Table 1

Selection of differentially expressed genes at T0-T1 generated by GeneChips and RNA-seq
Gene Verified/putative function Fc1↑up/↓down RPKM T0 RPKM T1 RPKM Fc ↑up/↓down
Gluconeogenesis/glyoxylate cycle
An04g05300 fructose bisphosphatase (A. nidulans acuG) ↓ 31.39 71.07 11.66 ↓ 6.09
An11g02550 phosphoenolpyruvate carboxykinase (A. nidulans acuF) ↓ 80.62 37.27 2.88 ↓ 12.94
An01g09270 isocitrate lyase (A. nidulans acuD) ↓ 20.47 627.18 93.74 ↓ 6.69
An15g01860 malate synthase (A. nidulans acuE) ↓ 40.61 28.52 3.68 ↓ 7.75
An12g01990 acyl-CoA synthetase ↓ 2.04 16.85 3.29 ↓ 5.12
An07g09190 acyl-CoA synthetase ↓ 6.07 23.8 10.77 ↓ 2.20
An08g04990 carnitine acetyl transferase (A. nidulans facC) ↓ 20.74 107.81 10.2 ↓ 10.56
An08g06580 facB, acetate regulatory DNA binding protein ↓ 2.09 16.27 0.99 ↓ 16.43
Metabolism of alternative carbon sources
An13g00480 triacylglycerol lipase ↓ 17.13 10.83 0.36 ↓ 30.08
An09g05120 triacylglycerol lipase ↓ 5.09 11.84 0.81 ↓ 14.62
An02g04680 lipase ↓ 4.93 19.39 4.46 ↓ 4.35
An07g04200 triacylglycerol lipase ↓ 3.32 123.82 6.02 ↓ 20.57
An18g06580 triacylglycerol lipase ↓ 3.21 58.96 3.63 ↓ 16.24
An16g05570 aspartate aminotransferase ↓ 11.93 31.74 1.9 ↓ 16.70
An14g01190 arginase ↓ 4.86 37.15 1.4 ↓ 26.53
An15g03260 threonine aldolase* ↓ 2.09 9.41 8.47 ↓ 1.11
Fermentation/glycolysis
An02g06820 pyruvate decarboxylase ↓ 17.56 111.28 6.39 ↓ 17.41
An08g01520 alcohol dehydrogenase ↓ 194.72 247.83 2 ↓ 123.91
An12g09950 alcohol dehydrogenase ↓ 118.28 92.97 0.62 ↓ 149.95
An04g02690 alcohol dehydrogenase ↓ 35.46 163.73 21.91 ↓ 7.47
An17g01530 adhA, alcohol dehydrogenase ↓ 21.35 71.04 5.21 ↓ 13.63
An09g03140 alcohol dehydrogenase ↓ 11.59 132.35 3.76 ↓ 35.19
An16g05420 glucose-6-phosphate isomerase ↓ 11.61 23.29 2.44 ↓ 9.54
An02g14380 hxkA, hexokinase ↓ 6.26 24.59 5.16 ↓ 4.76
An18g01670 pfkA, 6-phosphofructokinase ↓ 64.25 42.44 12.52 ↓ 3.38
An02g07470 fructose-bisphosphate aldolase ↓ 22.15 242.31 13.33 ↓ 18.17
An08g02260 pgkA, phosphoglycerate kinase ↓ 19.01 32.17 15.68 ↓ 2.05
An02g03830 creA, catabolite repressor ↑ 2.57 4.43 30.22 ↑ 6.82
An02g03540 hexose transport protein ↑ 42.48 33.08 523.81 ↑ 15.83
GABA shunt
An10g00090 glutamate dehydrogenase ↓ 89.12 246.31 3.87 ↓ 63.64
An15g04770 glutamate decarboxylase ↓ 63.83 62.34 2.3 ↓ 27.10
An08g08840 glutamate decarboxylase ↓ 5.74 16.85 3.14 ↓ 5.36
An17g00910 GABA transaminase ↓ 4.63 7.63 0 n/a
An14g02870 succinic semialdehyde dehydrogenase ↓ 31.91 274.43 2.34 ↓ 117.27
TCA cycle
An08g05580 isocitrate dehydrogenase ↑ 2.71 10.85 69.17 ↑ 6.37
An18g06760 isocitrate dehydrogenase ↑ 3.17 55.23 354.46 ↑ 6.41
An04g04750 oxoglutarate dehydrogenase ↑ 2.23 22.9 109.76 ↑ 4.79
An17g01670 succinyl-CoA synthetase ↑ 5.36 24.29 128.98 ↑ 5.31
Metabolism of internal carbohydrates
An01g09290 neutral trehalase (A. nidulans treB) ↓ 5.01 719.2 58.5 ↓ 12.29
An08g10510 tpsA, trehalose-6-phosphate synthase ↓ 48.49 124.99 2.69 ↓ 46.46
An07g08710 tpsB, trehalose-6-phosphate synthase ↓ 2.00 22.52 12.47 ↓ 1.80
An11g10990 trehalose-6-phosphate phosphatase ↓ 2.82 73.39 39.34 ↓ 1.86
An03g02430 mannitol dehydrogenase ↓ 14.61 74.76 31.38 ↓ 2.38
An02g05830 mpdA, mannitol-1-phosphate dehydrogenase ↓ 2.96 34.05 6.03 ↓ 5.64
An04g04890 glycerol kinase ↓ 24.53 209.95 50.67 ↓ 4.14
An08g00210 glycerol-3-phosphate dehydrogenase ↓ 16.76 80.42 25.23 ↓ 3.18
An14g04920 tpiA, triose-phosphate-isomerase ↓ 29.26 72.81 4.87 ↓ 14.95
An16g01830 gpdA, glyceraldehyde-3 phosphate dehydrogenase ↓ 14.75 107.99 19.98 ↓ 5.40
