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My Favorite Yeast ORF(s)!

Annotated Gene: CCL1/YPR025C    (YPD Protein Report)    Brief report of YPR025C 

Non-Annotated Gene:  YHR078W   (YPD Protein Report)     Brief report of YHR078W

Annotated Gene: CCL1/YPR025C    (YPD Protein Report)    

Saccharomyces cerevisiae  Chromosome XVI      

SGD: 50006229        Genbank: CAA89279.1         MIPS (PIR):539383      SWISSPROT: P37366  

Databases Searched  (All microarray data on this page comes from Expression Connection)

Scale used for all data: (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

Expression at different alpha-factor concentrations for CCL1/YPR025C (Rosetta Inpharmatics).

Orf Gene Process Function Component
YPR025C   CCL1     transcription initiation, from Pol II promoter*   general RNA polymerase II transcription factor*   transcription factor TFIIH
YMR005W   MPT1     transcription, from Pol II promoter   RNA polymerase II transcription factor   TFIID complex
YCR092C   MSH3     not yet annotated   not yet annotated   not yet annotated
YGR042W         biological_process unknown   molecular_function unknown   not yet annotated
YGL073W   HSF1     stress response*   transcription factor   nucleus
YMR029C         biological_process unknown   molecular_function unknown   not yet annotated
YOL091W   SPO21     not yet annotated   molecular_function unknown   not yet annotated
YHR057C   CPR2     stress response   peptidylprolyl isomerase   cellular_component unknown
YJL202C         biological_process unknown   molecular_function unknown   not yet annotated
YIR004W   DJP1     not yet annotated   molecular_function unknown   not yet annotated
YKR022C         biological_process unknown   molecular_function unknown   not yet annotated
YJR130C   STR2     not yet annotated   O-succinylhomoserine (thiol)-lyase   not yet annotated
YPL034W         biological_process unknown   molecular_function unknown   not yet annotated
YML002W         biological_process unknown   molecular_function unknown   not yet annotated
YDR230W         biological_process unknown   molecular_function unknown   not yet annotated
YBL080C   PET112     not yet annotated   not yet annotated   not yet annotated
YLL019C   KNS1     protein amino acid phosphorylation   protein serine/threonine kinase*   not yet annotated
YLR387C         biological_process unknown   molecular_function unknown   not yet annotated
YPL064C         biological_process unknown   molecular_function unknown   not yet annotated
YPR049C   CVT9     biological_process unknown   molecular_function unknown   not yet annotated
YDR108W   GSG1     meiosis   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

In response to varying degrees of pheromones, CCL1 is at first slightly repressed, but then gradually rises to be slightly induced, as does MPT1, which is also involved in transcription.  This makes sense as it is not involved in the mating process. After mating, however, it is needed to stimulate the promotor clearance and transcriptional elongation, which leads to an accumulation of G1 cells and an increase in cell size as Ohkuni K and I. Yamashita discovered.  It also follows that the greater amount of alpha-factor administered, the greater the transcription genes were induced.

Expression in response to alpha-factor for CCL1/YPR025C (Rosetta Inpharmatics).

Orf Gene Process Function Component
YPR025C   CCL1     transcription initiation, from Pol II promoter*   general RNA polymerase II transcription factor*   transcription factor TFIIH
YMR098C         biological_process unknown   molecular_function unknown   not yet annotated
YPL025C         biological_process unknown   molecular_function unknown   not yet annotated
YGL089C   MF(ALPHA)2     pheromone response (sensu Saccharomyces)   pheromone   extracellular
YPL065W   VPS28     not yet annotated   not yet annotated   not yet annotated
YHR171W   APG7     autophagy*   ubiquitin-like conjugating enzyme   cellular_component unknown
YNR073C         biological_process unknown   molecular_function unknown   not yet annotated
YDL154W   MSH5     DNA repair   not yet annotated   not yet annotated
YOL024W         biological_process unknown   molecular_function unknown   not yet annotated
YOR380W         biological_process unknown   molecular_function unknown   not yet annotated
YCL026C-A   FRM2     not yet annotated   molecular_function unknown   not yet annotated
YHR093W   AHT1     biological_process unknown   molecular_function unknown   not yet annotated
YKR015C         biological_process unknown   molecular_function unknown   not yet annotated
YLR302C         biological_process unknown   molecular_function unknown   not yet annotated
YLR125W         biological_process unknown   molecular_function unknown   not yet annotated
YHL037C         biological_process unknown   molecular_function unknown   not yet annotated
YGR219W         biological_process unknown   molecular_function unknown   not yet annotated
YCR081W   SRB8     repression of transcription, from Pol II promoter   RNA polymerase II transcription mediator   transcription factor complex
YFL015C         biological_process unknown   molecular_function unknown   not yet annotated
YER137C         biological_process unknown   molecular_function unknown   not yet annotated
YBR167C   POP7     rRNA processing*   ribonuclease P*   ribonuclease MRP*

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

In relation to the amount of time exposed to the alpha-factors, CCL1 and all of the genes clustered with it were slightly induced until just about 50 minutes, at which time the induction jumped up to 6.5-fold before falling equally sharply back down into repression.  This may correlate to the amount of time it takes yeast to mate and begin reproducing, thus making more cells in the G1 stage, or perhaps how long it takes for yeast to detect and respond to pheromones.

Expression in response to DNA-damaging agents for CCL1/YPR025C (Stanford University).

Orf Gene Process Function Component
YPR025C   CCL1     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

In wildtype yeast cells, CCL1 is generally repressed during methylation, which would make sense because it inhibits transcription.  It may be induced in the Mec1 mutant because while MMS inhibits transcription, TFIIH is involved with NER and the Mec1 pathway.  

Expression during the cell cycle  (Stanford University).

Name Score Peak
CCL1 0.756
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 CCL1 (YPR025C)


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).  CCL1 did not have a score high enough for us to generate such a list.

While CCL1 does not appear drastically affected by alpha-factors, which we already knew, elutriation or a cdc15 temperature-sensitive mutant, and as expected no trend of either strong induction or repression exists throughout the cell cycle.  As a type of cyclin, it seems a type of B-type Clb2p rather than the G1 cyclin Cln3p.  This may make sense as CCL1 is mainly a part of a kinase-cyclin protein involved with transcription that affects the number of cells in G1, but not the cell cycle directly. It is also possible and perhaps more likely that the nucleotide excision repair was needed, in which case TFIIH has been proven to inhibit transcription (You, Z., WJ Feaver et. al, 1998).  

Expression during the diauxic shift for CCL1/YPR025C (Stanford University).

Orf Gene Process Function Component
YPR025C   CCL1     transcription initiation, from Pol II promoter*   general RNA polymerase II transcription factor*   transcription factor TFIIH
YNL083W         biological_process unknown   molecular_function unknown   not yet annotated
YIL024C         biological_process unknown   molecular_function unknown   not yet annotated
YOR030W   DFG16     invasive growth   molecular_function unknown   not yet annotated
YDR270W   CCC2     not yet annotated   hydrogen/potassium-exchanging ATPase   not yet annotated
YNL072W   RNH35     DNA replication   ribonuclease H   cell
YDL089W         biological_process unknown   molecular_function unknown   not yet annotated
YGR101W         biological_process unknown   molecular_function unknown   not yet annotated
YKR017C         biological_process unknown   molecular_function unknown   not yet annotated
YIL036W   CST6     DNA metabolism   molecular_function unknown   cellular_component unknown
YJR152W   DAL5     not yet annotated   not yet annotated   not yet annotated
YKL123W         biological_process unknown   molecular_function unknown   not yet annotated
YPR023C   EAF3     biological_process unknown   not yet annotated   not yet annotated
YAL032C   PRP45     mRNA splicing   molecular_function unknown   spliceosome
YGR045C         biological_process unknown   molecular_function unknown   not yet annotated
YER181C         biological_process unknown   molecular_function unknown   not yet annotated
YGL222C   EDC1     mRNA processing   molecular_function unknown   not yet annotated
YHR033W         biological_process unknown   molecular_function unknown   not yet annotated
YNL133C   FYV6     biological_process unknown   molecular_function unknown   cellular_component unknown
YKL052C   ASK1     biological_process unknown   molecular_function unknown   not yet annotated
YMR141C         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

In the case of a diauxic shift, CCL1 is generally repressed until about it approches the 17th hour, when it becomes induced slightly.  Most of the genes it clustered with, including the annotated genes DFG16, RNH35, PRP45, and EDC1, are involved in some way with mRNA or growth, which support the findings that CCL1 is involved with transcription and NER.  

