This webpage was produced as an assignment for an undergraduate course at Davidson College.

 

EXPLORING GENE EXPRESSION OF MY FAVORITE YEAST ORFs, CDC28 and YBR161W, WITH DNA MIRCOARRAYS

 

 

CDC28.

 

       I saw previously that CDC28 is a cyclin-dependent kinase essential to the proliferation of Saccharomyces cerevisiae cells; this protein controls the essential process of yeast cells ‘deciding’ to replicate their DNA and enter mitosis.  I explored the expression patterns of CDC28 under different experimental conditions using the public database SGD Expression Connection (SGD, 2001; http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl). 

 

I found microarray data for the following conditions:

 

 

While there was a great deal of information to be found in the database results, I decided to focus my analysis on the experiments that pertained to the function of my gene.

 

I.  Expression at Different Alpha-Factor Concentrations.

 

     Alpha-factor is a pheromone that arrests yeast’s cell cycle in the G1 phase and induces genes necessary for mating (Zymo Research, 2001; http://www.zymor.com/y1001-frame.html).  In the life cycle of yeast, cells alternately undergo sexual and asexual reproduction; i.e., they alternate beteween meiosis and mitosis depending on environmental factors and subsequent gene expression.

 

Figure 1. The life cycle of yeast.  Yeast cells alternate between budding and mating, as well as mitosis and meiosis.  (With permission from Tom Manney, http://www.phys.ksu.edu/gene/Mating4.html).

 

If CDC28 is indeed responsible for controlling mitosis in budding yeast, it makes sense that this protein would be repressed as higher concentrations of  alpha pheromone trigger cells to arrest G1 phase and any subsequent mitotic division, and undergo meiosis.  The DNA microarray data supports this:

 

Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR160W

 

CDC28

 

 

protein amino acid phosphorylation*

 

cyclin-dependent protein kinase

 

cytoplasm

YOR372C

 

NDD1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YMR120C

 

ADE17

 

 

`de novo` IMP biosynthesis

 

IMP cyclohydrolase*

 

cytosol

YPL255W

 

BBP1

 

 

microtubule nucleation

 

structural protein of cytoskeleton

 

spindle pole body

YBR037C

 

SCO1

 

 

 

protein complex assembly*

 

molecular_function unknown

 

mitochondrial inner membrane

YOR373W

 

NUD1

 

 

 

microtubule nucleation

 

structural protein of cytoskeleton

 

spindle pole body

YNL030W

 

HHF2

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YBL002W

 

HTB2

 

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YBR010W

 

HHT1

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YJL092W

 

HPR5

 

 

DNA repair

 

DNA helicase

 

nucleus

YGR140W

 

CBF2

 

 

mitosis

 

not yet annotated

 

not yet annotated

YKR037C

 

SPC34

 

 

microtubule nucleation

 

structural protein of cytoskeleton

 

spindle pole body

YLR233C

 

EST1

 

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YNR009W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR307W

 

GAS1

 

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YBL003C

 

HTA2

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YDR225W

 

HTA1

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YBR009C

 

HHF1

 

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YDR224C

 

HTB1

 

 

chromatin assembly/disassembly

 

DNA binding

 

nucleosome

YNL031C

 

HHT2

 

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YLL002W

 

REM50

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated


* : indicates that more than one annotation exists for the gene.

 

Figure 2. Clustered data for expression at different alpha-factor concentrations. (SGD, 2001).

 

Figure 3.  Expression changes in CDC28 at different alpha-factor concentrations.  CDC28 is repressed to a nearly constant value relative to the control (SGD, 2001).

