Genome analyses genomics

M Schena, D Shalon, R Heller, A Chai, PO Brown, RW Davis. Parallel human genome analysis Microairay-based expression monitoring of 1000 genes. Pi oc Natl Acad Sci USA 93 10614-10619, 1996. 

D Shalon, SJ Smith, PO Brown. A DNA microairay system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6 639-645, 1996. MB Eisen, PT Spellman, PO Brown, D Botstem. Cluster analysis and display of genomewide expression patterns. Proc Natl Acad Sci USA 95 14863-14868, 1998. 

MQ Zhang. Large-scale gene expression data analysis A new challenge to computational biologists. Genome Res 9 681-688, 1999. 

Koonin, E. V., et al., 1996. Sequencing and analysis of bacterial genomes. Current Biology 6 404-416. 

Combined analysis of structural and genomic data will certainly get more importance in the near future. Protein folds can be analysed for whole genomes. 

Fredriksson R, Lagerstrom MC, Lundin LG et al (2003) The G-protein-coupled receptors in Hie human genome form five main families. Phylogenetic analysis, paralo-gon groups, and fingerprints. Mol Pharmacol 63 1256-1272... 

Histone Deacetylases (HDACs) catalyze the removal of the acetyl groups from lysines (see Fig. 1). Together with the HATs they are responsible for maintaining the level of histone acetylation throughout the genome. The family of HDAC proteins has been divided into four classes based on phylogenetic analysis and sequence comparison. HDACs of the classes I and II share the same Zn2+-based reaction and are evolutionary related. Class IV HDACs also possess a Zn2+-based reaction... 

Bjarnadottir TK, Gloriam DE, Hellstrand SH et al (2006) Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse. Genomics 88 263-273... 

Structural genomics aims to use high-throughput structure determination and computational analysis to provide structures and/or 3D-models of every tractable protein. The intention is to determine as many protein structures as possible and to exploit the solved structures for the assignment of biological function to hypothetical proteins. 

Classical global knockouts may have a developmental or lethal phenotype and thus preclude the analysis of the phenotypic consequences of the lack of a gene in specific tissues in adult animals. With the development of the cre/loxP and flp/FRT systems, it has become possible to excise defined DNA fragments from the genome of specified cells. Cre and Flp are bacterial and yeast recombinases, respectively, which recognize loxP and FRT sequences, respectively. The most common... 

---