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

MICROARRAY DATA FOR NON-ANNOTATED GENE YLR352W

Here I am presenting many of the same experiments as for my annotated gene.  I am trying to see if the microarray data can offer any insight into the function of this unknown gene. 

Expression at different alpha-factor concentrations for YLR352W

Scale : (fold repression/induction)

 

Orf

Gene

Process

Function

Component

YLR352W

 

biological_process unknown

molecular_function unknown

not yet annotated

YMR089C

YTA12

protein complex assembly*

adenosinetriphosphatase*

mitochondrial inner membrane

YNR005C

 

biological_process unknown

molecular_function unknown

not yet annotated

YKL167C

MRP49

protein biosynthesis

structural protein of ribosome

mitochondrial large ribosomal subunit

YJR086W

STE18

signal transduction of mating signal (sensu Saccharomyces)

heterotrimeric G-protein GTPase, gamma subunit

cytoplasm*

YKL190W

CNB1

cell wall organization and biogenesis*

calcium-dependent protein serine/threonine phosphatase

cytoplasm

YKL010C

UFD4

polyubiquitylation*

ubiquitin--protein ligase

cellular_component unknown

YGL153W

PEX14

protein-peroxisome targeting

protein binding

peroxisomal membrane

 

 

 

 

Expression in response to alpha-factor for YLR352W

Orf

Gene

Process

Function

Component

YLR352W

 

biological_process unknown

molecular_function unknown

not yet annotated

YPR026W

ATH1

stress response*

alpha,alpha-trehalase

vacuole

YDR074W

TPS2

stress response*

trehalose phosphatase

alpha,alpha-trehalose-phosphate synthase (UDP-forming)

 

 

 

Expression in response to DNA-damaging agents for YLR352W

 

Orf

Gene

Process

Function

Component

YLR352W

 

biological_process unknown

molecular_function unknown

not yet annotated

YLL019C

KNS1

protein amino acid phosphorylation

protein serine/threonine kinase*

not yet annotated

YDR001C

NTH1

stress response*

alpha,alpha-trehalase

 

 

 

 

 

Expression during the cell cycle

 

Name

Score

Peak

YLR352W

0.64

 

Reference Genes

 

CLN2

10.9

G1

HTA1

10.68

S

CLB4

3.08

G2

SWI5

6.726

M

ASH1

11.8

M/G1

 

Expression during sporulation for YLR352W

 

Orf

Gene

Process

Function

Component

YLR352W

 

biological_process unknown

molecular_function unknown

not yet annotated

YFL055W

AGP3

transport

general amino acid permease

not yet annotated

YOL060C

AMI3

not yet annotated

molecular_function unknown

not yet annotated

YFL025C

BST1

vesicle organization and biogenesis

molecular_function unknown

endoplasmic reticulum*

YPR167C

MET16

methionine metabolism*

phosphoadenylyl-sulfate reductase (thioredoxin)

cellular_component unknown

YIL033C

BCY1

stress response*

cAMP-dependent protein kinase inhibitor

nucleus

 

 

 

Expression in response to histone depletion for YLR352W

Orf

Gene

Process

Function

Component

YLR352W

 

biological_process unknown

molecular_function unknown

not yet annotated

YDR218C

SPR28

cell wall organization and biogenesis*

structural protein of cytoskeleton

septin ring (sensu Saccharomyces)

YML061C

PIF1

DNA recombination*

DNA helicase

mitochondrion

YPL147W

PXA1

transport

not yet annotated

not yet annotated

 

 

SUMMARY:

I HAD ORIGINALLY PREDICTED THAT MY NON-ANNOTATED GENE (YLR352W) WOULD HAVE A SIMILAR FUNCTION AS BUD8 BASED ON ITS LOCATION RIGHT NEXT TO BUD8 ON CHROMOSOME XII.  BUT, UPON EXAMINING THE MICROARRAY DATA, BUD8 AND YLR352W DO NOT APPEAR TO SHARE EXPRESSION PATTERNS IN ANY OF THE EXPERIMENTS PRESENTED.  I HAVE DELETED MOST OF THE OTHER NON-ANNOTATED GENES FROM THESE FIGURES , SO THAT ONLY THOSE GENES WHICH OFFER THE MOST INFORMATION ARE LEFT.  THE MOST INTERESTING THING TO NOTE IS THAT FOR THREE OF THE EXPERIMENTS (ALPHA-FACTOR, DNA-DAMAGING AGENTS, AND SPORULATION) GENES CLUSTERED THAT ARE INVOLVED IN STRESS RESPONSE.  ANOTHER CONNECTION BETWEEN EXPERIMENTS IS GENES INVOLVED IN PROTEIN BINDING AND STRUCTURE.  SO, PERHAPS THIS UNKNOWN GENE IS ALSO INVOLVED IN THESE PROCESSES.  THE CELL CYCLE EXPERIMENT WAS UNABLE TO PROVIDE ANY SIMILAR GENES, AND ALSO DID NOT REVEAL A PEAK OF EXPRESSION FOR YLR352W.

 

 

REFERENCE

 

http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl, accessed October 17, 2001.

 

 

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