 

          While CDC28 does not follow a linear pattern, it is repressed at different alpha-factor concentrations.  It is clustered with other genes that are highly repressed as alpha-factor concentration increases.  Many of these genes are non-annotated, but a few are structural proteins in the cytoskeleton.  This makes intuitive sense in that as the cells arrest mitosis and begin sexual reproduction, they do not need to form new cytoskeletons, and these structural genes should be repressed.  Interestingly, while CDC28 is a cytoplasmic protein, many of the genes that are co-regulated with it reside in various locations within the cell, such as the mitochondrial inner membrane and the nucleosome.  CDC28 is repressed to a nearly constant value and does not change with increasing concentrations of alpha-factor; once the signal is turned off, it stays off and does not fluctuate with increasing signal.

 

II.                Expression in Response to Alpha-Factor.

 

In this experimental condition, CDC28 is exposed to alpha-factor and its response is monitored over time.

 

Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR160W

 

CDC28

 

 

protein amino acid phosphorylation*

 

cyclin-dependent protein kinase

 

cytoplasm

YER177W

 

BMH1

 

 

pseudohyphal growth*

 

not yet annotated

 

not yet annotated

YLR463C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR090C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YFL068W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR219W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR102W

 

KIC1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YDR545W

 

YRF1-1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YAR002AC

 

 

 

 

 

 

 

 

 

YBR112C

 

CYC8

 

 

transcription

 

not yet annotated

 

not yet annotated

YPL230W

 

USV1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR467W

 

YRF1-5

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YCR093W

 

CDC39

 

 

 

cell cycle control*

 

molecular_function unknown

 

nucleus

YPR153W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YER189W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YCR050C

 

 

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YNL014W

 

HEF3

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR245C

 

CDD1

 

 

cytidine catabolism*

 

cytidine deaminase

 

cellular_component unknown

YLR437C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR177C

 

EHT1

 

 

lipid metabolism

 

molecular_function unknown

 

lipid particle

YJL019W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated


* : indicates that more than one annotation exists for the gene.
 

 

Figure 4.  Clustered data for CDC28 expression when exposed to alpha-factor over time (SGD, 2001). 

 

 

 

Figure 5.  CDC28 expression changes when exposed to alpha-factor over time (SGD, 2001). 

 

          The microarray data indicate that initially, CDC28 is repressed and then at the end of the time points taken, it is induced.  The genes CDC28 are clustered with exhibit similar expression profiles.  Most of these genes have unknown functions and are not yet annotated.  The genes that are annotated, however, play roles in essential cell cycling functions such as transcription and lipid metabolism.  These expression changes may be indicative of the trend that when initially exposed to alpha-factor, CDC28 is repressed for reasons explained above.  As time passes however, the cell may have completed meiosis and is ready to enter the cell cycle of mitosis and interphase again, and consequently CDC28 is induced. 

 

 

III.             Expression During the Cell Cycle.

 

This experiment attempted to catalog the different genes associated with the cell cycle.  The authors analyzed yeast cells under three different conditions: alpha-factor arrest, elutriation, and arrest of a CDC15 temperature-sensitive mutant.  They found 800 genes with significantly altered transcription levels over the course of the cell cycle.  More than half of these 800 genes responded to one or both of two important cyclins, CLN3 and CLB2, which are known to interact with CDC28 (Spellman et al., 1998; http://www.molbiolcell.org/cgi/content/full/9/12/3273).  

          The authors picked reference genes representative of each of the phases of the cell cycle: G1, S, G2 and mitosis.  These genes show a diagonal clustering; that is, they alternate with each other through each phase of the cell cycle, so the red and green stripes are diagonals leaning to the right across the page:

 

Name

Score

Peak

CDC28

0.66

 

Reference Genes

 

CLN2

10.9

G1

HTA1

10.68

S

CLB4

3.08

G2

SWI5

6.726

M

ASH1

11.8

M/G1

 

 

 

 

Plot of CDC28 (YBR160W)

 

Figure 6. Comparison of CDC28 expression to that of reference genes from each phase of the cell cycle.  Peaks and valleys in the graph indicate individual cycles of the cell (SGD, 2001).

