• Expression at different alpha-factor concentrations (Rosetta Inpharmatics)
• Expression in response to alpha-factor (Rosetta Inpharmatics)
• Expression in response to DNA-damaging agents (Stanford University)
• Expression during the diauxic shift (Stanford University)
• Evolution of expression during glucose limitation (Stanford University)
• Expression in response to environmental changes (Stanford University)
• Expression during the cell cycle (Stanford University, Cold Spring Harbor)
• Expression in response to histone depletion (The Whitehead Institute)
• Expression during sporulation (UCSF, Stanford University)

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

 

Expression at different alpha-factor concentrations for YDR466W

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
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.

Expression at different alpha-factor concentrations for YDR466W Visit the Website Browse clustered data

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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.

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

 

Expression in response to alpha-factor for YDR466W

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
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.

Expression in response to alpha-factor for YDR466W Visit the Website Browse clustered data

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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.

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

 

Expression in response to DNA-damaging agents for YDR466W

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.

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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.

Expression during the diauxic shift  (Stanford University).

 

Expression during the diauxic shift for YDR466W

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
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.

Expression during the diauxic shift for YDR466W Visit the Website Browse clustered data

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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.

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.

Expression in response to environmental changes  (Stanford University).

 

Expression in response to environmental changes for YDR466W

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.

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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.

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

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

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.

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

 

Expression in response to histone depletion for YDR466W

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
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.

Expression in response to histone depletion for YDR466W Visit the Website Browse clustered data

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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.

Expression during sporulation  (UCSF, Stanford University).

 

Expression during sporulation for YDR466W

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
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.

Expression during sporulation for YDR466W Visit the Website Browse clustered data

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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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Peter Lowry
pelowry@davidson.edu
Davidson College