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YDR466W Gene Expression in Saccharomyces cerevisiae  

Note:  My conclusions are displayed directly below each microarray data set, and final conclusions located at the bottom of the page.

 

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

 
Saccharomyces Genome Database

Expression at different alpha-factor concentrations for YDR466W

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

Orf Gene Process Function Component
YDR466W         biological_process unknown   molecular_function unknown   not yet annotated
YJL081C   ARP4     establishment and/or maintenance of chromatin architecture*   chromatin binding   chromatin
YFL002C   SPB4     35S primary transcript processing*   ATP dependent RNA helicase   nucleolus
YPL175W   SPT14     GPI anchor synthesis   not yet annotated   endoplasmic reticulum
YGR134W   CAF130     not yet annotated   not yet annotated   not yet annotated
YOR125C   CAT5     ubiquinone metabolism   not yet annotated   mitochondrial inner membrane
YKR064W         biological_process unknown   molecular_function unknown   not yet annotated
YDR258C   HSP78     stress response*   chaperone*   mitochondrial matrix
YLR071C   RGR1     transcription, from Pol II promoter   RNA polymerase II transcription mediator   mediator complex
YNL268W   LYP1     transport   lysine permease   not yet annotated
YPL020C   ULP1     G2/M transition of mitotic cell cycle   cysteine-type peptidase   nuclear membrane

* : 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 YDR466W

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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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The data set from the different Alpha factor concentrations has very little information contained in it.  It is impossible to deduce anything from seeing this microarray, because the amount of change in the expression of YDR466W is almost zero.  However, the genes to which YDR466W is compared show some interesting trends in their biological processes.  Most of the genes are involved in some aspect of the cell division or transcription.  This doesn't mean much, but it is possible to assume some relationship between the genes with which YDR466W is clustered.  Overall, though, it appears that the type of reproduction that the yeast undergoes does not affect the expression of YDR466W.


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

 
Saccharomyces Genome Database

Expression in response to alpha-factor for YDR466W

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

Orf Gene Process Function Component
YDR466W         biological_process unknown   molecular_function unknown   not yet annotated
YJR105W   ADO1     purine base metabolism   adenosine kinase   cellular_component unknown
YGL018C   JAC1     aerobic respiration   cochaperone   mitochondrion
YBR131W   CCZ1     not yet annotated   molecular_function unknown   not yet annotated
YEL032W   MCM3     DNA replication initiation*   chromatin binding*   cytoplasm*
YLR118C         biological_process unknown   molecular_function unknown   not yet annotated
YLR199C         biological_process unknown   molecular_function unknown   not yet annotated
YJR080C         biological_process unknown   molecular_function unknown   not yet annotated
YDL123W   SNA4     biological_process unknown   molecular_function unknown   not yet annotated
YDL053C         biological_process unknown   molecular_function unknown   not yet annotated
YNR015W   SMM1     not yet annotated   molecular_function unknown   not yet annotated
YJR025C   BNA1     not yet annotated   not yet annotated   not yet annotated
YBR162C   TOS1     not yet annotated   not yet annotated   not yet annotated
YKL190W   CNB1     cell wall organization and biogenesis*   calcium-dependent protein serine/threonine phosphatase   cytoplasm
YDL120W   YFH1     not yet annotated   not yet annotated   not yet annotated
YNL104C   LEU4     not yet annotated   2-isopropylmalate synthase   not yet annotated
YFL055W   AGP3     transport   general amino acid permease   not yet annotated
YBR026C   MRF1'     respiration   DNA binding   nucleus
YAL027W         biological_process unknown   molecular_function unknown   not yet annotated
YML039W            
YFL054C         biological_process unknown   molecular_function unknown   not yet annotated

* : 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 YDR466W

Visit the Website
Browse clustered data


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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Like above, YDR466W shows very little response to the Alpha factor.  However, it is again clustered with genes with biological processes that would not depend on the stage of the cell cycle.  This is consistent with the data (or lack thereof) from above, but it would be premature to make conclusions based on the two Alpha factor microarrays.


[X] Expression in response to DNA-damaging agents  (Stanford University).

