This web page was produced as an assignment for an undergraduate course at Davidson College
Expression of ASP3-4 and YLR161W
On this web page, I will analyze microarray data to determine the expression patterns for my annotated (ASP3-4) and non-annotated (YLR161W) yeast genes. Microarrays show the amount of transcription of genes in an organism's genome (which genes are turned on/off). In microarray experiments, the target organism is subjected to a certain environmental condition in order to determine the expression pattern for certain genes in this condition. Through analysis of the microarrays, one can determine which genes are regulated in the same way, and thus have similar or redundant functions. If the function of a gene is unknown, one can analyze microarray data and make an educated guess as to the function of the gene through guilt by association. Guilt by association means that if a non-annotated gene is regulated in a similar fashion compared to a group of annotated genes, then it has a similar function to the annotated genes. I will try to make a prediction of the function of my non-annotated gene through guilt by association. For a review of the function and predicted function for ASP3-4 and YLR161W, respectively, go here .
Fig.1- The scale used to show the amount of expression determined by microarrays. Image used courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl
ASP3-4 Expression in Varying Environmental Conditions
In this experiment, several generations of yeast were cultivated to determine the genes transcribed when glucose is limited. ASP3-4 was repressed throughout this experiment (Fig. 2).
Fig. 2- ASP3-4 expression pattern during glucose limitation and 20 genes with similar expression patterns. Image used courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YLR160C&dataset=evolution&type=similar
Along with being repressed during this experiment, the genes associated with ASP3-4's expression pattern either have no data (grey portion of scale) or are not transcribed (black portion) according to their expression pattern scale. Also, there is no apparent association with regards to function or cellular component between ASP3-4 and the gene's with similar expresion patterns. Overall finding from this experiment with regards to ASP3-4: this gene is repressed during glucose limitation. For what reason is it repressed? ASP3-4 is involved in breaking down Asparagine for nitrogen and is only needed in times of nitrogen starvation.
Sporulation refers to the production of haploid cells through meiosis and morphogenesis. ASP3-4 shows some induction at the beginning of this process, but is repressed for the majority of the rest of the process.
Fig. 3- The expression pattern for ASP3-4 and 20 genes with similar patterns. Image used courrtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YLR160C&dataset=sporulation&type=similar
Fig. 4- Expression graph for ASP3-4 during sporulation. Image used courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?id=23621&dataset=sporulation&type=graph
From Fig. 3 and 4, one can see that ASP3-4 is only induced at the very beginning of sporulation and is repressed for the majority of the process. From this data one can conclude that ASP3-4 has no significant role in sporulation. The genes with similar regulation patterns are not closely related to the function or cellular component of ASP3-4, so no significant conclusions can be drawn from this data either.
The diauxic shift refers to yeast's switch from the process of anaerobic fermentation (conversion of glucose to ethanol) to aerobic respiration (conversion of ethanol into energy). Because this is a major switch in metabolic pathways, several genes are turned on/off during this process.
Fig. 5- Expression pattern for ASP3-4 during diauxic shift and 20 genes with similar expression patterns. Image used courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YLR160C&dataset=diauxic&type=similar
Fig. 6- A graph of the expression pattern for ASP3-4 during the diauxic shift. Image courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?id=23621&dataset=diauxic&type=graph
ASP3-4 is induced in the diauxic shift most notably around the 12th and 19th hours of the shift. The GO term finder is a function that takes the clustered genes and determines if the terms used to describe the biological process, molecular function, or cellular component are statistically significant when compared to the entire genome (meaning: the similar biological process found among the clustered genes is found in only a specific amount of genes found in the genome, which means these genes are regulated in a similar way for a specific purpose during the diauxic shift).
