Topic Name Description
Topic 1 File An Overview of Functional Genomic Data
File Data Integration: An Example Using GenePattern
In this short demonstration, we will use the GenePattern server {Reich, 2006} on a set of yeast data mapped to human orthologs to detect enriched gene sets using GSEA {Subramanian, 2003}. We will also obtain inter-species orthology mappings from InParanoid {Berglund, 2008} and gene identifier mappings from BioMart {Haider, 2009}.
File Genomic Data Resources
File A Quick Guide to Large Scale Genomic Data Mining
With almost every type of biological data accumulating at an exponential rate, large scale genomic data mining is increasingly becoming a necessity. For computational investigators, this represents a clear opportunity for methodology development; since data are becoming available at a rate that outpaces even Moore's law, it is not enough to wait for faster computers to execute longer and longer queries, and new bioinformatic tools must be developed with an eye to scalability and efficiency (e.g. through massive parallization). However, the opportunity for biological investigation is at least as large. Nature has already harnessed scalability to her own advantage, and the combinatorics of the genetic code, multimodal and combinatorial regulation, cellular differentiation, and temporal development ensure that even our current wealth of data provides an incomplete view of biological complexity. A simple justification for broad-ranging computational screens of genomic data is their speed and low cost as a precursor to more extensive laboratory work. An even more compelling motivation, though, is the fact that the extent and complexity of biological systems may best be discovered by simultaneously considering a wide range of genome-scale data.
File A Quick Guide to Large Scale Genomic Data Mining:
An example using multiple genome-scale data repositories to determine potential kinase-target interactions active during the S. cerevisiae cell cycle.
File Data Integration: An Example Using GenePattern (Results)
Folder Papers
Topic 2 File How to Understand the Cell by Breaking It
File How to Understand the Cell by Breaking It
File How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens
Functional genomics has demonstrated considerable success in inferring the inner working of a cell through analysis of its response to various perturbations. In recent years several technological advances have pushed gene perturbation screens to the forefront of functional genomics. Most importantly, modern technologies make it possible to probe gene function on a genome-wide scale in many model organisms and human. For example, large collections of knock-out mutants play a prominent role in the study of Saccharomyces cerevisiae, and RNA interference (RNAi) has become a widely used high-throughput method to knock-down target genes in a wide range of organisms, including Drosophila melanogaster, Caenorhabditis elegans, and human.