 
Saccharomyces Genome Database

Expression in response to DNA-damaging agents for YDR466W

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Scale : (fold repression/induction)

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

Orf Gene Process Function Component
YDR466W         biological_process unknown   molecular_function unknown   not yet annotated

* : 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 DNA-damaging agents for YDR466W

Visit the Website


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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YDR466W again shows nearly no response to the stresses put upon it in these microarrays.  There are no more than three or four spots out of the many in these microarrays that show real deviation from the control expression.  No conclusions can be made from this microarray set.


[X] Expression during the diauxic shift  (Stanford University).

 
Saccharomyces Genome Database

Expression during the diauxic shift for YDR466W

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

Orf Gene Process Function Component
YDR466W         biological_process unknown   molecular_function unknown   not yet annotated
YHR022C         biological_process unknown   molecular_function unknown   not yet annotated
YIL003W         biological_process unknown   molecular_function unknown   not yet annotated
YLR362W   STE11     protein amino acid phosphorylation*   MAP kinase kinase kinase   cytoplasm
YJR152W   DAL5     not yet annotated   not yet annotated   not yet annotated
YGR030C   POP6     rRNA processing*   ribonuclease P*   ribonuclease MRP*
YLR034C   SMF3     not yet annotated   not yet annotated   not yet annotated
YPL067C         biological_process unknown   molecular_function unknown   not yet annotated
YDL159W   STE7     protein amino acid phosphorylation*   MAP kinase   not yet annotated
YDR521W         biological_process unknown   molecular_function unknown   not yet annotated
YJL149W         biological_process unknown   molecular_function unknown   not yet annotated
YOR329C   SCD5     not yet annotated   not yet annotated   not yet annotated
YDR113C   PDS1     cell cycle   not yet annotated   not yet annotated
YOR196C   LIP5     fatty acid metabolism   not yet annotated   not yet annotated
YFR004W   RPN11     ubiquitin-dependent protein degradation   multicatalytic endopeptidase   19S proteasome regulatory particle
YGR002C         biological_process unknown   molecular_function unknown   not yet annotated
YDL001W         biological_process unknown   molecular_function unknown   not yet annotated
YPL101W   ELP4     biological_process unknown   molecular_function unknown   not yet annotated
YDR004W   RAD57     not yet annotated   not yet annotated   not yet annotated
YML050W         biological_process unknown   molecular_function unknown   not yet annotated
YOR231W   MKK1     protein amino acid phosphorylation*   MAP kinase kinase   cellular_component unknown

* : indicates that more than one annotation exists for the gene.
See the Summary of the Gene Ontology annotations for this gene group

Expression during the diauxic shift for YDR466W

Visit the Website
Browse clustered data


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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YDR466W again returned a mostly black row of spots of information, meaning that the change from anaerobic to aerobic respiration meant little for the expression of YDR466W.  This would signal that the gene does not control a vital cell process such as cell division or protein synthesis.  So, for the first time, real assumptions can be made - but instead of being able to assume what the YDR466W gene does, it is only possible to say what it probably doesn't do using this test.


[X] Evolution of expression during glucose limitation  (Stanford University).


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Name Process Function
YDR466W biological_process unknown molecular_function unknown
TFC3 transcription initiation, from Pol III promoter RNA polymerase III transcription factor
YFR038W biological_process unknown molecular_function unknown
GEA1 ER to Golgi transport* ARF small monomeric GTPase
KEL1 biological_process unknown not yet annotated
YCG1 mitotic chromosome condensation molecular_function unknown
SHE4 not yet annotated molecular_function unknown
YDR049W biological_process unknown molecular_function unknown
YGR004W biological_process unknown molecular_function unknown
YOL032W biological_process unknown molecular_function unknown
PAK1 protein amino acid phosphorylation* protein kinase
YOL099C biological_process unknown molecular_function unknown
RAD53 not yet annotated protein kinase
YNL338W biological_process unknown molecular_function unknown
MRS2 mRNA splicing* magnesium ion transporter
TFA1 transcription initiation, from Pol II promoter general RNA polymerase II transcription factor
PAU2 biological_process unknown molecular_function unknown
YBR030W biological_process unknown molecular_function unknown
YGR068C biological_process unknown molecular_function unknown
CAF4 not yet annotated not yet annotated
TIR1 cell wall organization and biogenesis* cell wall structural protein