 

          By reading across each row and comparing how each of the reference genes is expressed with how CDC28 is expressed, CDC28 expresses similarly to CLN2 and HTA1; these genes are co-regulated so they each induce and repress at the same time.  CDC28 is expressed inversely to ASH1; when CDC28 is induced, ASH1 is repressed and vice versa.  CLB4 and SWI5 don’t seem to co-regulate with CDC28; the colors were too close to black, i.e. with ratios too close to 1, to make out appreciable differences.

These statements are approximations; CDC28 was not largely induced or repressed for any of these experimental conditions.  This may be due to the fact that since CDC28 is such an important protein in the signaling process of cell cycling, only slight changes in its induction and repression cause significant changes in many other proteins in a complex cascade.  Hence, it is not necessary for CDC28 to be largely induced or repressed when so many other proteins depend on it for activation and deactivation.

 

IV. Expression During Sporulation.

          This experiment measured gene expression during sporulation.  Given that yeast produce spores by undergoing meiotic division, we would expect the data to be similar to that of II above. 

 

Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR160W

 

CDC28

 

 

protein amino acid phosphorylation*

 

cyclin-dependent protein kinase

 

cytoplasm

YOR340C

 

RPA43

 

 

transcription, from Pol I promoter

 

DNA-directed RNA polymerase I

 

DNA-directed RNA polymerase I

YJL094C

 

KHA1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL158W

 

APE2

 

 

peptide metabolism

 

leucyl aminopeptidase

 

cytoplasm*

YML116W

 

ATR1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YDR485C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL201W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR064W

 

RPS13

 

 

protein biosynthesis

 

structural protein of ribosome

 

cytosolic small ribosomal (40S) subunit

YML117W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR062C

 

BUD28

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown

YMR157C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR121C

 

RPL15B

 

 

protein biosynthesis

 

structural protein of ribosome*

 

cytosolic large ribosomal (60S) subunit

YBR182C

 

SMP1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YLR061W

 

RPL22A

 

 

protein biosynthesis

 

structural protein of ribosome

 

cytosolic large ribosomal (60S) subunit

YDL031W

 

DBP10

 

 

35S primary transcript processing*

 

ATP dependent RNA helicase

 

nucleolus

YLR342W

 

FKS1

 

 

cell wall organization and biogenesis*

 

1,3-beta-glucan synthase

 

actin cap (sensu Saccharomyces)*

YDL061C

 

RPS29B

 

 

protein biosynthesis

 

structural protein of ribosome

 

cytosolic small ribosomal (40S) subunit

YJL096W

 

MRPL49

 

 

protein biosynthesis

 

structural protein of ribosome

 

mitochondrial large ribosomal subunit

YOR147W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL044C

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL079C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated


* : indicates that more than one annotation exists for the gene.

 

Figure 7.  Microarray data for sporulation over time.  Notice similarities to data from exposure to alpha-factor over time above. 

 

 

Figure 8. Response of CDC28 to sporulation over time.  Note similarity to Figure 5 (SGD, 2001).

 

          This experiment was similar to a previous experiment monitoring gene response to alpha-factor over time in that above, alpha-factor was signaling cells to mate, where here, sporulation entails the yeast cells forming spores necessary for mating.  While CDC28 is regulated similarly as seen in Figure 8, it was interesting to find how many more annotated genes clustered with CDC28 in Figure 7.  Many of these genes are involved with such processes as RNA transcription, peptide metabolism and biosynthesis, as well as cell wall biogenesis.  It appears that many more proteins are worked out in this signaling pathway relative to previous ones.

 

Conclusions.

          For many of the non-annotated genes, because they exhibit similar expression profiles, they may have similar functions to CDC28.  While many were more intensely induced or repressed than my gene, this is expected given that a cell should have very few critical proteins for complex signaling like CDC28. 

 

 

YBR161W.

 

       Previously, I found that YBR161W is an ORF located in close proximity to CDC28 on chromosome II.  Based on sequence similarity, it may be a functional homolog to the yeast gene Sur1, which has been found to play a key role in cell wall formation. 