An07g05790 osmoregulator (S. cerevisiae SGD1) ↑ 11.18 3.14 96.62 ↑ 30.7
Nitrogen metabolism
An14g02720 neutral amino acid transporter ↑ 13.44 3.02 313.74 ↑ 103.89
An15g07550 neutral amino acid transporter ↑ 2.59 32.67 398.48 ↑ 12.20
An16g05880 neutral amino acid transporter ↑ 37.51 14.66 907.29 ↑ 61.89
An03g05360 neutral amino acid transporter ↑ 3.97 5.05 127.9 ↑ 25.33
An04g09420 neutral amino acid transporter ↑ 58.88 0 126.15 n/a
An17g00860 translation initiation factor (A. fumigatus cpcC) no change2 45.91 60.85 ↑ 1.32
An01g07900 cpcA, transcription factor ↑ 3.55 18.59 123.24 ↑ 6.62
An01g08850 transcription factor (A. nidulans cpcB) ↑ 3.86 23.52 530.23 ↑ 22.54
An11g06180 transcription factor (A. nidulans prnA) ↑ 2.59 20.6 101.93 ↑ 4.94
An11g06160 proline oxidase (A. nidulans prnD) ↑ 5.49 25.16 248.82 ↑ 9.88
An11g06150 proline permease (A. nidulans prnB) ↑ 2.10 0 9.34 n/a
An11g06140 proline utilisation protein (A. nidulans prnC) ↑ 3.67 1.68 70.97 ↑ 42.24
An12g08960 areA, transcription factor no change2 23.9 12.21 ↓ 1.95
An11g00450 nitrate transport protein ↑ 79.28 8.41 909.98 ↑ 108.20
An08g05610 niaD, nitrate reductase ↑ 5.51 2.19 22.31 ↑ 10.18
An08g05640 niiA, nitrite reductase* ↑ 2.61 7.34 7.97 ↑ 1.08
An18g02330 transcription factor (A. nidulans nirA) present T0, absent T1 45.17 15.7 ↓ 2.88
An04g00990 gdhA, NADP-dependent glutamate dehydrogenase ↑ 9.61 48.66 1066.53 ↑ 21.91
An03g05590 uracil transporter ↑ 28.54 14.71 384.05 ↑ 26.11
An11g04340 uracil transporter ↑ 9.43 2.43 28.05 ↑ 11.54
An07g01950 uracil transporter (A. nidulans uapC) ↓ 8.95 69.95 1.51 ↓ 46.32
An01g08050 uaY, transcription factor ↓ 5.75 57.87 15.15 ↓ 3.82
An14g03370 allantoinase* ↑ 27.48 7.64 16.23 ↑ 2.12
Mitochondria/respiration
An12g01480 Aminoacyl-tRNA biosynthesis ↑ 2.85 20.41 36.35 ↑ 1.78
An08g02450 ATP synthase complex assembly ↑ 2.63 4.82 51.51 ↑ 10.69
An15g01710 atp7, F1Fo-ATP synthase ↑ 2.29 31.59 265.5 ↑ 8.40
An01g10880 F1Fo-ATP synthase ↑ 4.53 13.27 427.48 ↑ 32.21
An11g04370 cytochrome b5 ↑ 65.60 4.32 84.98 ↑ 19.67
An02g04330 cytochrome C oxidase ↑ 5.29 0.72 140.73 ↑195.46
An08g08720 cytochrome C peroxidase ↑ 11.09 11.03 148.09 ↑13.43
An14g00240 holocytochrome-c synthase ↑ 2.50 16.53 48.96 ↑ 2.96
An02g12620 mitochondrial respiratory chain complex IV ↑ 5.93 25.57 238.28 ↑ 9.32
An08g04150 mitochondrial ribosomal protein ↑ 9.46 7.78 316.39 ↑ 40.67
An15g05790 mitochondrial RNA polymerase ↑ 2.56 122.85 236.49 ↑ 1.93
An04g02550 mitochondrial translation elongation factor ↑ 33.29 13.97 1080.27 ↑ 77.33
An01g10190 mitochondrial transport protein ↑ 41.01 14.25 555.87 ↑ 39.01
An08g04240 NADH:ubiquinone reductase ↑ 16.45 4.44 470.4 ↑ 105.94
An02g12510 plasma membrane H(+)-ATPase pmaA ↑ 65.65 24.33 1271.65 ↑ 52.27
An04g05220 ubiquinol-cytochrome C reductase ↑ 2.95 13.09 213.13 ↑ 16.28

Fc1 = Fold change based on GeneChip data.

No change2 = fold change < 2.

The RPKM values shown are from the combined mapping scores of two distinct biological samples at each time point. Three statistical significance tests were applied to changes in gene expression measured by RNA-seq, the Likelihood Ratio Test [53], Fisher’s Exact Test [54], and an MA-plot-based method with Random Sampling model [52]. All changes in gene transcription, between T0 and T1, listed for RNA-seq data scored a p-value of < 0.001 for all three statistical tests, other than those genes highlighted with a *.

Novodvorska et al.

Novodvorska et al. BMC Genomics 2013 14:246   doi:10.1186/1471-2164-14-246

Open Data