Expression in response to histone depletion for CCL1/YPR025C (The Whitehead Institute)

Orf Gene Process Function Component
YPR025C   CCL1     transcription initiation, from Pol II promoter*   general RNA polymerase II transcription factor*   transcription factor TFIIH
YOL079W         biological_process unknown   molecular_function unknown   not yet annotated
YBR138C   HDR1     meiosis   molecular_function unknown   not yet annotated
YNR066C         biological_process unknown   molecular_function unknown   not yet annotated
YLR255C         biological_process unknown   molecular_function unknown   not yet annotated
YDR102C         biological_process unknown   molecular_function unknown   not yet annotated
YML005W         biological_process unknown   molecular_function unknown   not yet annotated
YAR064W         biological_process unknown   molecular_function unknown   not yet annotated
YDR018C         biological_process unknown   molecular_function unknown   not yet annotated
YIL132C   CSM2     biological_process unknown   molecular_function unknown   not yet annotated
YHR125W         biological_process unknown   molecular_function unknown   not yet annotated
YOL016C   CMK2     protein amino acid phosphorylation*   calcium/calmodulin-dependent protein kinase   cytoplasm
YBR174C         biological_process unknown   molecular_function unknown   not yet annotated
YCL004W   PGS1     not yet annotated   CDP-diacylglycerol-serine O-phosphatidyltransferase   not yet annotated
YNL041C   TFI2     biological_process unknown   molecular_function unknown   not yet annotated
YMR297W   PRC1     not yet annotated   carboxypeptidase C   not yet annotated
YGR202C   PCT1     not yet annotated   cholinephosphate cytidylyltransferase   not yet annotated
YML099C   ARG81     arginine metabolism   transcription factor   not yet annotated
YGR255C   COQ6     ubiquinone metabolism   not yet annotated   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

In response to histone depletion, CCL1 fell into the category with 75% of the yeast genes that did not show more than a 3-fold repression or induction at any point in the six hours that were recorded.  It does, however, cluster with genes that show similar trends in times of induction and repression.  Most of these genes' biological processes are unknown, but one of them is meiosis, which would obviously be affected by the depletion of histone, which represses genes around telomeres.  It has also been suggested that nucleosomes do not regulate genes as dominantly as transcription activators do, of which CCL1 is believed to be a part (Wyrick and Holstege 1999).

Non-Annotated Gene:  YHR078W   (YPD Protein Report)     Brief report of YHR078W

S. cerevisiae  Chromosome VIII

SGD: S0001120    Genbank: AAB68887.1    MIPS (PIR): S46809        SWISS-PROT: P38799

Databases Searched  (All microarray data on this page comes from Expression Connection)

Expression at different alpha-factor concentrations for YHR078W (Rosetta Inpharmatics).

Orf Gene Process Function Component
YHR078W         biological_process unknown   molecular_function unknown   not yet annotated
YJL102W   MEF2     protein synthesis elongation   translation elongation factor   mitochondrion
YDL111C   RRP42     35S primary transcript processing*   3'-5' exoribonuclease   nuclear exosome (RNase complex)*
YIL078W   THS1     not yet annotated   threonine--tRNA ligase   not yet annotated
YDL164C   CDC9     nucleotide-excision repair*   DNA ligase (ATP)   replication fork
YDR036C         biological_process unknown   molecular_function unknown   not yet annotated
YJR090C   GRR1     ubiquitin-dependent protein degradation*   ubiquitin--protein ligase*   nuclear ubiquitin ligase complex
YLR078C   BOS1     ER to Golgi transport   v-SNARE   endoplasmic reticulum membrane
YDL096C         biological_process unknown   molecular_function unknown   not yet annotated
YLR344W   RPL26A     protein biosynthesis   structural protein of ribosome*   cytosolic large ribosomal (60S) subunit
YOR199W         biological_process unknown   molecular_function unknown   not yet annotated
YOR065W   CYT1     oxidative phosphorylation   cytochrome c1   not yet annotated
YLR397C   AFG2     biological_process unknown   not yet annotated   not yet annotated
YNL315C   ATP11     protein complex assembly   chaperone   mitochondrial matrix
YMR037C   MSN2     stress response   not yet annotated   not yet annotated
YKL144C   RPC25     transcription, from Pol III promoter   DNA-directed RNA polymerase III   DNA-directed RNA polymerase III
YMR087W         biological_process unknown   molecular_function unknown   not yet annotated
YLR360W   VPS38     not yet annotated   molecular_function unknown   not yet annotated
YCR063W   BUD31     biological_process unknown   molecular_function unknown   cellular_component unknown
YJL042W   MHP1     cell wall organization and biogenesis*   structural protein of cytoskeleton   microtubule

