Team:Alberta/Project/Gene Selection
From 2009.igem.org
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Literature ReviewThere were four primary literature sources which were used for the determination of the essential genome. These genes were analyzed to construct a preliminary essential gene list
Each gene list was determined in a variety of ways and there results show very little consistency. The number of genes from each source varies greatly. When the lists are compared to one another, there is very little overlap noted. Please see below: Venn Diagram of the Number of Essential Genes Shared Between Lists in the LiteratureThe maximum number of genes in common between any two literature lists is 205, which is between Baba et al 2006 and Gerdes et al 2003. Only 48 genes were present in all four lists. The lack of consensus between these literature lists makes it very unreliable to use these genes in an essential genome. Still, these lists provide an important foundation for basic components that are required in an essential genome list. |
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Constructing the BioBytes Preliminary Essential Gene ListThe preliminary essential gene list is based on literature sources. As described in the modeling section of this wiki, the metabolic genes from this preliminary list were used as a starting point for the computer model and were greatly altered based on the model's suggestions. The following criteria were used for selecting genes from a literature source: Criteria for Gene Selection
The basic functional groups of genes which were selected can be seen in the next chart and a detailed list of processes which were included follow.
Genes for the following processes were included:
RNAs:The rrnC operon supplies all the rRNA’s and three of the tRNAs. This operon was selected because it includes the great number of tRNA’s. To select the other tRNA’s, all tRNA’s listed as essential in PEC were first included. One tRNA was then selected for each anticodon that differed on one of the last two bases. Differences in the first base can be accommodated by anticodon 'wobble'. At least one tRNA was included for each amino acid. The complete list of essential RNA’s can be found here . |
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Statistics on BioBytes Preliminary Essential Gene ListTotal genes in Ecoli: 4762 Total protein coding genes in BioBytes preliminary essentials list: 332 Total number of RNA genes in BioBytes preliminary essentials list: 29 |
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BioBytes Final Essential Gene List
A final list of essential genes was produced from the literature review and the computer model.
Number of genes in list created from literature: 332 Number of additional genes suggested by model: 116 Number of genes in final essential genes list: 448 Number of genes in our essential gene list not classified as essential in the literature: 117 |