 

          Again, I searched SGD’s Expression Connection Database, and yielded a great deal of information on the expression profiles of my non-annotated gene.  I focused my analysis on the experiments that gave the most insight into potential functions and processes associated with YBR161W.

 

I.                   Expression at Different Alpha-Factor Concentrations.

 

Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR161W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR110W

 

ERP5

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YLR376C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL066W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL157C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL181W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL224C

 

SDT1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YFR041C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL165C

 

MCD4

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YML101C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAL044C

 

GCV3

 

 

glycine metabolism

 

not yet annotated

 

not yet annotated

YBL031W

 

SHE1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YGR109C

 

CLB6

 

 

G1/S transition of mitotic cell cycle*

 

cyclin

 

cellular_component unknown

YDR133C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR050C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR098W

 

MMS4

 

 

DNA repair

 

transcription co-activator

 

nucleus

YAR007C

 

RFA1

 

 

nucleotide-excision repair*

 

RNA binding*

 

DNA replication factor A complex

YFR027W

 

ECO1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YOL090W

 

MSH2

 

 

DNA repair

 

not yet annotated

 

not yet annotated

YER149C

 

PEA2

 

 

establishment of cell polarity (sensu Saccharomyces)*

 

cytoskeletal regulatory protein binding

 

actin cap (sensu Saccharomyces)*

YMR301C

 

ATM1

 

 

iron homeostasis

 

ATP-binding cassette (ABC) transporter

 

mitochondrial inner membrane


* : indicates that more than one annotation exists for the gene.

 

Figure 9.  Clustering data for YBR161W when exposed to increasing concentrations of alpha-factor (SGD, 2001).

 

 

Figure 10.  Response of YBR161W to increasing alpha-factor concentrations (SGD, 2001).

 

     Interestingly, YBR161W is regulated similarly to CDC28 under this experimental condition.  Also of note, YBR161W clustered with one of the 9 essential cyclins, CLB6, that CDC28 is known to activate and deactivate.  CLB6 is one of the key genes responsible for signaling the end of G1 and the beginning of S phase.  If YBR161W is also involved in the cell’s ‘decision’ to undergo DNA replication, it makes sense that these other genes involved in DNA repair and establishment of cell polarity should be clustered here as well.

 

II.                Expression in Response to Alpha-Factor.

 

Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR161W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR518W

 

EUG1

 

 

not yet annotated

 

protein disulfide isomerase

 

not yet annotated

YFR042W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR025W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR204W

 

 

 

 

biological_process unknown

 

DNA helicase

 

cellular_component unknown

YKR068C

 

BET3

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YDR189W

 

SLY1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YIL026C

 

IRR1

 

 

mitotic sister chromatid cohesion*

 

molecular_function unknown

 

cohesin

YHR007C

 

ERG11

 

 

ergosterol biosynthesis

 

lanosterol 14-alpha-demethylase

 

endoplasmic reticulum

YGL009C

 

LEU1

 

 

not yet annotated

 

3-isopropylmalate dehydratase

 

not yet annotated

YOL003C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR304W

 

ISW2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML012W

 

ERV25

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YDR105C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR047C

 

NUP116

 

 

mRNA-nucleus export*

 

structural protein

 

nuclear pore

YNR016C

 

ACC1

 

 

 

fatty acid biosynthesis*

 

acetyl-CoA carboxylase*

 

cytosol*

YAR003W

 

SWD1

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YER026C

 

CHO1

 

 

phosphatidylserine biosynthesis

 

CDP-diacylglycerol-serine O-phosphatidyltransferase

 

endoplasmic reticulum

YDL102W

 

CDC2

 

 

nucleotide-excision repair*

 

delta DNA polymerase

 

delta DNA polymerase

YOR110W

 

TFC7

 

 

transcription initiation, from Pol III promoter

 

RNA polymerase III transcription factor

 

transcription factor TFIIIC

YPR202W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown


* : indicates that more than one annotation exists for the gene.

