The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties

By Nicholas M. Luscombe, J. Qian, Zhaolei Zhang, Ted Johnson, Mark Gerstein. 2002

130 citations recorded by the source corpus.

BackgroundThe sequencing of genomes provides us with an inventory of the 'molecular parts' in nature, such as protein families and folds, and their functions in living organisms. Through the analysis of such inventories, it has been shown that different genomes have very different usage of parts; for example, the common folds in the worm are very different from those in Escherichia coli.ResultsDespite these differences, we find that the genomic occurrence of generalized parts follows a well-known mathematical framework called the power law, with a few parts occurring many times and most occurring only a few times. This observation is true in a wide variety of genomic contexts. Earlier studies found power laws in a few specific cases, such as the occurrence of protein families. Here, we find many further cases of power-law behavior, for example in the occurrence of pseudogenes and in levels of gene expression. We show comprehensively that this behavior applies across many different genomes, for many different types of parts (DNA words, InterPro families, protein superfamilies and folds, pseudogene families and pseudomotifs), and for the many disparate attributes associated with these parts (their functions, interactions and expression levels).ConclusionsPower-law behavior provides a concise mathematical description of an important biological feature: the sheer dominance of a few members over the overall population. We present this behavior in a unified framework and propose that all these observations are connected to an underlying DNA duplication process as genomes evolved to their current state.

Subfields: Genetics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches (2014, background): “Malde and Furmanek (2013) showed that using UniRef50 as an intermediate database can increase sequence search sensitivity when compared with directly searching the target database.”
Scaling Laws in the Functional Content of Genomes (2003, background): “For instance, it is shown in [13] that the number of genomic occurrences of DNA words, protein folds, superfamilies, and families all follow power-law distributions.”
Identification and distribution of protein families in 120 completed genomes using Gene3D (2005, background): “41 In Pfam there is some deviation from power-law behavior as small families are greatly underrepresented in Pfam.”
Grammar of protein domain architectures (2019, background): “Power-law distributions have been found in numerous natural and social contexts, including a broad variety of biological systems (14 – 16).”
Beyond Gaussian averages: redirecting international business and management research toward extreme events and power laws (2007, background): “…and Podladchikov (1994) Hughes and Nathan (1994); Marsili and Zhang (1996) Hughes et al. (2003) Baryshev and Teerikorpi (2002) Selvam (2002) Luscombe et al. (2002) Barabási (2002) Song et al. (2005); Wuchty and Almaas (2005) West et al. (1997) Wax et al. (2002) Roberts (1979) West et al.…”
The structure of the protein universe and genome evolution (2002, background): “and subsequently in detailed studies by Gerstein and colleague”
Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins (2017, background): “A power-law distribution is widely found in genomics 44, 46 and it has been successfully explained by simple generative models 41, 44 , which indicate that a larger community is generally older than a smaller one.”