Table 2

Comparison of genes determined to be DE in the ALS experiment by each method using either 12 or 22 samples
List of DE genes Gene/Accession Description p-value/SAM score
LO/W12 FTH1/NM_002032 Ferritin, heavy polypeptide 1 1.59E-3
JUNB/NM_002229 Jun B proto-oncogene 3.67 E-3
B2M/NM_004048 Beta-2-microglobulin 1.54 E-3
ACTG1/NM_001614 Poly(A) binding protein, cytoplasmic 1 3.7 E-3
SLC25A3
    /
NM_005888
solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 4.46 E-3
LO/W22 EXOC3L2/NM_138568 Exocyst complex component 3 like 2 5.73 E-3
FAU/NM_001997 Finkel-Biskis-Reilly murine sarcoma virus 1.96 E-3
GLTSCR1/AF182077 Glioma tumor suppressor candidate region gene 1 2.56 E-3
JUNB/NM_002229 Jun B proto-oncogene 1.24 E-3
IRS2/NM_003749 Insulin receptor substrate 2 1.66 E-3
TM4/W12 CSE1L/NM_001316 CSE1 chromosome segregation 1-like (yeast) 3.95E-3
NUP88/NM_002532 Nucleoporin 88 kDa 3.95E-3
PARP1/
NM_001618 poly (ADP-ribose) polymerase 1 3.95E-3
DYNC1I2/NM_001378 Dynein, cytoplasmic 1, intermediate chain 2 6.17E-3
DYNLT1/NM_006519 Dynein, light chain, Tctex-type 1 6.48E-3
TM4/W22 IRS2/NM_003749 Insulin receptor substrate 2 1.22E-04
SKIV2L2/NM_015360 Superkiller viralicidic activity 2-like 2 (S. cerevisiae) 1.22E-04
DYNLT1/NM_006519 Dynein, light chain, Tctex-type 1 1.60E-04
C12orf35/NM_018169 Chromosome 12 open reading frame 35 2.07E-04
TARDBP/NM_007375 TAR DNA binding protein 2.68E-04
SAM/W12 FTH1/NM_002032 Ferritin, heavy polypeptide 1 1.628
JUNB/NM_002229 Jun B proto-oncogene 1.429
B2M/NM_004048 Beta-2-microglobulin 1.452
ACTG1/NM_001614 Poly(A) binding protein, cytoplasmic 1 1.234
SLC25A3
    /
NM_005888
solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 1.057
SAM/W22 IRS2/NM_003749 Insulin receptor substrate 2 1.182
GLTSCR1/AF182077 Glioma tumor suppressor candidate region gene 1 1.165
FAU/NM_001997 Finkel-Biskis-Reilly murine sarcoma virus 1.165
EXOC3L2/NM_138568 Exocyst complex component 3-like 2 1.099
JUNB/NM_002229 Jun B proto-oncogene 1.034

Genes were selected based on FDR significance (p < 0.05). Methods include: LO-BaFL-Wilcoxon (LO/W12, LO/W22), TM4-SAM-Wilcoxon (TM4/W12, TM4/W22) and LO-BaFL-SAM-Wilcoxon (SAM/W12, SAM/W22) as described in the text.

Baciu et al.

Baciu et al. BMC Bioinformatics 2012 13:244   doi:10.1186/1471-2105-13-244

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