*This website was created as an assignment for an undergraduate course*
Expression profile for TKL1: I investigaged the expression profile of TKL1, an yeast geen known to produce transketolase protein 1 which is involved in the phophate pentose patheway. For more information on TKL1 please see my previous web assignment.
To begin this investigation I went to Expression Connection. This website searches "gene expression data from multiple microarray studies." Using this website I searched each study for the TKL1 gene. I found TKL1 in a number of microarray studies that can be seen below.
figure 1. This is the scale used in the expression connection microarray studies. This scale shows the relative induction or repression that which correlates to particular colors.
Diauxic Shift:
The first study I looked at examined TKL1 expression during the diauxic shift. To see the abstract of the paper associated with this study click here.
Figure 2: 20 genes with similar expression profiles to TKL1 in the diauxic shift response. (http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl?orf=YPR074C&dataset=diauxic&type=similar).
TLK1 is involed in transketolase activity and its process is in the pentose-phosphate shunt. The pentose phosphate pathway is used in tissues which tissues actively synthesizing fatty acids and steroids. This pathway is also used in the biosynthesis of nucleic acids and the generation of pentoses (Nelson et al 2003). Many of the associated genes appear to be involved in protein biosynthesis and glycolysis. These genes' function correlate with the pentose-phosphate pathway and follow the guilt by association inference.
DNA Damage: The microarray response in TKL1 associated with 8 genes when DNA damage expression profiles were observed. To see the abstract of the DNA damage paper click here.
figure 3: 8 genes associated with similar expression profiles as TKL1 when exposed to DNA damage. (http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl?orf=YPR074C&dataset=DNAdamage&type=similar)
The data presented in this figure again shows a correlation between the expression patterns of TKl1 and other genes involved in metabolism and anabolism. For the majority of these DNA damage situations TKL1 is repressed inidicating a reduction in biosyntheis when DNA is damaged.
Environmental Conditions: Finaly I examined TKL1's expression response to many environmental conditions. In order to see the abstarct associated with this study please click here.
Figure 4: This data is an selection from the environmental conditions microarray study. In this figure only the expression profiles and gene ontology profiles from genes associated with TKl1 under heat shock conditions are shown. (http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl?orf=YPR074C&dataset=stressResponse&type=similar).
Under heat shock conditions TKL1 is represed between ten and forty minutes. It then begins to return to a normal expression ratio. The other genes shown in figure 4 are also repressed under heat shock conditions. Many of these genes are repressed at the greatest levels between 10 and forty minutes and then begin to decrease their repression levels. Like the previous two studies TKL1 expression profile for heat shock associates with protiens involved in metabolism and biosynthesis.
Conclusion:
Micorarray data can be used to verify a suggested biological function for a gene. Guilt by association is a theory that uses microarray data to hypothesize a gene's function. Guilt by association groups genes that are repressed and induced similarly under the same conditions and hypotheszies that these genes will have similar functions. Following this theory the TKL1 gene appears to be involved in biosynthesis and metabolism. In the three studies examined TKL1 had correlations to genes involved in biosynthesis and metabolism. This micorarray data supports the hypothesize that TKL1 encode transketolase-1 which is involved in the pentose phosphate shunt.
References:
Nelson D.L. and M.M. Cox. 2003 Lehninger Principles of Biochemistry third edition. Worth Publishers.
Expression Connection 2003. http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl