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

    YAL011w is an unannotated ORF that could hint at its own function as more data is collected from microarrays.  This
 ORF is coordinately expressed with other genes in response to a changing cellular environment.  Here is some information that
    reveals clustered expression of YAL011w with other genes.  “Guilt by association” implies that genes showing similar
 expression patterns may have similar functions but various patterns of clustering require a more analysis to elucidate the function of a gene.  The true source of data for clustering of YAL011w in response to changing cellular and environmental conditions can be found at this website after running a search with YAL011w: <http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl> Please read my other link on
         YAL011w if you are totally unfamiliar with this ORF.  The microarray clustering of Yal011w should appear similar the figure below:

I) Expression of YAL011w in response to different concentrations of alpha factor

    YAL011w clusters very weakly with two annotated genes SEC11 and PRP38 during exposure to alpha factor.  These two
genes are responsible for protein
modification and RNA splicing respectively.

II) Timed expression of YAL011w in response to a constant concentration of alpha factor

    YAL011w clusters with RPS0B and TAF145 after 60 minutes exposure to alpha factor.  RPS0B and TAF145 function as
kinases and RNA transcription regulators respectively.  Because YAL01w is a mitochondrial transmembrane protein, it may
modify a cytosolic protein kinase that in turn exerts feedback in transcription.

III) Expression of YAL011w in response to DNA damaging agents

     The microarray data for the expresison of YAL011w for the dun1 mutant tells an interesting story.  Genomic DNA
hybridizes with strong induction of YAL011w when the dun1 gene is deleted.  Thus dun1 mutants may be viable only when
another part of the chromosome containing YAL011w is duplicated.  Dun1 is a protein kinase that is responsible for repairing
damaged DNA < http://genome-www4.stanford.edu/cgi-bin/SGD/YPD/ypd.pl?sgdid=S0002259>.  YAL011w most likely
does not complement the dun1 mutation beause it is located in the mitochondrial membrane, not the nucleus.  However, it may
be that YAL011w modifies another protein that can complement the dun1 mutation.

IV) Expression of YAL011w during the cell cycle

    The microarray data for YAL011w indicate that it is not involved in the cell cyle. There is onne point where YAL011w is
slightly inducted but this is most likely the result of mitochondria dividing so as to equip the new daughter cell with these
organelles.  As the mitochondria divide, their integral membrane proteins must be transcribed again and this transcription most
likely results in the peak for YAL011w.

V) Expression of YAL011w during the diauxic shift

    During the diauxic shift, the yeast are transferred from an anaerobic to an aerobic environment.  YAL011w clusters most
closely during this environmental change with two genes of unknown function.  The most similarly clustered annotated gene
(RGR1) is involved in assisting RNA polymerase II.  This is the third time
that YAL011w has clustered with a gene involved in regulating transcription.  The other two transcription regulators were
PRP38 and TAF145.
It may be that the protein modified by YAL011w, if YAL011w does indeed modify a protein involved in transcription, has a
unique tertiary
structure as a result of the interaction that allows it to enter the nucleus and work on RNA.

VI) Expression of YAL011w during sporulation

    Once again, we have a case here where YAL011w clusters with a gene known to regulate mRNA splicing (SYF2).  SYF2
is also a participant in the cell
cycle < http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=SYF2>, which might lead credence to the notion that
the induction of YAL011w does not
simply correspond with the division of mitochondria during cell division.

VII) Expression of YAL011w during histone depletion

    The expression of YAL011w is seriously repressed in response to histone depletion.  This phenomenon leads credence to
the notion that YAL011w modifies transcription indirectly by regulating other transcription factors.  During histone depletion,
DNA may be damaged since histones regulate the chromatin that maintains the integrity of DNA structure.  Since the cell does
not want to transcribe damaged DNA, it follows that YAL011w would be repressed during histone depletion if it was
indirectrly involved in RNA transcription.

VIII) Other expression patterns of YAL011w

    The expression pattern of YAL011w does not change significantly in response to the environmental changes induced by the
authors of the microarray data at:<http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl>.
Tup1 deletions and Yap1 overexpression neither change significantly the expression patter of YAL011w.
<http://cmgm.stanford.edu/pbrown/explore/tupsearch.html>

                                         References Cited

   1)      Saccharomyces Genome Database [online database]. Available from:
http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl Accessed 2001 Oct17

  2)  Saccharomyces Genome Database [online databse]. Available from: <http://genome-www4.stanford.edu/cgi-bin/SGD/YPD/ypd.pl?sgdid=S0002259> Accessed 2001 Oct 17

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