Paper: Unifying measures of gene function and evolution

Proceedings of the Royal Society B: Biological Sciences
ISSN: 0962-8452 (Paper) 1471-2954 (Online)
Issue: Volume 273, Number 1593 / June 22, 2006

Pages: 1507 - 1515
DOI: 10.1098/rspb.2006.3472

Unifying measures of gene function and evolution

Yuri I. Wolf, Liran Carmel, Eugene V. Koonin

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.

Abstract and Full Text Links at The Royal Society
http://tinyurl.com/j8x65

Posted by
Robert Karl Stonjek


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