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

MICROARRAY ANALYSIS OF

THE YEAST GENE YDR078C

*Below each data set review the analysis section for an explanation and discussion of the data presented above*


Experiments:

Expression at different alpha-factor concentrations

Expression in response to alpha-factor

Yeast cell-cycle experiment

Yeast sporulation

Expression in response to histone depletion

 


[X] Expression at different alpha-factor concentrations  (Rosetta Inpharmatics).

Saccharomyces Genome Database

Expression at different alpha-factor concentrations for YDR078C

Help



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

YDR078C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHL035C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR048W

 

TAH18

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR196W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

nucleus

YDR100W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLL042C

 

APG10

 

 

autophagy*

 

ubiquitin-like conjugating enzyme

 

soluble fraction

YPR098C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YNL249C

 

MPA43

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJR108W

 

ABM1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YHR184W

 

SSP1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YMR059W

 

SEN15

 

 

tRNA splicing

 

tRNA-intron endonuclease

 

nuclear inner membrane*

YKL110C

 

KTI12

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YHL039W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML107C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML050W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YNL001W

 

DOM34

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YIL098C

 

FMC1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YOR160W

 

MTR10

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YKL106W

 

AAT1

 

 

aspartate catabolism

 

aspartate aminotransferase

 

mitochondrion

YLR105C

 

SEN2

 

 

tRNA splicing

 

tRNA-intron endonuclease

 

nuclear inner membrane*

YMR283C

 

RIT1

 

 

tRNA processing

 

not yet annotated

 

not yet annotated

 

Analysis:  Although this microarray is devoid of informative information, it is a perfect example of why YDR078C is a non-annotated gene.  There is not induction or repression relative to the control and most of the genes that express this pattern are also unknown.  Although, it is likely that YDR078C is not involved in the pheromone response pathway.  Microarrays, even non-indicative plates, can at least help to narrow the playing field.


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

See the Summary of the Gene Ontology annotations for this gene group

 

Expression at different alpha-factor concentrations for YDR078C

Visit the Website
Browse clustered data

 

 



[X] Expression in response to alpha-factor  (Rosetta Inpharmatics).

Saccharomyces Genome Database

Expression in response to alpha-factor for YDR078C

Help



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

YDR078C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML050W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL264C

 

 

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YDR369C

 

XRS2

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YGR071C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL015W

 

BAR1

 

 

pheromone degradation

 

aspartic-type endopeptidase

 

periplasmic space (sensu Fungi)

YJL041W

 

NSP1

 

 

mRNA-nucleus export*

 

structural protein

 

nuclear pore

YDR506C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR003W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR288C

 

APM3

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YML087C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLL005C

 

SPO75

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR147W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL100W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR168C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAL047C

 

SPC72

 

 

microtubule nucleation*

 

structural protein of cytoskeleton

 

outer plaque of spindle pole body

YDR220C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR250C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL102W

 

MEF2

 

 

protein synthesis elongation

 

translation elongation factor

 

mitochondrion

YPL166W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YFL050C

 

ALR2

 

 

di-, tri-valent inorganic cation transport

 

di-, tri-valent inorganic cation transporter

 

plasma membrane

 

Analysis:  This microarray is interesting in comparison the previous one because induction is shown in the middle of the experiment.  We can begin to hypothesize that YDR078C might play a role in pheromone degradation as BAR1 does or even spindle formation as SPC72 does.  Further, more specific tests are required to determine its function, but we can now focus the search.  Performing the same microarray with shorter time intervals might give more information as well.


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

See the Summary of the Gene Ontology annotations for this gene group

 

Expression in response to alpha-factor for YDR078C

Visit the Website
Browse clustered data

 

 



[X] Expression during the cell cycle  (Stanford University).


Home | Search | Figures | Data | Info | Links | SGD | Microarray_Homepage


Name

Score

Peak

YDR078C

0.062

 

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 YDR078C

Analysis:  YDR078C is not substantially induced or repressed by these pheromones.  Data is not available for cdc15.  We can infer from this microarray that the expression of YDR078C is constant, and, therefore, not directly involved in cell-cycle activities.  Also, as mentioned below, YDR078C has not been clustered with other genes because of it’s low “aggregate CDC score.”



Note: We only generated a list of genes with similar patterns of expression for genes whose "aggregate CDC scores" were in the top 1200 (Score >= 0.95).  YDR078C did not have a score high enough for us to generate such a list.




[X] Expression during sporulation  (Stanford University).

