Table 1

Significantly induced genes of Saccharomyces cerevisiae by HMF during the lag phase

Systematic Name

Standard Name

Description

Fold change


0.2 h

0.5 h

1 h

2 h


Reductase

YCR105W

ADH7

NADPH-dependent medium chain alcohol dehydrogenase with broad substrate specificity

+38.4

+60.3

+81.3

+39.5

YGL157W

ARI1

NADPH-dependent aldehyde reductase

+12.3

+21.3

+29.2

+27.2

YOL151W

GRE2

3-methylbutanal reductase and NADPH-dependent methylglyoxal reductase (D-lactaldehyde dehydrogenase)

+8.0

+7.6

+10.4

+12.0

YOR374W

ALD4

NAD(P)-dependent mitochondrial aldehyde dehydrogenase

+4.3

+3.2

+2.7

+3.2

PDR family

YOR153W

PDR5

Plasma membrane ATP-binding cassette (ABC) transporter

+30.0

+19.0

+30.6

+23.7

YPL058C

PDR12

Plasma membrane ATP-binding cassette (ABC) transporter

+7.1

+4.1

+6.2

+3.3

YDR406W

PDR15

Plasma membrane ATP binding cassette (ABC) transporter

+9.5

+3.5

+5.4

+7.3

YDR011W

SNQ2

Plasma membrane ATP-binding cassette (ABC) transporter

+4.7

+3.8

+6.4

+4.1

YGR281W

YOR1

Plasma membrane ATP-binding cassette (ABC) transporter

+4.7

+3.0

+4.4

+3.5

YOR049C

RSB1

Suppressor of sphingoid long chain base (LCB) sensitivity of an LCB-lyase mutation

+15.7

+6.9

+9.5

+8.6

YLR099C

ICT1

Lysophosphatidic acid acyltransferase

+3.4

+2.9

+4.8

+6.2

YER142C

MAG1

3-methyl-adenine DNA glycosylase involved in protecting DNA against alkylating agents

+4.3

+4.5

+5.1

+3.7

YER143W

DDI1

DNA damage-inducible v-SNARE binding protein

+2.4

+2.2

+2.4

+1.7

YLL028W

TPO1

Polyamine transporter that recognizes spermine, putrescine, and spermidine

+4.5

+3.3

+5.1

+4.3

YOR273C

TPO4

Polyamine transporter that recognizes spermine, putrescine, and spermidine

+2.7

+2.0

+3.0

+2.6

YDL020C

RPN4

Transcription factor that stimulates expression of proteasome genes

+1.9

+2.5

+2.8

+3.3

YGR035C

YGR035C

Putative protein of unknown function

+3.1

+3.8

+4.1

+5.9

YLL056C

YLL056C

Putative protein of unknown function

+2.0

+2.0

+5.8

+6.2

YMR102C

YMR102C

Putative protein of unknown function

+1.8

+1.6

+2.2

+2.9

Proteasome and ubiquitin

YER012W

PRE1

Beta 4 subunit of the 20 S proteasome

+2.7

+2.4

+2.1

+1.8

YJL001W

PRE3

Beta 1 subunit of the 20 S proteasome

+3.0

+3.0

+2.6

+2.1

YOL038W

PRE6

Alpha 4 subunit of the 20 S proteasome

+2.0

+2.2

+2.8

+2.3

YBL041W

PRE7

Beta 6 subunit of the 20 S proteasome

+3.5

+2.6

+2.6

+1.9

YOR362C

PRE10

Alpha 7 subunit of the 20 S proteasome

+2.4

+2.2

+2.2

+1.9

YER094C

PUP3

Beta 3 subunit of the 20 S proteasome involved in ubiquitin-dependent catabolism

+2.4

+2.2

+2.9

+2.1

YDR427W

RPN9

Non-ATPase regulatory subunit of the 26 S proteasome

+2.7

+2.4

+2.4

+2.1

YFR052W

RPN12

Subunit of the 19 S regulatory particle of the 26 S proteasome lid

+2.8

+2.4

+2.6

+2.5

YHL030W

ECM29

Major component of the proteasome

+4.6

+3.3

+3.6

+2.6

YDL007W

RPT2

One of six ATPases of the 19 S regulatory particle of the 26 S proteasome involved in the degradation of ubiquitinated substrates

+3.3

+2.6

+2.6

+2.4

YDR394W

RPT3

One of six ATPases of the 19 S regulatory particle of the 26 S proteasome involved in the degradation of ubiquitinated substrates

+2.9

+2.0

+2.5

+2.5

YOR259C

RPT4

One of six ATPases of the 19 S regulatory particle of the 26 S proteasome involved in the degradation of ubiquitinated substrates

+3.1

+2.6

+3.2

+2.5

YBL058W

SHP1

UBX (ubiquitin regulatory X) domain-containing protein that regulates Glc7p phosphatase activity and interacts with Cdc48p

