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*
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]](./YDR078Cdraft_files/image001.gif)
Expression at different alpha-factor
concentrations (Rosetta Inpharmatics).
Expression at different alpha-factor concentrations for YDR078C |
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 |
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
TAH18 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
nucleus |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
APG10 |
|
|
|
autophagy* |
|
ubiquitin-like conjugating enzyme |
|
soluble fraction |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
MPA43 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
ABM1 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
SSP1 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
SEN15 |
|
|
|
tRNA splicing |
|
tRNA-intron endonuclease |
|
nuclear inner membrane* |
|
|
|
KTI12 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
DOM34 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
FMC1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
MTR10 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
AAT1 |
|
|
|
aspartate catabolism |
|
aspartate aminotransferase |
|
mitochondrion |
|
|
|
SEN2 |
|
|
|
tRNA splicing |
|
tRNA-intron endonuclease |
|
nuclear inner membrane* |
|
|
|
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.
|
Expression at
different alpha-factor concentrations for YDR078C |
|
|
Expression in response to alpha-factor
(Rosetta Inpharmatics).
Expression in response to alpha-factor for YDR078C |
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 |
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
not yet annotated |
|
not yet annotated |
|
|
|
XRS2 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
BAR1 |
|
|
|
pheromone degradation |
|
aspartic-type endopeptidase |
|
periplasmic space (sensu Fungi) |
|
|
|
NSP1 |
|
|
|
mRNA-nucleus export* |
|
structural protein |
|
nuclear pore |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
APM3 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
SPO75 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
SPC72 |
|
|
|
microtubule nucleation* |
|
structural protein of cytoskeleton |
|
outer plaque of spindle pole body |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
MEF2 |
|
|
|
protein synthesis elongation |
|
translation elongation factor |
|
mitochondrion |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
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.
|
Expression in
response to alpha-factor for YDR078C |
|
|
Expression during the cell cycle
(Stanford University).
Home | Search | Figures | Data | Info | Links | SGD | Microarray_Homepage
|
Name |
Score |
Peak |
|
|
0.062 |
|
|
|
|
Reference Genes |
|
||
|
10.9 |
G1 |
|
|
|
10.68 |
S |
|
|
|
3.08 |
G2 |
|
|
|
6.726 |
M |
|
|
|
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.
Expression during
sporulation (Stanford University).
Expression during sporulation for YDR078C |
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 |
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
BET2 |
|
|
|
C-terminal protein
geranylgeranylation |
|
RAB-protein
geranylgeranyltransferase |
|
not yet annotated |
|
|
|
SEC59 |
|
|
|
not yet annotated |
|
dolichol kinase |
|
not yet annotated |
|
|
|
EXO70 |
|
|
|
establishment of cell
polarity (sensu Saccharomyces)* |
|
not yet annotated |
|
actin cap (sensu
Saccharomyces)* |
|
|
|
HNT2 |
|
|
|
biological_process unknown |
|
not yet annotated |
|
not yet annotated |
|
|
|
SKI7 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
SGT1 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
OGG1 |
|
|
|
DNA repair |
|
8-oxoguanine DNA
glycosylase |
|
not yet annotated |
|
|
|
ICS3 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
OST1 |
|
|
|
N-linked glycosylation |
|
dolichyl-diphosphooligosaccharide-protein
glycosyltransferase |
|
endoplasmic reticulum lumen |
|
|
|
PIF1 |
|
|
|
DNA recombination* |
|
DNA helicase |
|
mitochondrion |
|
|
|
IKS1 |
|
|
|
not yet annotated |
|
protein kinase |
|
not yet annotated |
|
|
|
TPT1 |
|
|
|
tRNA splicing |
|
tRNA 2'-phosphotransferase |
|
nucleus |
|
|
|
SHE1 |
|
|
|
biological_process unknown |
|
not yet annotated |
|
not yet annotated |
|
|
|
TFI2 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
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.
|
Expression during
sporulation for YDR078C |
|
|
Expression
in response to histone depletion (The Whitehead Institute).
Expression in response to histone depletion for YDR078C |
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 |
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
SWR1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
AEP1 |
|
|
|
protein biosynthesis |
|
molecular_function unknown |
|
cellular_component unknown |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
ZMS1 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
STB5 |
|
|
|
transcription |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
RSM24 |
|
|
|
protein biosynthesis |
|
structural protein of
ribosome |
|
mitochondrial small
ribosomal subunit |
|
|
|
PRP19 |
|
|
|
mRNA splicing |
|
molecular_function unknown |
|
spliceosome |
|
|
|
MED1 |
|
|
|
transcription, from Pol II
promoter |
|
RNA polymerase II
transcription mediator |
|
mediator complex |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
CBP2 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
BEM4 |
|
|
|
establishment of cell polarity
(sensu Saccharomyces)* |
|
molecular_function unknown |
|
cellular_component unknown |
|
|
|
CAC2 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
ECM31 |
|
|
|
not yet annotated |
|
3-methyl-2-oxobutanoate
hydroxymethyltransferase |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
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.
|
Expression in
response to histone depletion for YDR078C |
|
|
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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