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Table 1 Most consistently dysregulated chromosome 21 genes based on their p-values from ANOVA and after 5% false discovery rate cut-off

From: Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart

Gene name Accession number Chromosome number p value (ANOVA) Cerebrum Cerebellum Astrocyte Heart
     Control TS21 Control TS21 Control TS21 Control TS21
Pituitary tumor-transforming 1 interacting protein (PTTG1IP) NM_004339 21 1.50E-07 582.6 888.1 830.9 1176.9 2355.5 3896.0 1153.0 2003.5
ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit (ATP5O) NM_001697 21 5.11E-07 1509.0 2553.5 1331.5 2327.1 1552.9 2086.3 2375.0 4002.1
SH3 domain binding glutamic acid-rich protein (SH3BGR) NM_007341 21 7.12E-07 20.5 44.5 21.2 48.4 38.2 130.2 606.8 1937.5
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6 (ATP5J) NM_001685 21 2.47E-06 624.4 1148.8 723.1 1013.6 881.3 1331.5 916.4 2046.7
Down syndrome critical region gene 3 (DSCR3) NM_006052 21 1.44E-05 51.7 94.3 49.8 92.6 49.7 169.0 72.9 71.1
Chromosome 21 segment HS21C048, zinc finger protein 294 (ZNF294) NM_015565 21 3.39E-05 165.7 283.0 161.6 228.9 78.6 127.8 107.5 178.0
Superoxide dismutase 1 (SOD1) NM_000454 21 5.62E-05 1176.2 2493.4 1816.7 2860.4 2482.7 3853.6 1789.7 3110.8
ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit (ATP5O) NM_001697 21 6.94E-05 203.7 335.9 219.1 342.7 124.5 258.4 342.4 521.4
Cystatin B (stefin B) (CSTB) NM_000100 21 7.75E-05 412 695.0 584.6 868.9 855.1 1007.3 797.4 1034.7
Phosphofructokinase, liver (PFKL) BC006422 21 1.93E-04 411 476.9 255.8 492.1 247.3 397.9 390.0 433.1
Pyridoxal (pyridoxine, vitamin B6) kinase (PDXK) NM_003681 21 2.82E-04 50.3 137.4 70.1 149.4 118.4 261.6 96.6 139.3
Collagen, type VI, alpha 1 (COL6A1) AA292373 21 5.04E-04 559.4 963.1 1019 1417 573.7 834.4 3003.5 4177.7
Transmembrane protein 1 (TMEM1) U61500 21 5.25E-04 68.4 83.6 45.0 90.8 34.5 88.5 6.6 62.8
Ubiquitin specific protease 16 (USP16) NM_006447 21 5.33E-04 189.8 318.8 223.1 306.5 272.5 513.4 180.0 320
SMT3 suppressor of mif two 3 homolog 1 (yeast) (SMT3H1) NM_006936 21 6.27E-04 704.0 1181.5 823.4 1233.1 698.7 1092.9 484.6 676.5
SON DNA binding protein (SON) X63071 21 7.28E-04 701.5 975.7 807.4 870.3 781.2 1181.3 761.7 924.7
Mitochondrial ribosomal protein L39 (MRPL39) NM_017446 21 7.48E-04 195.2 281.5 256.7 266.2 250.6 310.1 274.1 385.9
Interferon gamma receptor 2 (IFNGR2) NM_005534 21 8.16E-04 553.5 754.3 507.5 692.0 881.2 1307.9 639.5 811.15
Human homolog of ES1 (zebrafish) protein (C21orf33) D86062 21 1.02E-03 175.5 260.5 163.5 280.1 190.0 202.1 188.4 374.7
Chaperonin containing TCP1, subunit 8 (theta) (CCT8) NM_006585 21 1.45E-03 1098 1520.4 743.6 956.3 619.0 1200.8 615.1 1089.8
Chromosome 21 open reading frame 108 (C21orf108) AI803485 21 1.53E-03 52.5 101.9 61.9 91.8 60.7 105.4 25.6 71.3
Tryptophan rich basic protein (WRB) NM_004627 21 2.18E-03 759.6 1439.2 926.4 1182.4 728.6 1336.5 291.9 566.5
SMT3 suppressor of mif two 3 homolog 1 (yeast) (SMT3H1) BG338532 21 3.15E-03 204.0 274.6 186.6 294.2 252.2 352.2 157.3 263.7
HMT1 hnRNP methyl-transferase-like 1 (HRMT1L1) NM_001535 21 3.62E-03 670.0 920.5 584.2 843.2 489.1 471.6 363.0 525.2
Human homolog of ES1 (zebrafish) protein (C21orf33) NM_004649 21 4.00E-03 491.8 818.2 589.7 918.9 455.9 665.6 713.3 1039.4
Stress 70 protein chaperone, microsome-associated, 60 kDa (STCH) AI718418 21 4.43E-03 276.2 477.5 289 308.5 418.2 738.6 59.0 111.4
  1. The average expression values are for the probe sets corresponding to the genes (from MAS5 software). Two genes (ATP5O and C21orf33) each have two probe sets on this list. TS21, trisomy 21.