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

Varying degrees of alpha-factor concentrations only slightly induce YHR078W, which means that if this ORF codes for a protein at all, it is probably not related to mating.   In fact, as the concentration increases past 175 nM, the induction ratio drops.  The genes clustered with YHR078W seem random when looking at the expression patterns, except for the ones that are also as unaffected, like RRP42, BOS1, RPL26A, and CYT1, which have been found to be involved in various processes like ER to Golgi transport, protein biosynthesis, 35S primary transcript processing, and oxidative phosphorylation.  

Expression in response to alpha-factor for YHR078W (Rosetta Inpharmatics).

Orf Gene Process Function Component
YHR078W         biological_process unknown   molecular_function unknown   not yet annotated
YIL159W   BNR1     osmotic response*   molecular_function unknown   cytokinetic ring (sensu Saccharomyces)
YIL090W         biological_process unknown   molecular_function unknown   not yet annotated
YDR075W   PPH3     not yet annotated   protein serine/threonine phosphatase   not yet annotated
YGL035C   MIG1     transcription regulation, from Pol II promoter*   DNA binding*   nucleus*
YGL065C   ALG2     oligosaccharide-lipid intermediate assembly   glycolipid mannosyl transferase   not yet annotated
YDR390C   UBA2     ubiquitin cycle   ubiquitin activating enzyme   nucleus
YPL066W         biological_process unknown   molecular_function unknown   not yet annotated
YBR029C   CDS1     phosphatidylglycerol biosynthesis*   phosphatidate cytidylyltransferase   mitochondrion*
YPR119W   CLB2     G2/M transition of mitotic cell cycle*   G2/M-specific cyclin   cellular_component unknown
YER149C   PEA2     establishment of cell polarity (sensu Saccharomyces)*   cytoskeletal regulatory protein binding   actin cap (sensu Saccharomyces)*
YHR023W   MYO1     cytokinesis*   microfilament motor   cytokinetic ring (sensu Saccharomyces)
YJL183W   MNN11     biological_process unknown   not yet annotated   not yet annotated
YKL085W   MDH1     tricarboxylic acid cycle*   malic enzyme   mitochondrial matrix
YBR054W   YRO2     biological_process unknown   not yet annotated   not yet annotated
YKL014C         biological_process unknown   molecular_function unknown   not yet annotated
YMR290C   HAS1     biological_process unknown   RNA helicase   not yet annotated
YGR228W         biological_process unknown   molecular_function unknown   not yet annotated
YER145C   FTR1     transport   not yet annotated   not yet annotated
YDL155W   CLB3     G1/S transition of mitotic cell cycle*   G2/M-specific cyclin   cellular_component unknown
YJR031C   GEA1     ER to Golgi transport*   ARF small monomeric GTPase   Golgi vesicle

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

Again, over time YHR078W does not seem to respond much to pheromones, although it does show slight repression.  It clusters here with an equal variety of gene functions and locations, but ER to Golgi transport does show up again, which may indicate a similar function.  A few genes also function in the cell cycle and various assembly lines, which are also possibilities.  

Expression during the diauxic shift for YHR078W (Stanford University).

Orf Gene Process Function Component
YHR078W         biological_process unknown   molecular_function unknown   not yet annotated
YDR180W   SCC2     mitotic sister chromatid cohesion   molecular_function unknown   cohesin
YKL081W   TEF4     protein synthesis elongation   translation elongation factor   ribosome
YGR034W   RPL26B     protein biosynthesis   structural protein of ribosome*   cytosolic large ribosomal (60S) subunit
YCL053C            
YGR285C   ZUO1     protein folding   chaperone   cytosol*
YML016C   PPZ1     sodium ion homeostasis   protein serine/threonine phosphatase   nucleus
YDR447C   RPS17B     protein biosynthesis*   structural protein of ribosome   cytosolic small ribosomal (40S) subunit
YMR321C         biological_process unknown   molecular_function unknown   not yet annotated
YOL077C   BRX1     biological_process unknown   molecular_function unknown   not yet annotated
YHR089C   GAR1     rRNA modification*   small nuclear ribonucleoprotein   box H+ACA snoRNP protein
YLR285W         biological_process unknown   molecular_function unknown   not yet annotated
YPL198W   RPL7B     protein biosynthesis   structural protein of ribosome   cytosolic large ribosomal (60S) subunit
YMR146C   TIF34     not yet annotated   not yet annotated   not yet annotated
YDR449C         biological_process unknown   molecular_function unknown   not yet annotated
YDL208W   NHP2     rRNA modification*   small nuclear ribonucleoprotein   box H+ACA snoRNP protein
YPL131W   RPL5     protein biosynthesis*   structural protein of ribosome*   cytosolic large ribosomal (60S) subunit
YNL065W   AQR1     biological_process unknown   molecular_function unknown   cellular_component unknown
YKR095W   MLP1     protein-nucleus import   molecular_function unknown   nuclear membrane*
YNL087W         biological_process unknown   molecular_function unknown   not yet annotated
YKR094C   RPL40B     protein biosynthesis*   structural protein of ribosome   cytosolic large ribosomal (60S) subunit

