Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks.
BACKGROUND
Genes and proteins are organized into functional modular networks in which the network context of a gene or protein has implications for cellular function. Highly connected hub proteins, largely responsible for maintaining network connectivity, have been found to be much more likely to be essential for yeast survival.


RESULTS
Here we investigate the properties of weighted gene co-expression networks formed from multiple microarray datasets. The constructed networks approximate scale-free topology, but this is not universal across all datasets. We show strong positive correlations between gene connectivity within the whole network and gene essentiality as well as gene sequence conservation. We demonstrate the preservation of a modular structure of the networks formed, and demonstrate that, within some of these modules, it is possible to observe a strong correlation between connectivity and essentiality or between connectivity and conservation within the modules particularly within modules containing larger numbers of essential genes.


CONCLUSIONS
Application of these techniques can allow a finer scale prediction of relative gene importance for a particular process within a group of similarly expressed genes.
Carlson
Marc R J
MR
Gonda (Goldschmied) Neuroscience and Genetics Research Center, Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095-7088, USA. mrjcarlson@mednet.ucla.edu
Zhang
Bin
B
Fang
Zixing
Z
Mischel
Paul S
PS
Horvath
Steve
S
Nelson
Stanley F
SF
D001483:Base Sequence; D002453:Cell Cycle / Q000235:genetics; D017124:Conserved Sequence; D004249:DNA Damage; D004271:DNA, Fungal / Q000737:chemistry; D005656:Fungal Proteins / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D023281:Genomics; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D012440:Saccharomyces / Q000235:genetics* / Q000378:metabolism
D004271:DNA, Fungal; D005656:Fungal Proteins