Unifying measures of gene function and evolution Export

@article{citeulike:672193, abstract = {Recent genome analyses revealed intriguing correlations between variables characterizing the functioning of a gene, such as expression level (EL), connectivity of genetic and protein–protein interaction networks, and knockout effect, and variables describing gene evolution, such as sequence evolution rate (ER) and propensity for gene loss. Typically, variables within each of these classes are positively correlated, e.g. products of highly expressed genes also have a propensity to be involved in many protein–protein interactions, whereas variables between classes are negatively correlated, e.g. highly expressed genes, on average, evolve slower than weakly expressed genes. Here, we describe principal component (PC) analysis of seven genome-related variables and propose biological interpretations for the first three PCs. The first PC reflects a gene's 'importance', or the 'status' of a gene in the genomic community, with positive contributions from knockout lethality, EL, number of protein–protein interaction partners and the number of paralogues, and negative contributions from sequence ER and gene loss propensity. The next two PCs define a plane that seems to reflect the functional and evolutionary plasticity of a gene. Specifically, PC2 can be interpreted as a gene's 'adaptability' whereby genes with high adaptability readily duplicate, have many genetic interaction partners and tend to be non-essential. PC3 also might reflect the role of a gene in organismal adaptation albeit with a negative rather than a positive contribution of genetic interactions; we provisionally designate this PC 'reactivity'. The interpretation of PC2 and PC3 as measures of a gene's plasticity is compatible with the observation that genes with high values of these PCs tend to be expressed in a condition- or tissue-specific manner. Functional classes of genes substantially vary in status, adaptability and reactivity, with the highest status characteristic of the translation system and cytoskeletal proteins, highest adaptability seen in cellular processes and signalling genes, and top reactivity characteristic of metabolic enzymes.}, author = {Wolf, Yuri and Carmel, Liran and Koonin, Eugene V.}, citeulike-article-id = {672193}, citeulike-linkout-0 = {http://www.journals.royalsoc.ac.uk/(1s4thz45413rms550kxn2krx)/app/home/contribution.asp?referrer=parent&backto=issue,11,20;journal,2,223;linkingpublicationresults,1:102024,1}, citeulike-linkout-1 = {http://dx.doi.org/10.1098/rspb.2006.3472}, doi = {10.1098/rspb.2006.3472}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {evolution-gene, gene-expression, gene\_function}, pages = {1507--1515}, posted-at = {2006-05-27 20:19:19}, priority = {2}, title = {Unifying measures of gene function and evolution}, url = {http://dx.doi.org/10.1098/rspb.2006.3472}, volume = {273}, year = {2006} }

TY - JOUR ID - citeulike:672193 L3 - citeulike-article-id:672193 N2 - Recent genome analyses revealed intriguing correlations between variables characterizing the functioning of a gene, such as expression level (EL), connectivity of genetic and protein–protein interaction networks, and knockout effect, and variables describing gene evolution, such as sequence evolution rate (ER) and propensity for gene loss. Typically, variables within each of these classes are positively correlated, e.g. products of highly expressed genes also have a propensity to be involved in many protein–protein interactions, whereas variables between classes are negatively correlated, e.g. highly expressed genes, on average, evolve slower than weakly expressed genes. Here, we describe principal component (PC) analysis of seven genome-related variables and propose biological interpretations for the first three PCs. The first PC reflects a gene's ‘importance’, or the ‘status’ of a gene in the genomic community, with positive contributions from knockout lethality, EL, number of protein–protein interaction partners and the number of paralogues, and negative contributions from sequence ER and gene loss propensity. The next two PCs define a plane that seems to reflect the functional and evolutionary plasticity of a gene. Specifically, PC2 can be interpreted as a gene's ‘adaptability’ whereby genes with high adaptability readily duplicate, have many genetic interaction partners and tend to be non-essential. PC3 also might reflect the role of a gene in organismal adaptation albeit with a negative rather than a positive contribution of genetic interactions; we provisionally designate this PC ‘reactivity’. The interpretation of PC2 and PC3 as measures of a gene's plasticity is compatible with the observation that genes with high values of these PCs tend to be expressed in a condition- or tissue-specific manner. Functional classes of genes substantially vary in status, adaptability and reactivity, with the highest status characteristic of the translation system and cytoskeletal proteins, highest adaptability seen in cellular processes and signalling genes, and top reactivity characteristic of metabolic enzymes. JF - Proceedings of the Royal Society B: Biological Sciences EP - 1515 TI - Unifying measures of gene function and evolution VL - 273 SP - 1507 KW - evolution-gene KW - gene-expression KW - gene_function AU - Wolf, Yuri AU - Carmel, Liran AU - Koonin, Eugene PY - 2006/// UR - http://dx.doi.org/10.1098/rspb.2006.3472 ER -