene Regulation (Informatics)

The Genome Sciences Centre is developing bioinformatic approaches for the derivation of cis-regulatory elements in mammalian genomes. We are developing methodologies to combine comparative genomic data, gene expression data and existing algorithmic approaches. We have developed an software platform, Sockeye, which provides access to comparative genomic analysis tools , gene expression data and a number of existing cis-regulatory element detection tools. We are also working with the Encode consortium to refine methods in the 1% of the human being studied by this project.

This project is funded by Genome Canada.

Sockeye

This is a 3D genomic viewer which data viewer is being developed in Java for the Bioinformatics of Mammalian Gene Expression project. This uses the Ensembl database to provide genomic information and provide a platform to perform and visualise a number of bioinformatic analyses, focussing on cis-regulatory element detection. More information on this application is available on the Sockeye page.

Chinook

This is a peer-to-peer bioinformatics platform. The goal of the Chinook is to facilitate exchange of analysis techniques within a local community and/or worldwide. Chinook has been developed to support the algorithmic and CPU requirements of the Sockeye application. Allowing tasks to be distributed easily locally, eg. across a compute cluster or between remote servers anywhere in the world. More information is available on the Chinook page.

Human Expression Resources

To provide easily available resources for the determination of co-expressed genes, the Genome Sciences Centre has begun collecting publicly available data for large-scale global co-expression analyses. Oligonucleotide probe intensities, cDNA microarray hybridization ratios, or SAGE tag counts are used to calculate expression similarity metrics (e.g. Pearson Correlation) between each gene. More information is available here.