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Table 4 Fold changes of gene expression in three datasets reanalyzed by CANEapp and compared to qRT-PCR results

From: CANEapp: a user-friendly application for automated next generation transcriptomic data analysis

Gene Name Cuffdiff edgeR_GML edgeR_et DESeq2 QRT-PCR
Alzheimer’s disease dataset
 SERPINE1 1.41 1.71 1.54 0.98 1.66
 TAC1 −1.77 −1.65 −1.85 −1.56 −0.42
 ID2 0.98 1.07 0.88 −0.73 1.17
 GRM2 0.86 0.98 0.78 0.63 0.44
 LINC01314 −0.25 −1.19 −1.38 −1.05 −0.50
 RP11-87E22.2 3.63 2.01 1.85 1.31 2.30
Mouse cortex dataset
 Vax1 −2.12 −2.02 −1.74 −1.71 −3.18
 Caly 1.93 1.79 2.08 2.09 2.10
 Igf2bp1 −9.40 −8.72 −8.45 −8.16 −5.61
 Draxin −5.98 −5.26 −4.98 −4.94 −6.80
 Nrp1 −2.17 −2.22 −1.94 −1.92 −2.46
 Ttr 11.04 11.18 11.46 11.28 11.63
 Mobp 12.44 12.08 12.36 12.24 12.69
 Wipf1 2.22 1.74 2.02 2.03 1.71
Rat liver dataset
 Bax-AFL 1.78 1.86 1.75 1.96 2.62
 Cdkn1a-AFL 4.19 4.28 3.30 8.00 23.50
 Myc-AFL 0.97 1.03 0.82 0.99 2.10
 Met-AFL −1.02 −0.94 −0.88 −0.89 −1.90
 Bax-NIT 1.62 1.22 1.19 1.25 1.98
 Cdkn1a-NIT 3.22 2.82 2.56 3.05 8.07
 Figf-NIT 4.18 3.76 3.51 3.72 10.27
 Fzd4-NIT −0.30 −0.70 −0.69 −0.73 −2.07