 

Figure 11.  Clustering data for YBR161W when exposed to alpha-factor over time (SGD, 2001).

 

 

Figure 12.  Response of YBR161W to alpha-factor over time (SGD, 2001).

 

     Interestingly, here my favorite non-annotated gene is clustering with other genes involved in DNA replication, but intead of repair functions, these genes are involved in a variety of functions such as cohesion of sister chromatids, ergosterol biosynthesis, mRNA-nucleus export, fatty acid biosynthesis, transcription initiation, as well as one gene involved in necleotide-excision repair.  This is not the same gene involved in nucleotide-excision repair from above; that gene was involved in RNA binding, where this gene is a DNA polymerase. There don’t appear to be significant correlations between these 2 experiments except to say that YBR161W has something to do with DNA replication.

 

III.             Expression During the Cell Cycle.

 

Name

Score

Peak

YBR161W

1.851

G1

Reference Genes

 

CLN2

10.9

G1

HTA1

10.68

S

CLB4

3.08

G2

SWI5

6.726

M

ASH1

11.8

M/G1

 

 

 

 

Plot of YBR161W

 

Figure 13.  Comparison of YBR161W to reference genes from each phase of the cell cycle.  Peaks and valleys of the graph indicate a full cycle for the cell.

 

     Interestingly, the reference genes follow a diagonal pattern as before, indicating induction and repression as the cell cycles through the 4 phases of G1, DNA replication, G2 and mitosis.  Readingly across as above, it appears that YBR161W is co-regulated with CLN2 and HTA1.  There is too much black in the strip for YBR161W to determine which of these 2 genes, and hence which phase, it is more closely imitating.  YBR161W co-regulates with CLB4 in some of the mutant conditions but not all.  YBR161W is oppositely regulated with SWI5 and ASH1;  that is, when SWI5 and ASH1 are induced, YBR161W is repressed and vice versa, though these correlations are not precise across each row.

     As before, these generalizations are approximate; YBR161W was not strongly induced or repressed for many of the time points or mutants, therefore, strict correlations are difficult to extract.

 

IV.             Expression During the Diauxic Shift.

This experiment measured gene expression responses to changes in available glucose.  We saw in class that when yeast cells were placed under this environmental stress, they responded by consuming as much glucose as possible and reproducing as quickly as possible to safeguard against possible starvation.

 

Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR161W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL131W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL209C

 

IPL1

 

 

not yet annotated

 

protein kinase

 

not yet annotated

YBL074C

 

AAR2

 

 

mRNA splicing

 

molecular_function unknown

 

cellular_component unknown

YGL133W

 

ITC1

 

 

biological_process unknown

 

molecular_function unknown

 

nucleus

YDR480W

 

DIG2

 

 

invasive growth

 

not yet annotated

 

not yet annotated

YFL064C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHL049C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR213W

 

UPC2

 

 

steroid metabolism

 

RNA polymerase II transcription factor

 

cellular_component unknown

YHL027W

 

RIM101

 

 

meiosis

 

transcription factor

 

not yet annotated

YEL053C

 

MAK10

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YBR027C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR166C

 

TYR1

 

 

not yet annotated

 

prephenate dehydrogenase (NADP+)

 

not yet annotated

YBR168W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YEL006W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL095W

 

YJU2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR090C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR524C

 

AGE1

 

 

ER to Golgi transport*

 

ARF GTPase activator

 

cellular_component unknown

YFR025C

 

HIS2

 

 

histidine biosynthesis

 

histidinol-phosphatase

 

cell

YNL094W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR041W

 

BUD9

 

 

polar budding

 

molecular_function unknown

 

cell


* : indicates that more than one annotation exists for the gene.

 

Figure 14.  Clustering data for YBR161W when exposed to limited glucose (SGD, 2001).

 

 

Figure 15.  Time response of YBR161W to diauxic shift (SGD, 2001).

