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Table 2 Biologically-verified data on transcription factors that act on genes also found in Additional file 1: transcript dependence on HAP4 over-expression.

From: Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1

ORF

GENE

FACTOR CHANGE IN GENE EXPRESSION FROM V5 TO V5.TM6*P

FACTOR CHANGE IN GENE EXPRESSION FROM WT TO A HAP4 OVER-EXPRESSION STRAIN[19]

Glycolysis

YCL040W

GLK1

3.8

0.4

Alternative carbon source utilization

YML054C

CYB2

10.1

5.0

TCA cycle

YIL125W

KGD1

2.2

2.2

YDR148C

KGD2

3.5

4.4

YFL018C

LPD1

2.0

2.2

YKL085W

MDH1

3.6

2.2

YKL148C

SDH1

4.6

4.7

YLL041C

SDH2

4.1

3.9

YKL141W

SDH3

3.7

2.3

YDR178W

SDH4

5.3

3.2

Glyoxylate cycle

YIR029W

DAL2

3.0

3.0

Respiratory chain

YPL078C

ATP4

2.1

2.0

YKL016C

ATP7

2.3

2.4

YPR020W

ATP20

2.5

3.4

YGR174C

CBP4

2.8

2.1

YBL045C

COR1

2.0

2.0

YGL187C

COX4

2.0

2.3

YNL052W

COX5A

2.0

2.1

YHR051W

COX6

2.1

2.2

YLL009C

COX17

2.8

4.7

YOR065W

CYT1

2.5

2.3

YKL087C

CYT2

2.2

2.8

YIL098C

FMC1

2.5

2.3

YDL181W

INH1

2.2

5.5

YBR185C

MBA1

2.3

2.3

YML120C

NDI1

4.1

4.4

YEL024W

RIP1

2.3

2.4

YPR151C

SUE1

2.2

3.0

Plasma membrane transport

YLL052C

AQY2

3.0

3.0

YLR411W

CTR3

3.0

0.5

YGL255W

ZRT1

0.5

0.1

Mitochondrial transport

YNR002C

ATO2

3.8

3.8

YKL217W

JEN1

10.3

2.9

YPL134C

ODC1

6.3

3.3

Transcriptional regulation

YOL071W

EMI5

2.1

2.9

YNL333W

SNZ2

3.0

6.4

Fatty acid metabolism

YKL150W

MCR1

3.1

2.8

Biosynthesis

YFL030W

AGX1

3.6

7.8

Ribosomal proteins in the mitochondria or cytosol

YDR296W

MHR1

2.0

2.5

YGL068W

MNP1

2.1

2.4

YDR116C

MRPL1

2.6

3.5

YKL138C

MRPL31

2.2

2.8

YGR165W

MRPS35

2.0

2.7

YHR038W

RRF1 (FIL1)

2.2

4.8

YDR041W

RSM10

2.1

2.4

YDR175C

RSM24

2.4

2.9

YFR049W

YMR31

2.5

2.6

Other

YBR262C

AIM5

2.3

2.1

YFR011C

AIM13

2.1

3.4

YLR168C

AIM30

2.6

3.3

YML087C

AIM33

4.2

11.6

YBR230C

OM14

3.3

2.4

YDL104C

QRI7

2.1

2.7

YOR187W

TUF1

2.3

2.4

YKL067W

YNK1

3.1

2.1

Not characterized

YGR110W

N/A

2.3

2.0

  1. Genes were tabulated and sorted according to their roles in yeast cellular physiology, as described in the legend for Additional file 1. Note that the seven hexose transporter genes, HXT1-7, are deleted in the V5.TM6*P with the amino-terminal half of HXT1 and the carboxy-terminal half of HXT7 reincorporated as the TM6* chimera. In the 'Factor Change' column, change is expressed as a factor, where that factor is x when a gene expressed with intensity '1' in V5 is expressed with intensity 'x' in V5.TM6*P. All T-tests were jointly adjusted for multiple testing using the false discovery rate method (disregarding correlations between genes): p-values were adjusted so that when selecting all genes with p-values less than a threshold q, a proportion of q false positives would be expected amongst these genes. The genes shown have p-values < 0.05, and thus the expected false discovery rate is 5%. The factor in the final column is taken from Lascaris et al [19]. †Note that due to overall high homology within the hexose transporter family, changes were still observed on the cDNA array for HXT4 (YHR092C) even though it is deleted as already mentioned.
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BMC Genomics

ISSN: 1471-2164

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