+2.5

+2.0

+2.1

+2.8

YFL044C

OTU1

Deubiquitylation enzyme that binds to the chaperone-ATPase Cdc48p

+2.3

+1.9

+3.3

+2.3

Amino acids

YLR142W

PUT1

Proline oxidase

+4.8

+6.9

+10.8

+43.0

YHR037W

PUT2

Delta-1-pyrroline-5-carboxylate dehydrogenase

+3.7

+3.7

+4.7

+3.3

YJR010W

MET3

ATP sulfurylase

+2.5

+2.7

+3.3

+3.6

YKL001C

MET14

Adenylylsulfate kinase

+1.7

+2.6

+2.8

+3.2

YCL064C

CHA1

Catabolic L-serine (L-threonine) deaminase, catalyzes the degradation of both L-serine and L-threonine

+13.3

+17.7

+15.8

+7.3

YLR089C

ALT1

Alanine transaminase

+2.9

+3.1

+4.1

+4.9

YPL111W

CAR1

Arginase, responsible for arginine degradation

+3.4

+2.2

+1.9

+1.6

Stress

YBR072W

HSP26

Small heat shock protein (sHSP) with chaperone activity

+10.8

+1.8

+2.0

+8.0

YER103W

SSA4

Heat shock protein that is highly induced upon stress

+13.2

+1.5

+2.0

+2.6

Transcription factors

YML007W

YAP1

Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance

+3.3

+2.1

+2.5

+2.2

YDL020C

RPN4

Transcription factor that stimulates expression of proteasome genes

+1.9

+2.5

+2.8

+3.3

Others

YPL171C

OYE3

Conserved NADPH oxidoreductase containing flavin mononucleotide (FMN)

+5.9

+3.9

+5.3

+17.7

YOR306C

MCH5

Plasma membrane riboflavin transporter

+2.6

+4.9

+7.8

+7.2

YAR073W

IMD1

Nonfunctional protein with homology to IMP dehydrogenase

+2.2

+2.1

+3.4

+2.7

YBL078C

ATG8

Component of autophagosomes and Cvt vesicles

+4.5

+3.3

+2.7

+3.5

YBR062C

YBR062C

Hypothetical protein

+2.5

+2.4

+2.4

+2.1

YML130C

ERO1

Thiol oxidase required for oxidative protein folding in the endoplasmic reticulum

+2.3

+2.4

+2.8

+2.3

YBR114W

RAD16

Protein that recognizes and binds damaged DNA in an ATP-dependent manner (with Rad7p) during nucleotide excision repair

+2.8

+2.1

+2.8

+1.7

YBR170C

NPL4

Endoplasmic reticulum and nuclear membrane protein

+2.4

+2.7

+2.2

+1.5

YDL021W

GPM2

Homolog of Gpm1p phosphoglycerate mutase

+3.5

+1.6

+1.7

+2.8

YBL101W-A

YBL101W-A

Retrotransposon TYA Gag gene co-transcribed with TYB Pol

+1.4

+1.6

+2.6

+6.4

YDR210W-B

YDR210W-B

Retrotransposon TYA Gag and TYB Pol genes

+1.9

+1.7

+2.6

+4.4

YDR316W-B

YDR316W-B

Retrotransposon TYA Gag and TYB Pol genes

+1.8

+1.8

+2.6

+3.2

YDR365W-B

YDR365W-B

Retrotransposon TYA Gag and TYB Pol genes

+1.7

+1.7

+2.2

+4.3

YDR515W

SLF1

RNA binding protein that associates with polysomes

+2.7

+2.7

+2.4

+2.7

YOR009W

TIR4

Cell wall mannoprotein of the Srp1p/Tip1p family of serine-alanine-rich proteins

-1.3

+1.3

+4.6

+5.9

YPL156C

PRM4

Pheromone-regulated protein proposed to be involved in mating

+3.4

+2.8

+3.5

+3.5

YGL062W

PYC1

Pyruvate carboxylase isoform

+2.3

+2.6

+3.1

+2.1

YOR007C

SGT2

Glutamine-rich cytoplasmic protein of unknown function

+2.8

+2.5

+2.9

+3.0

YOR052C

YOR052C

Nuclear protein of unknown function

+4.1

+2.6

+1.8

+2.4

YDR034W-B

YDR034W-B

Protein of unknown function

+7.2

+5.0

+3.6

+4.5

YML125C

PGA3

Putative cytochrome b5 reductase

+1.6

+2.7

+3.0

+2.4

YBL107C

YBL107C

Putative protein of unknown function

+2.4

+2.6

+2.1

+2.9

YBR255C-A

YBR255C-A

Putative protein of unknown function

+4.0

+2.0

+1.8

+2.1

YER137C

YER137C

Putative protein of unknown function

+2.9

+2.4

+2.5

+3.6

YGR111W

YGR111W

Putative protein of unknown function

+2.1

+2.2

+4.3

+7.1

YHR138C

YHR138C

Putative protein of unknown function

+4.2

+2.8

+2.4

+2.8

YKR011C

YKR011C

Putative protein of unknown function

+4.6

+2.3

+1.9

+1.3

YNL155W

YNL155W

Putative protein of unknown function

+3.7

+2.4

+2.2

+1.9

YOR059C

YOR059C

ORF, Uncharacterized

+2.1

+2.6

+2.2

+2.2


Ma and Liu BMC Genomics 2010 11:660   doi:10.1186/1471-2164-11-660

Open Data