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

A stronger, but not highly conclusive, repression result clusters YHR078W with many genes involved in protein biosynthesis or post translational modification.  These are the strongest clustering results connecting this unannotated hypothetical ORF to any kind of function.  This is, however, only one test, and far from conclusive.  

Expression in response to histone depletion for YHR078W (The Whitehead Institute).

Orf Gene Process Function Component
YHR078W         biological_process unknown   molecular_function unknown   not yet annotated
YMR132C         biological_process unknown   molecular_function unknown   not yet annotated
YML005W         biological_process unknown   molecular_function unknown   not yet annotated
YFL055W   AGP3     transport   general amino acid permease   not yet annotated
YMR190C   SGS1     not yet annotated   not yet annotated   not yet annotated
YGR266W         biological_process unknown   molecular_function unknown   not yet annotated
YIL084C   SDS3     not yet annotated   not yet annotated   not yet annotated
YDR265W   PEX10     peroxisome organization and biogenesis   molecular_function unknown   cellular_component unknown
YGR190C         biological_process unknown   molecular_function unknown   not yet annotated
YIR031C   DAL7     allantoin catabolism   malate synthase   peroxisomal matrix
YHR035W         biological_process unknown   molecular_function unknown   not yet annotated
YGL057C         biological_process unknown   molecular_function unknown   not yet annotated
YIL132C   CSM2     biological_process unknown   molecular_function unknown   not yet annotated
YHR080C         biological_process unknown   molecular_function unknown   not yet annotated
YPR080W   TEF1     protein synthesis elongation   translation elongation factor   ribosome
YMR148W         biological_process unknown   molecular_function unknown   not yet annotated
YML099C   ARG81     arginine metabolism   transcription factor   not yet annotated
YGL185C         biological_process unknown   molecular_function unknown   not yet annotated
YMR192W         biological_process unknown   molecular_function unknown   not yet annotated
YCL004W   PGS1     not yet annotated   CDP-diacylglycerol-serine O-phosphatidyltransferase   not yet annotated
YAR064W         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

While not induced or repressed 3-fold or more, YHR078W is definitely affected by the loss of histones, most markedly induced at around the 2 hour mark.  The induction-repression pattern falls on the opposite times as CCL1 and its related genes, which are involved with transcription, so we may be able to set transcription aside as a possible function of YHR078W.  Transport comes up again, which may make a stronger case for it.
References:

Ohkuni, K, and I. Yamashita.  30 June, 2000.  A transcriptional autoregulatory loop for KIN28-CCL1 and SRB10-SRB11, each encoding RNA polymerase II CTD kinas-cyclin pair, stimulates the meiotic development of S. cerevisiae.  Yeast, Vol 16(9): 829 - 46.  29 September, 2001. <http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&uid=10861906&dopt=r>

You, Zhaoyang, William J. Feaver, and Errol C. Friedberg.  May 1998.  Yeast RNA polymerase II transcription in vitro is inhibited in the presence of nucleotide excision repair: complementation of inbibitors by Holo-TFIIH and requirement for RAD26.  Molecular Cell Biology, Vol. 18(5):2668-76.  30 September, 2001. <http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&uid=98226539&dopt=r>

Wyrick, John, Frank Holstege et. al.  25 November, 1999.  Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast.  Nature, Vol. 402: 418-421.  18 October, 2001.  <http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v402/n6760/full/402418a0_fs.html>


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