Fig. 7- GO term finder results for the clustered genes' biological process. P-values relate to the significance of biological process term as compared to the entire yeast genome. A lower p-value means greater significance. Image used courtesy: http://db.yeastgenome.org/cgi-bin/GO/goTermFinder
Figure 7 shows that the genes clustered together with similar expression patterns are also involved in similar biological processes. These data show that ASP3-4 is regulated along with several other genes with a similar biological process in the later stages of the diauxic shift.
Response to Alpha-Factor:
ASP3-4 has no involvement in alpha- factor response, which is related to cell cycling and phereomone production.
Fig. 8- Expression pattern for ASP3-4 in respone to alpha-factor. Image used courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?dataset=alpha_time&id=23621&type=enlarge&expts=7
Response to various environmental conditions:
The most notable section is this expression pattern is the section with nitrogen depletion over time and during the stationary phase. The known function of ASP3-4 is further confirmed by this expression pattern as ASP3-4 is heavily induced during nitrogen depletion.
Fig. 9- Section of expression pattern in which ASP3-4 is most heavily induced. Image used courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?dataset=stressResponse&id=23621&type=enlarge&expts=174
This further confirms ASP3-4's role as a response to environments without an adequate nitrogen supply.
Predicted Function of YLR161W through Microarray Analysis:
The only two experiments that gave siginificant expression pattern data for YLR161W were the experiments involved with the unfolded protein response and the response to alpha-factor over time.
Unfolded Protein Response:
This experiment looked at gene expression in response to stress on the endoplasmic reticulum. When there is an accumulation of unfolded proteins in a cell, the cell must upregulate certain genes to deal with these unfolded protiens and start folding the proteins in a correct fashion.
Fig. 10- The expression pattern for YLR161W along with 20 other genes with similar expression patterns in respone to unfolded proteins. Image used courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?orf=YLR161W&dataset=unfolded_protein_response&type=similar
The expression pattern shows that YLR161W is induced in response to a certain type of unfolded protein but not all types used in the experiment. The GO term finder function produces this table, which helps shine some light on YLR161W's biological process.
Fig. 11- GO term finder for biological process for genes clustered with YLR161W. Image used courtesy: http://db.yeastgenome.org/cgi-bin/GO/goTermFinder
From figure 11 one can make the prediction that YLR161W is involved with protein glycosylation, biosynthesis, or metabolism.
Response to alpha-factor:
YLR161W was repressed throughout this experiment. Looking at the GO term finder shows that YLR161W may be involved in the cell cycle and cell proliferation.
Fig. 12- The GO term finder results for the alpha-response for YLR161W and the genes it's clustered with. Image used courtesy: http://db.yeastgenome.org/cgi-bin/GO/goTermFinder
Response to various environments:
One section of the expression pattern shows a resmblance to ASP3-4.
Fig. 13- Part of the expression pattern for various environmental conditions including nitrogen depletion for YLR161W. Image used courtesy: http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl?dataset=stressResponse&id=2889&type=enlarge&expts=174
Through guilt by association, YLR161W appears to be involved in either protein regulation, the cell cycle, and/ or response to nitrogen depletion.
1) Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I (1998) The transcriptional program of sporulation in budding yeast. Science
2) DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278(5338):680-6
3) Dolinski, K. et. al. (2003). Saccharomyces Genome Database. <http://www.yeastgenome.org/> Accessed 2004 21 Oct.
4)Ferea TL, Botstein D, Brown PO, Rosenzweig RF (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl
Acad Sci U S A 96(17):9721-6
5)Gene Ontology Software Group. 2003. Gene Ontology Database.<http://www.godatabase.org/dev/database/> Accessed 2004 21 Oct.
6) Travers KJ, Patil CK, Wodicka L, Lockhart DJ, Weissman JS, Walter P (2000) Functional and genomic analyses reveal an essential coordination between
the unfolded protein response and ER-associated degradation. Cell 101(3):249-58
Questions or comments? email me: firstname.lastname@example.org
Genomics Home Page
Davidson College Home Page
John Bunton's Genomics Home Page