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YDR466W, like a broken record, keeps returning a constant expression.  In all of the previous tests, this is the case.  This means again that the stresses inflicted upon the yeast do not affect the level of YDR466W expression.  Specifically in this microarray, the level of expression was examined during glucose limitation.  The fact that YDR466W expression was not significantly affected signifies again that it is not involved in controlling a vital biological process.  Also, the amount of energy that the cell has to use does not affect expression.  This probably means that the biological process for YDR466W is fairly "inexpensive" biologically.

[X] Expression in response to environmental changes  (Stanford University).

 
Saccharomyces Genome Database

Expression in response to environmental changes for YDR466W

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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
YDR466W         biological_process unknown   molecular_function unknown   not yet annotated

* : 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 environmental changes for YDR466W

Visit the Website


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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Again, no change in the expression of YDR466W was observed for the majority of the stresses for this microarray set.  However, YDR466W did finally return some data for some of the stresses, including nitrogen depletion.  However, with no other genes to compare YDR466W to, it is difficult to guess what function the YDR466W gene actually has.   This microarray could be helpful in concert with other arrays, but by itself it is fairly inconclusive.

[X] Expression during the cell cycle  (Stanford University, Cold Spring Harbor).


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Name Score Peak
YDR466W 0.436
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 YDR466W


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).  YDR466W did not have a score high enough for us to generate such a list.

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YDR466W again produced spots that showed no significant change throughout the cell cycle.  One of the only conclusions that can be reached from this array is the fact that YDR466W does not control a process that occurs in a specific stage in the cell cycle.  It is also noted that YDR466W did not cluster with any genes which showed an aggregate CDC score >.95.  Therefore, little can be drawn from this array set.


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

 
Saccharomyces Genome Database

Expression in response to histone depletion for YDR466W

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Scale : (fold repression/induction)

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

Orf Gene Process Function Component
YDR466W         biological_process unknown   molecular_function unknown   not yet annotated
YHR102W   KIC1     not yet annotated   not yet annotated   not yet annotated
YLL047W         biological_process unknown   molecular_function unknown   not yet annotated
YGR224W   AZR1     transport   transporter   membrane
YKR067W   GPT2     biological_process unknown   molecular_function unknown   not yet annotated
YDR142C   PEX7     protein-peroxisome targeting*   peroxisome targeting signal receptor   peroxisomal matrix
YKL057C   NUP120     mRNA-nucleus export*   structural protein   nuclear pore
YKR037C   SPC34     microtubule nucleation   structural protein of cytoskeleton   spindle pole body
YMR019W   STB4     transcription   not yet annotated   not yet annotated
YLR107W   REX3     RNA processing   3'-5' exonuclease   cellular_component unknown
YGR270W   YTA7     not yet annotated   not yet annotated   not yet annotated
YLR225C         biological_process unknown   molecular_function unknown   not yet annotated
YGR213C   RTA1     not yet annotated   molecular_function unknown   not yet annotated
YIL171W   HXT12        
YGL233W   SEC15     establishment of cell polarity (sensu Saccharomyces)*   not yet annotated   actin cap (sensu Saccharomyces)*
YLL043W   FPS1     transport*   transporter   integral plasma membrane protein
YMR316C-A         biological_process unknown   molecular_function unknown   not yet annotated
YLR246W   ERF2     not yet annotated   molecular_function unknown   not yet annotated
YPL196W   OXR1     biological_process unknown   molecular_function unknown   not yet annotated
YLR071C   RGR1     transcription, from Pol II promoter   RNA polymerase II transcription mediator   mediator complex
YDR460W   TFB3     transcription initiation, from Pol II promoter*   general RNA polymerase II transcription factor   transcription factor TFIIH

* : 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 YDR466W

Visit the Website
Browse clustered data


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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YDR466W revealed some relevant data in this microarray, testing the effects of histone depletion on expression.  Initially, YDR466W was greatly repressed, but leveled off and became induced, peaking at 4 hours.  YDR466W is clustered with several genes of unknown function and several with functions involving transcription and transport.  One would expect that genes would show some change in expression if involved in any transcription with this array, because changes in the histone concentrations would affect the yeast's ability to continue cellular pathways involving DNA replication or DNA-RNA translation.  These pathways could also potentially affect the expression of translation factors by downregulating some transcription factors, causing an absence of the RNA. The cell could then try to compensate for this lack of the protein by trying to upregulate translation factors, when in fact the cause could be farther upstream.