Saccharomyces Genome Database

Expression during sporulation for YDR078C

Help



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

YDR078C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR176C

 

BET2

 

 

C-terminal protein geranylgeranylation

 

RAB-protein geranylgeranyltransferase

 

not yet annotated

YMR013C

 

SEC59

 

 

not yet annotated

 

dolichol kinase

 

not yet annotated

YJL085W

 

EXO70

 

 

establishment of cell polarity (sensu Saccharomyces)*

 

not yet annotated

 

actin cap (sensu Saccharomyces)*

YDR305C

 

HNT2

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YOR076C

 

SKI7

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YER010C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR057W

 

SGT1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YML060W

 

OGG1

 

 

DNA repair

 

8-oxoguanine DNA glycosylase

 

not yet annotated

YJL077C

 

ICS3

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YHR045W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR181W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR083W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL178C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL002C

 

OST1

 

 

N-linked glycosylation

 

dolichyl-diphosphooligosaccharide-protein glycosyltransferase

 

endoplasmic reticulum lumen

YML061C

 

PIF1

 

 

DNA recombination*

 

DNA helicase

 

mitochondrion

YJL057C

 

IKS1

 

 

not yet annotated

 

protein kinase

 

not yet annotated

YOL102C

 

TPT1

 

 

tRNA splicing

 

tRNA 2'-phosphotransferase

 

nucleus

YBL031W

 

SHE1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YNL041C

 

TFI2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL217C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

 

Analysis:  Although we are faced with yet another minimal information microarray, the genes clustered with YDR078C are interesting.  DNA repair, polarity establishment and DNA recombination are important and ubiquitous functions.  We cannot infer that YDR078C has a related function, although its universal, consistent expression does no eliminated the possibility of an “omniscient, ever-necessary” role, i.e., a critical, albeit small function.  Of course, as the second project found, null mutants are, in fact, viable, so it cannot be absolutely critical, but perhaps “secondarily important.”


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

See the Summary of the Gene Ontology annotations for this gene group

 

Expression during sporulation for YDR078C

Visit the Website
Browse clustered data

 

 


 


[X] Expression in response to histone depletion  (The Whitehead Institute).

Saccharomyces Genome Database

Expression in response to histone depletion for YDR078C

Help



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

YDR078C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML122C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR334W

 

SWR1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YKL098W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR064W

 

AEP1

 

 

protein biosynthesis

 

molecular_function unknown

 

cellular_component unknown

YDL071C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR160W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR003C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJR127C

 

ZMS1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL146W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR178W

 

STB5

 

 

transcription

 

molecular_function unknown

 

not yet annotated

YDR175C

 

RSM24

 

 

protein biosynthesis

 

structural protein of ribosome

 

mitochondrial small ribosomal subunit

YLL036C

 

PRP19

 

 

mRNA splicing

 

molecular_function unknown

 

spliceosome

YPR070W

 

MED1

 

 

transcription, from Pol II promoter

 

RNA polymerase II transcription mediator

 

mediator complex

YDR430C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHL038C

 

CBP2

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YPL161C

 

BEM4

 

 

establishment of cell polarity (sensu Saccharomyces)*

 

molecular_function unknown

 

cellular_component unknown

YML102W

 

CAC2

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YBR176W

 

ECM31

 

 

not yet annotated

 

3-methyl-2-oxobutanoate hydroxymethyltransferase

 

not yet annotated

YMR265C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL216C

 

 

 

 

not yet annotated

 

alpha-glucosidase

 

not yet annotated

 

Analysis:  Our final microarray displays clear induction and repression.  Unfortunately, the pattern is only similar to other non-annotated genes.  Interestingly, the expression pattern oscillates through repression and induction for the points available.  Because histones normally can effect gene expression, deletion of histones can demonstrate novel gene expression patterns.  As we have seen,YDR078C does not show much variation in expression levels.  A possible hypothesis, based on this data, is that YDR078C is repressed by histones in wild-type organisms.

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

See the Summary of the Gene Ontology annotations for this gene group

 

Expression in response to histone depletion for YDR078C

Visit the Website
Browse clustered data

 

 




 

NOTE: ALL MICROARRAY DATA IS COURTESY OF SACCHROMYCES GENOME DATABASE , SPECIFICALLY, THE "EXPRESSION CONNECTION" OF STANFORD UNIVERISTY. PLEASE SEE LINKS BELOW FOR MORE INFORMATION.


SGDtm pages Database Copyright © 1997-2001 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.


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Email the author at: amhartman@davidson.edu

 

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