 

          Here, YBR161W clustered with genes involved in meiosis, mRNA splicing, polar budding and RNA polymerase transcription factor.  Again, these clustering data indicate that YBR161W probably serves some function in the DNA replication process.

 

V.                Expression During Sporulation.

 

Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR161W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR016W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL037C

 

EGD1

 

 

nascent polypeptide association

 

chaperone

 

nascent polypeptide-associated complex

YGR061C

 

ADE6

 

 

not yet annotated

 

phosphoribosylformylglycinamidine synthase

 

not yet annotated

YER020W

 

GPA2

 

 

pseudohyphal growth*

 

heterotrimeric G-protein GTPase

 

cellular_component unknown

YML115C

 

VAN1

 

 

not yet annotated

 

mannosyltransferase

 

not yet annotated

YHR195W

 

NVJ1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YOL027C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOL148C

 

SPT20

 

 

not yet annotated

 

not yet annotated

 

SAGA complex

YPR092W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR155C

 

CPR1

 

 

biological_process unknown

 

peptidylprolyl isomerase

 

cytoplasm

YNL133C

 

FYV6

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown

YMR124W

 

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR248C

 

HIS7

 

 

histidine biosynthesis

 

imidazoleglycerol-phosphate synthase

 

cell

YPL198W

 

RPL7B

 

 

protein biosynthesis

 

structural protein of ribosome

 

cytosolic large ribosomal (60S) subunit

YLR150W

 

STM1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YER102W

 

RPS8B

 

 

protein biosynthesis

 

structural protein of ribosome

 

cytosolic small ribosomal (40S) subunit

YHL020C

 

OPI1

 

 

phospholipid metabolism

 

not yet annotated

 

not yet annotated

YNL098C

 

RAS2

 

 

pseudohyphal growth*

 

RAS small monomeric GTPase

 

plasma membrane

YDR385W

 

EFT2

 

 

protein synthesis elongation

 

translation elongation factor

 

ribosome

YLR076C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated


* : indicates that more than one annotation exists for the gene.

 

Figure 16.  Clustering data for YBR161W during sporulation (SGD, 2001).

 

 

Figure 17.   Expression response of YBR161W to sporulation over time (SGD, 2001).

 

          Again, the annotated genes YBR161W clustered with all seem to pertain to DNA replication, for example, protein biosynthesis, protein synthesis elongation and translation elongation, as well as nascent polypeptide formation.  Also, for the first time, YBR161W has clustered with genes involved in cell wall production, i.e. phospholipid metabolism.  Recall that previous BLAST searches suggested YBR161W was a functional homolog to Sur1, a gene involved in the production of phospholipids in the cellular membrane.

 

Conclusions.

          While YBR161W consistently clustered with annotated genes involved in DNA replication for each experimental condition, it did not cluster with the same gene several times, nor with different genes but the same specific function.  While it may have coding similarities to the gene Sur1, it never clustered with that gene, indicating that they may not be regulated similarly.  To conclude with confidence that YBR161W is a functional homolog of any of these genes, more experimental evidence will be necessary.  Though it may be reasonable to assume that YBR161W plays a role in DNA replication, what that specific role may be has yet to be determined.

 

References.

1.     SGD, Expression Connection. 2001. < http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl> Accessed 2001 Oct 16.

 

2.    Spellman P, Sherlock G, Zhang M, Vishwanath R, Anders K, Eisen M, Brown P, Botstein D, Futcher B.  1998.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.  Molecular Biology of the Cell 9(12). <http://www.molbiolcell.org/cgi/content/full/9/12/3273>  Accessed 2001 Oct 16.

 

3.    Zymo Research. 2001.  Alpha-factor mating pheromone. <http://www.zymor.com/y1001-frame.html>.  Accessed 2001 Oct 16.

 

 

 

 

Emily Oldham's Home Page

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Department of Biology, Davidson College, Davidson, NC 28036

Send comments, questions, and suggestions to: emoldham@davidson.edu