[X] Expression during sporulation  (UCSF, Stanford University).

 
Saccharomyces Genome Database

Expression during sporulation for YDR466W

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Scale : (fold repression/induction)

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

Orf Gene Process Function Component
YDR466W         biological_process unknown   molecular_function unknown   not yet annotated
YBR296C   PHO89     phosphate metabolism   not yet annotated   not yet annotated
YOL087C         biological_process unknown   molecular_function unknown   not yet annotated
YMR164C   MSS11     not yet annotated   not yet annotated   not yet annotated
YPL202C   AFT2     biological_process unknown   molecular_function unknown   not yet annotated
YDL140C   RPO21     transcription, from Pol II promoter   DNA-directed RNA polymerase II   DNA-directed RNA polymerase II, core
YNL006W   LST8     transport   molecular_function unknown   cellular_component unknown
YGR061C   ADE6     not yet annotated   phosphoribosylformylglycinamidine synthase   not yet annotated
YLR442C   SIR3     chromatin silencing at HML and HMR (sensu Saccharomyces)*   not yet annotated   nucleolus*
YOR133W   EFT1     protein synthesis elongation   translation elongation factor   ribosome
YJL143W   TIM17     mitochondrial translocation   protein transporter   mitochondrial inner membrane translocase complex
YMR124W         biological_process unknown   molecular_function unknown   not yet annotated
YKR073C         biological_process unknown   molecular_function unknown   not yet annotated
YOR023C   AHC1     nucleosome disassembly   molecular_function unknown   Ada2/Gcn5/Ada3 transcription activator complex
YLR167W   RPS31     protein biosynthesis*   structural protein of ribosome   cytosolic small ribosomal (40S) subunit
YNL093W   YPT53     endocytosis   not yet annotated   not yet annotated
YOL065C   INP54     not yet annotated   inositol-1,4,5-triphosphate 5-phosphatase   not yet annotated
YHL020C   OPI1     phospholipid metabolism   not yet annotated   not yet annotated
YLR058C   SHM2     not yet annotated   glycine hydroxymethyltransferase   not yet annotated
YOL063C         biological_process unknown   molecular_function unknown   not yet annotated
YPL136W         biological_process unknown   molecular_function unknown   not yet annotated

* : 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 YDR466W

Visit the Website
Browse clustered data


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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YDR466W shows a repression for nearly every time point (excluding 11.5 hours) in the sporulation microarray.  Initially, the repression is small, then becomes more pronounced, and again approaches zero for time=11.5 hours.  Overall, the repression is less pronounced than in many other genes, which show a fold repression of >2.8.  The peak for YDR466W repression is slightly >0.5 at time=7.0 hours.  YDR466W clusters with many genes of more significant repression, but many of them have functions having to do with protein synthesis.  This is consistent with the arrays above both in the relatively low amount of change in the expression of YDR466W and in the biological functions of the genes with which YDR466W clusters.

 

CONCLUSIONS

Through the limited data that was received through these microarrays, one must be careful not to assume too much, or assume to confidently about the funtion of YDR466W.  However, YDR466W is consistent in the fact that it shows little response to nearly all environmental stresses and cell cycle stage changes.  Therefore it could be assumed that the function of YDR466W is not a vital one, and not one that fluctuates throughout the cell cycle.  Also, YDR466W continually clusters with other genes that have roles in protein synthesis.  YDR466W could have a role in this area, but the variability of the protein's presence would have to be low.  Therefore, I will assume that the role of YDR466W is a structural protein (low variability of expression) for either a ribosome or for endoplasmic reticulum (both involved in protein synthesis).

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This page was created by:
Peter Lowry
pelowry@davidson.edu
Davidson College